Re: [Ifeffit] MBACK and Athena
Chris, I measured the spectra of copper foil which gave me Cu foil Then I changed the sample to Sample 1 and did 3 successive scans. Sample1_scan1 Sample1_scan2 Sample1_scan3 Thanks. Cyril -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Christopher Patridge Sent: Friday, March 08, 2013 3:43 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] MBACK and Athena Cyril, Is the copper foil a separate file or is this file imported together with the other scans as a reference channel? If separate files, then there is not a clear relationship between sample and the foil since these were collected at different times and hence corrections for drift or other gremlins will not be the same. Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 3/8/2013 2:49 AM, Bajamundi Cyril wrote: > Dear Bruce, > > The motivation for the question is that I'm concerned whether the shift in E > values after calibration is conserved when the calibrated data has been saved > in the .xmu file. > But thanks to the link you have sent to me and your previous answer in the > mailing list archive > <<http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02755.html>> > things are a bit clearer now. > So here's a follow up. I have taken the following scans successively > Cu foil > Sample1_scan1 > Sample1_scan2 > Sample1_scan3 > I then process the data in Athena, to begin I calibrated the Cu foil > spectrum, such that the nice orange circle falls at the tabulated value of > 8979 eV. This in turn gives some "eshift" value of -0.360. What is the > relationship of this eshift to the spectra of sample 1, should I apply this > eshift to the scans for sample 1 as? Definitely I can't apply the E0. > > This is still a bit vague in my mind, even after reading the basic data > processing section in the documentation. > Thank you in advance. > > Warm regards, > Cyril > > -Original Message- > From: ifeffit-boun...@millenia.cars.aps.anl.gov > [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Bruce > Ravel > Sent: Thursday, March 07, 2013 3:55 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] MBACK and Athena > > On Thursday, March 07, 2013 12:10:26 PM Bajamundi Cyril wrote: >> 1. Is this procedure valid? In the sense that no information or features >> of the spectrum are lost from merge.xmu to merged.xmu.mnor file. > Do you have some reason to believe that might be happening? If so, perhaps > you could ask a more explicit question. > >> 2. How will the procedure affect this procedure? > Calibration, as it is defined in Athena, is a procedure that changes *both* > the E0 and the Eshift values so that a selected point in the spectrum has a > selected energy value. > >http://bruceravel.github.com/demeter/aug/process/cal.html > > I'm not certain I've answered your question, but I am unclear what is > motivating your question. > > B > > > -- > Bruce Ravel bravel at bnl.gov > > National Institute of Standards and Technology Synchrotron Methods > Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, > 11973 > > My homepage:http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] MBACK and Athena
Cyril, Is the copper foil a separate file or is this file imported together with the other scans as a reference channel? If separate files, then there is not a clear relationship between sample and the foil since these were collected at different times and hence corrections for drift or other gremlins will not be the same. Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 3/8/2013 2:49 AM, Bajamundi Cyril wrote: Dear Bruce, The motivation for the question is that I'm concerned whether the shift in E values after calibration is conserved when the calibrated data has been saved in the .xmu file. But thanks to the link you have sent to me and your previous answer in the mailing list archive <<http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02755.html>> things are a bit clearer now. So here's a follow up. I have taken the following scans successively Cu foil Sample1_scan1 Sample1_scan2 Sample1_scan3 I then process the data in Athena, to begin I calibrated the Cu foil spectrum, such that the nice orange circle falls at the tabulated value of 8979 eV. This in turn gives some "eshift" value of -0.360. What is the relationship of this eshift to the spectra of sample 1, should I apply this eshift to the scans for sample 1 as? Definitely I can't apply the E0. This is still a bit vague in my mind, even after reading the basic data processing section in the documentation. Thank you in advance. Warm regards, Cyril -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: Thursday, March 07, 2013 3:55 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] MBACK and Athena On Thursday, March 07, 2013 12:10:26 PM Bajamundi Cyril wrote: 1. Is this procedure valid? In the sense that no information or features of the spectrum are lost from merge.xmu to merged.xmu.mnor file. Do you have some reason to believe that might be happening? If so, perhaps you could ask a more explicit question. 2. How will the procedure affect this procedure? Calibration, as it is defined in Athena, is a procedure that changes *both* the E0 and the Eshift values so that a selected point in the spectrum has a selected energy value. http://bruceravel.github.com/demeter/aug/process/cal.html I'm not certain I've answered your question, but I am unclear what is motivating your question. B -- Bruce Ravel bravel at bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage:http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] MBACK and Athena
Dear Bruce, The motivation for the question is that I'm concerned whether the shift in E values after calibration is conserved when the calibrated data has been saved in the .xmu file. But thanks to the link you have sent to me and your previous answer in the mailing list archive <<http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02755.html>> things are a bit clearer now. So here's a follow up. I have taken the following scans successively Cu foil Sample1_scan1 Sample1_scan2 Sample1_scan3 I then process the data in Athena, to begin I calibrated the Cu foil spectrum, such that the nice orange circle falls at the tabulated value of 8979 eV. This in turn gives some "eshift" value of -0.360. What is the relationship of this eshift to the spectra of sample 1, should I apply this eshift to the scans for sample 1 as? Definitely I can't apply the E0. This is still a bit vague in my mind, even after reading the basic data processing section in the documentation. Thank you in advance. Warm regards, Cyril -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: Thursday, March 07, 2013 3:55 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] MBACK and Athena On Thursday, March 07, 2013 12:10:26 PM Bajamundi Cyril wrote: > 1. Is this procedure valid? In the sense that no information or features > of the spectrum are lost from merge.xmu to merged.xmu.mnor file. Do you have some reason to believe that might be happening? If so, perhaps you could ask a more explicit question. > 2. How will the procedure affect this procedure? Calibration, as it is defined in Athena, is a procedure that changes *both* the E0 and the Eshift values so that a selected point in the spectrum has a selected energy value. http://bruceravel.github.com/demeter/aug/process/cal.html I'm not certain I've answered your question, but I am unclear what is motivating your question. B -- Bruce Ravel bravel at bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage:http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] MBACK and Athena
On Thursday, March 07, 2013 12:10:26 PM Bajamundi Cyril wrote: > 1. Is this procedure valid? In the sense that no information or features > of the spectrum are lost from merge.xmu to merged.xmu.mnor file. Do you have some reason to believe that might be happening? If so, perhaps you could ask a more explicit question. > 2. How will the procedure affect this procedure? Calibration, as it is defined in Athena, is a procedure that changes *both* the E0 and the Eshift values so that a selected point in the spectrum has a selected energy value. http://bruceravel.github.com/demeter/aug/process/cal.html I'm not certain I've answered your question, but I am unclear what is motivating your question. B -- Bruce Ravel bravel at bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage:http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] MBACK and Athena
Hello Chris, I have short-range spectra for my standards and that I am having challenges in normalizing them. It has been suggested before in the previous thread that MBACK, although not absolutely, "will sort of solve the problem in the sense that it offers a somewhat more stable way of dealing with short-range data" -thus this interest in normalizing the my standards spectra using MBACK. Regards, Cyril From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Christopher Patridge Sent: Thursday, March 07, 2013 3:22 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] MBACK and Athena Hello Cyril, Is there a particular reason for moving the data to Matlab and using MBACK rather than the built-in procedure in Athena? From your email, it seems that you have the raw data which you then merge. I would feel confident in performing all the data processing in Athena. Your hope in merging data is remove noise and improve the confidence that features seen in the data are real. Someone may be able to comment on the impact of MBACK, but questions here mostly deal with ifeffit. Good luck, Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 3/7/2013 7:10 AM, Bajamundi Cyril wrote: [cid:image001.gif@01CE1B4A.F709D670] Hello, I have 3 spectra taken from a single sample, I align, merge and save the merged data as merge.xmu file. I then normalize this merged data using the MBACK algorithm in Matlab, the results of which is stored as merged.xmu.mnor file. This file, I then import to ATHENA using the instructions in http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03523.html. I do this for all my samples and standards in order for me to perform LCF. My questions are 1. Is this procedure valid? In the sense that no information or features of the spectrum are lost from merge.xmu to merged.xmu.mnor file. 2. How will the procedure affect this procedure? Thank you for your time in answering my questions. Regards, Cyril PS: This query is in relation to my previous question [Ifeffit] Basic question in normalization and background removal ___ 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 <>___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] MBACK and Athena
Hello Cyril, Is there a particular reason for moving the data to Matlab and using MBACK rather than the built-in procedure in Athena? From your email, it seems that you have the raw data which you then merge. I would feel confident in performing all the data processing in Athena. Your hope in merging data is remove noise and improve the confidence that features seen in the data are real. Someone may be able to comment on the impact of MBACK, but questions here mostly deal with ifeffit. Good luck, Chris Christopher J. Patridge, PhD NRC Post Doctoral Research Associate Naval Research Laboratory Washington, DC 20375 Cell: 315-529-0501 On 3/7/2013 7:10 AM, Bajamundi Cyril wrote: Hello, I have 3 spectra taken from a single sample, I align, merge and save the merged data as merge.xmu file. I then normalize this merged data using the MBACK algorithm in Matlab, the results of which is stored as merged.xmu.mnor file. This file, I then import to ATHENA using the instructions in http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03523.html. I do this for all my samples and standards in order for me to perform LCF. My questions are 1. Is this procedure valid? In the sense that no information or features of the spectrum are lost from merge.xmu to merged.xmu.mnor file. 2. How will the procedure affect this procedure? Thank you for your time in answering my questions. Regards, Cyril PS: This query is in relation to my previous question [Ifeffit] Basic question in normalization and background removal ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] MBACK and Athena
Hello, I have 3 spectra taken from a single sample, I align, merge and save the merged data as merge.xmu file. I then normalize this merged data using the MBACK algorithm in Matlab, the results of which is stored as merged.xmu.mnor file. This file, I then import to ATHENA using the instructions in http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03523.html. I do this for all my samples and standards in order for me to perform LCF. My questions are 1. Is this procedure valid? In the sense that no information or features of the spectrum are lost from merge.xmu to merged.xmu.mnor file. 2. How will the procedure affect this procedure? Thank you for your time in answering my questions. Regards, Cyril PS: This query is in relation to my previous question [Ifeffit] Basic question in normalization and background removal <>___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
