Dear all I agree with Mike and Scott too. I might suggest Schalken, M. J. and Chantler, C. T. "Preservation of uncertainty in experiment: structures of Ni (II) coordination complexes" (2018) J. Synchrotron Rad., 25, 920-934 as a partial discussion around this topic if people are interested.
It could be read as 'don't smooth data if you can avoid it'. Very best wishes to all Chris -------------------------------------------------------------------------------------- Christopher Chantler, Professor, FAIP, Fellow American Physical Society Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS; CIT, CCN IPP, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chant...@unimelb.edu.au<https://owa.unimelb.edu.au/owa/redir.aspx?C=c7BoS0kVVkC1_S95-9x9l5cBu6YTjdAITgSrfUpfDAUV5oUH1LFYBcz08w8xvHMJoosZRdagfQM.&URL=mailto%3achantler%40unimelb.edu.au> chant...@me.com<https://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.html<https://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.html<https://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 <ifeffit-boun...@millenia.cars.aps.anl.gov> on behalf of ifeffit-requ...@millenia.cars.aps.anl.gov <ifeffit-requ...@millenia.cars.aps.anl.gov> Sent: Thursday, 23 January 2020 4:05 PM To: ifeffit@millenia.cars.aps.anl.gov <ifeffit@millenia.cars.aps.anl.gov> Subject: Ifeffit Digest, Vol 203, Issue 5 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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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. smoothing XAS data (Daria Boglaienko) 2. Re: smoothing XAS data (Carlo Segre) 3. Re: smoothing XAS data (Scott Calvin) 4. Re: smoothing XAS data (Mike Massey) 5. Re: smoothing XAS data (Will Bennett) ---------------------------------------------------------------------- Message: 1 Date: Wed, 22 Jan 2020 17:38:43 -0800 From: Daria Boglaienko <dbogl...@fiu.edu> To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] smoothing XAS data Message-ID: <caacwq8bmjfr0qnuhk1yrsb7w3blghzyus9pxow0ng+er3ea...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello, In what case smoothing of the data is OK? My data have a lot of noise and smoothing really helps (visually). I compared fit done in Artemis for smoothed and non-smoothed data sets and the result is very similar, however when I searched about it online, it looks like it is not recommended. What is a good way to justify it? Thank you! -Daria -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20200122/f5449543/attachment-0001.html> ------------------------------ Message: 2 Date: Wed, 22 Jan 2020 19:44:22 -0600 (CST) From: Carlo Segre <se...@iit.edu> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] smoothing XAS data Message-ID: <alpine.deb.2.22.394.2001221942280.10...@hydride.segre.home> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Daria: I smooth (or boxcar average) the data which it is oversampled, such as in a continuous scan where the data in the exafs region is spaced closer than the usual delta k of 0.05. I generally don't like to smooth XANES data since smoothing does tend to attenuate sharp features such as the ones which exist near the absorption edge. Carlo On Wed, 22 Jan 2020, Daria Boglaienko wrote: > Hello, > > In what case smoothing of the data is OK? My data have a lot of noise and > smoothing really helps (visually). I compared fit done in Artemis for > smoothed and non-smoothed data sets and the result is very similar, however > when I searched about it online, it looks like it is not recommended. > What is a good way to justify it? > > Thank you! > > -Daria > -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Directory, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 se...@iit.edu http://phys.iit.edu/~segre se...@debian.org ------------------------------ Message: 3 Date: Wed, 22 Jan 2020 23:01:23 -0500 From: Scott Calvin <dr.scott.cal...@gmail.com> To: Carlo Segre <se...@iit.edu>, XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] smoothing XAS data Message-ID: <2cfe75b8-59d9-472f-95e0-2c618fd3b...@gmail.edu> Content-Type: text/plain; charset="utf-8" Not only can smoothing XANES data attenuate sharp features, it can also shift them, since many XANES features, particularly in the ?pre-edge? region, are significantly asymmetric about their peak. That can make analysis quite confusing, since, e.g., the size of the boxcar ends up affecting the position of the peak! Best, Scott Calvin Lehman College of the City University of New York > On Jan 22, 2020, at 8:44 PM, Carlo Segre <se...@iit.edu> wrote: > > I generally don't like to smooth XANES data since smoothing does tend to > attenuate sharp features such as the ones which exist near the absorption > edge. -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20200122/4e427a6e/attachment-0001.html> ------------------------------ Message: 4 Date: Wed, 22 Jan 2020 20:50:51 -0800 From: Mike Massey <mmas...@gmail.com> To: Carlo Segre <se...@iit.edu>, XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] smoothing XAS data Message-ID: <e369e515-d6b6-4e74-8ae5-7d91a3177...@gmail.com> Content-Type: text/plain; charset=utf-8 At this juncture, I'd like to bring up a "rule" I've made for myself regarding data quality and smoothing: I'd rather walk away from a beam run with one good spectrum than a hundred poor ones. Meaning, for me anyway, if the data aren't smooth enough on their own, I'd rather spend more precious time counting than move on. I'd count for three days on a sample if I had to (I've never had to). While it has been proven that, contrary to the popular saying, one _can_ polish a turd, I'd personally rather not try. I realize this approach was more difficult when I was a grad student and everyone in the research group was clamoring for data, but even in that situation, good data > not-good data. Apologies for the tangent, but I hope someone out there might find it useful. Cheers, Mike > On Jan 22, 2020, at 5:44 PM, Carlo Segre <se...@iit.edu> wrote: > > ? > Hi Daria: > > I smooth (or boxcar average) the data which it is oversampled, such as in a > continuous scan where the data in the exafs region is spaced closer than the > usual delta k of 0.05. > > I generally don't like to smooth XANES data since smoothing does tend to > attenuate sharp features such as the ones which exist near the absorption > edge. > > Carlo > >> On Wed, 22 Jan 2020, Daria Boglaienko wrote: >> >> Hello, >> >> In what case smoothing of the data is OK? My data have a lot of noise and >> smoothing really helps (visually). I compared fit done in Artemis for >> smoothed and non-smoothed data sets and the result is very similar, however >> when I searched about it online, it looks like it is not recommended. >> What is a good way to justify it? >> >> Thank you! >> >> -Daria >> > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics > Directory, Center for Synchrotron Radiation Research and Instrumentation > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > se...@iit.edu http://phys.iit.edu/~segre se...@debian.org > _______________________________________________ > Ifeffit mailing list > 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 ------------------------------ Message: 5 Date: Thu, 23 Jan 2020 05:05:37 +0000 From: Will Bennett <w.benn...@griffith.edu.au> To: Mike Massey <mmas...@gmail.com>, Carlo Segre <se...@iit.edu>, XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] smoothing XAS data Message-ID: <sy4p282mb1051aeaf3f19ee9a41f026a4a8...@sy4p282mb1051.ausp282.prod.outlook.com> Content-Type: text/plain; charset="utf-8" I entirely agree with Mike and Scott. I never smooth data because it is a slippery slope to start on! How much should you smooth? Should you only smooth data if it looks "bad"? What does "bad data" look like anyway? If the only point of smoothing is to improve the visual look of data, then you are doing it for the wrong reason - it is better to present the true data and let the reader decide if your interpretation is robust. In my view, smoothing data is somewhat scientifically dishonest unless you have a strong justification that extends beyond trying to make the data look "better"... As someone who works with environmental samples at low concentrations, I'm very used to seeing noisy data. You just have to get used to long count times and lots of replicate scans! Cheers, Will Dr William W. Bennett Senior Lecturer Environmental Futures Research Institute School of Environment and Science Griffith University Gold Coast, Queensland, Australia M +61 401 186 488 w.benn...@griffith.edu.au Assistant Professor Nordcee, Department of Biology University of Southern Denmark Odense, Denmark M +45 8193 8111 wbenn...@biology.sdu.dk ________________________________ From: Ifeffit <ifeffit-boun...@millenia.cars.aps.anl.gov> on behalf of Mike Massey <mmas...@gmail.com> Sent: Thursday, 23 January 2020 2:50 PM To: Carlo Segre <se...@iit.edu>; XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] smoothing XAS data At this juncture, I'd like to bring up a "rule" I've made for myself regarding data quality and smoothing: I'd rather walk away from a beam run with one good spectrum than a hundred poor ones. Meaning, for me anyway, if the data aren't smooth enough on their own, I'd rather spend more precious time counting than move on. I'd count for three days on a sample if I had to (I've never had to). While it has been proven that, contrary to the popular saying, one _can_ polish a turd, I'd personally rather not try. I realize this approach was more difficult when I was a grad student and everyone in the research group was clamoring for data, but even in that situation, good data > not-good data. Apologies for the tangent, but I hope someone out there might find it useful. Cheers, Mike > On Jan 22, 2020, at 5:44 PM, Carlo Segre <se...@iit.edu> wrote: > > ? > Hi Daria: > > I smooth (or boxcar average) the data which it is oversampled, such as in a > continuous scan where the data in the exafs region is spaced closer than the > usual delta k of 0.05. > > I generally don't like to smooth XANES data since smoothing does tend to > attenuate sharp features such as the ones which exist near the absorption > edge. > > Carlo > >> On Wed, 22 Jan 2020, Daria Boglaienko wrote: >> >> Hello, >> >> In what case smoothing of the data is OK? My data have a lot of noise and >> smoothing really helps (visually). I compared fit done in Artemis for >> smoothed and non-smoothed data sets and the result is very similar, however >> when I searched about it online, it looks like it is not recommended. >> What is a good way to justify it? >> >> Thank you! >> >> -Daria >> > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics > Directory, Center for Synchrotron Radiation Research and Instrumentation > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > se...@iit.edu http://phys.iit.edu/~segre<http://phys.iit.edu/~segre> > se...@debian.org > _______________________________________________ > Ifeffit mailing list > Ifeffit@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<http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> _______________________________________________ Ifeffit mailing list Ifeffit@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<http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20200123/ffb88fc8/attachment.html> ------------------------------ Subject: Digest Footer _______________________________________________ Ifeffit mailing list 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 ------------------------------ End of Ifeffit Digest, Vol 203, Issue 5 ***************************************
_______________________________________________ Ifeffit mailing list 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
