Re: [Ifeffit] How to perform normalisation and background removal of data containing L3 and L2 edges
In checking the literature, has anyone indicated what data collection ranges they used, and what pre- and post-edge regions were selected for normalisation? Do you have more data below 2800eV that you are not showing? Starting data collection only 50 eV or so below the edge can be problematic for estimating background, particularly so if a large feature (white line) is present at the edge. Around 2810 eV, the step size has changed from coarser to finer steps in energy: and that seems to be associated with a change in slope, but with more noise in the coarser step range. If I had to pick something with just this data, I could tolerate using the first 10 eV of the scan for the pre-edge... If it is just this one sample, and you aren't trying to conclude anything from absolute intensities, this could be reasonable. If you are comparing, be consistent in how you treat the data, and understand (and admit in presenting the data) that there can be errors associated with normalisation. If I vary the post-edge values a few eV to either direction, the edge step changes by +/- 0.03 (0.90+/-0.03). The variation is even larger if I push the pre-edge upper limit to closer to the edge. (and I can convince myself that the 1st ~15 eV of the scan are reasonable, for an edge step closer to 0.94) Generally, for this and future reference, make sure you have sufficient data range for processing. This will vary depending on what edge you are studying, but here, I would have started at least 100 eV below the edge. Understand that processing has an element of subjective interpretation to it - asking yourself what is reasonable. Treat similar data consistently. Probably paraphrasing Bruce a bit, but he has a mantra of "Data handling and interpretation should be done in a manner that is reasonable, plausible, and defensible." Over time, through experience, you can gain an understanding of what constitutes reasonable, plausible and defensible. Practice on some standards at different edges to get a feel for it. Some more unsolicited advice: Avoid bias - let the data tell their story. Explain how the data were collected. Describe in detail how the spectra were processed. Discuss the results - what you observe, how it compares to literature. If you see differences, report differences, and consider what might be plausible explanations. On 2020-12-07 8:55 a.m., Deka, N. wrote: Dear all I am a student trying to learn Athena for XAS data processing. Attached is a data file which contains L3 and L2 edge of Ru. What should be the right parameters for background removal and normalization of this data set? In the videos from Bruce Ravel, I could not find any example for such a data set containing two edges. Thank you Best Regards, Nipon Deka Leiden University ___ 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 ___ 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
Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported data
Likeliest reason: https://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units Make sure "xmu" is selected in the indicated menu. Good luck, B On 12/7/20 10:26 AM, Deka, N. wrote: > Dear all > > I am a new student trying to work with Athena for XAS data processing. > Attached is a data file which when I import does not show the background > and also Athena cannot plot “k” , “q” , “R” plots for the data. Please > suggest me a possible solution. > > Thank you > > Best Regards, > > Nipon Deka > > Leiden University > > > ___ > 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 > -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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
[Ifeffit] How to perform normalisation and background removal of data containing L3 and L2 edges
Dear all I am a student trying to learn Athena for XAS data processing. Attached is a data file which contains L3 and L2 edge of Ru. What should be the right parameters for background removal and normalization of this data set? In the videos from Bruce Ravel, I could not find any example for such a data set containing two edges. Thank you Best Regards, Nipon Deka Leiden University RuOxAA_200mV_combined.dat Description: RuOxAA_200mV_combined.dat ___ 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
Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported data
Data is just XANES at Ru L2...be better if it went to higher E for normalisation purposes Why are you trying to plot XANES data in k,q or R? On 2020-12-07 7:38 a.m., Ravel, Bruce wrote: Likeliest reason: https://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units Make sure "xmu" is selected in the indicated menu. Good luck, B On 12/7/20 10:26 AM, Deka, N. wrote: Dear all I am a new student trying to work with Athena for XAS data processing. Attached is a data file which when I import does not show the background and also Athena cannot plot “k” , “q” , “R” plots for the data. Please suggest me a possible solution. Thank you Best Regards, Nipon Deka Leiden University ___ 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 ___ 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
Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported
Dear Fred I did not completely understand what you meant. How do I change the data type? And to which data type should I change to? mu(e)(e)?? Thanks Nipon Deka -Original Message- From: Ifeffit On Behalf Of Mosselmans, Fred (DLSLtd,RAL,SCI) Sent: maandag 7 december 2020 16:34 To: 'ifeffit@millenia.cars.aps.anl.gov' Subject: Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported Dear Nipon, I suspect you have read the spectrum in as XANEs if you change the data type to mu(e)(e) it should give you what you want Thanks Fred Mosslemans Message: 2 Date: Mon, 7 Dec 2020 15:26:19 + From: "Deka, N." To: "ifeffit@millenia.cars.aps.anl.gov" Subject: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported data Message-ID: <3088c35cdc4c4e488b2782623526d...@lic.leidenuniv.nl> Content-Type: text/plain; charset="us-ascii" Dear all I am a new student trying to work with Athena for XAS data processing. Attached is a data file which when I import does not show the background and also Athena cannot plot "k" , "q" , "R" plots for the data. Please suggest me a possible solution. Thank you Best Regards, Nipon Deka Leiden University -- next part -- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20201207/b51a474e/attachment.htm> -- next part -- A non-text attachment was scrubbed... Name: RuOxAA_200mV_L2.dat Type: application/octet-stream Size: 17670 bytes Desc: RuOxAA_200mV_L2.dat URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20201207/b51a474e/attachment.obj> -- 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 214, Issue 2 *** -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom ___ 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 ___ 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
Re: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported
Dear Nipon, I suspect you have read the spectrum in as XANEs if you change the data type to mu(e)(e) it should give you what you want Thanks Fred Mosslemans Message: 2 Date: Mon, 7 Dec 2020 15:26:19 + From: "Deka, N." To: "ifeffit@millenia.cars.aps.anl.gov" Subject: [Ifeffit] Unable to see background and "k", "q", "R" plots for imported data Message-ID: <3088c35cdc4c4e488b2782623526d...@lic.leidenuniv.nl> Content-Type: text/plain; charset="us-ascii" Dear all I am a new student trying to work with Athena for XAS data processing. Attached is a data file which when I import does not show the background and also Athena cannot plot "k" , "q" , "R" plots for the data. Please suggest me a possible solution. Thank you Best Regards, Nipon Deka Leiden University -- next part -- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20201207/b51a474e/attachment.htm> -- next part -- A non-text attachment was scrubbed... Name: RuOxAA_200mV_L2.dat Type: application/octet-stream Size: 17670 bytes Desc: RuOxAA_200mV_L2.dat URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20201207/b51a474e/attachment.obj> -- 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 214, Issue 2 *** -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom ___ 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
[Ifeffit] Unable to see background and "k", "q", "R" plots for imported data
Dear all I am a new student trying to work with Athena for XAS data processing. Attached is a data file which when I import does not show the background and also Athena cannot plot "k" , "q" , "R" plots for the data. Please suggest me a possible solution. Thank you Best Regards, Nipon Deka Leiden University RuOxAA_200mV_L2.dat Description: RuOxAA_200mV_L2.dat ___ 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
