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

Re: Ifeffit Digest, Vol 1, Issue 123
by Grant Bunker 14 Mar '03

14 Mar '03

HI, Irit - well, I'm sure the whole EXAFS community wishes you the best in delivery of your third child! And the whole world hopes the Bush/Saddam war will be short with minimum casualties on both sides. (I'll continue the conversation without the whole world listening) best wishes - grant ps congratulations on your Nature paper On Fri, 14 Mar 2003 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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: Ifeffit Digest, Vol 1, Issue 121 (Irit Sagi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 Mar 2003 21:07:04 +0200 > From: "Irit Sagi" <cssagi(a)wisemail.weizmann.ac.il> > Subject: [Ifeffit] Re: Ifeffit Digest, Vol 1, Issue 121 > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <se70f2fb.035(a)wisemail.weizmann.ac.il> > Content-Type: text/plain; charset=US-ASCII > > Oops, I see that the whole EXAFS community saw this mail.......Oh well, SHALOM from Israel. Irit. > > > > > > > > Dr. Irit Sagi > Department of structural Biology > The Weizmann Institute of Science > ISRAEL > Tel/Fax 972-8-9342130 > e-mail: irit.sagi(a)weizmann.ac.il > > >>> cssagi(a)wisemail.weizmann.ac.il 03/13/03 08:56pm >>> > Hi Grant > I read your e-mails regarding IFEFFIT and I could not help myself to ask how are you doing and how are things. > We are all OK here in Israel, as much as we can of course. I am pregnant with my third child and I am due by the end of the month. Besides this, we are well prepared for the USA-Iraq war. In fact we are expecting it to start on Monday. > I was invited to give a talk in the APS workshop this year but I will not be able to make due to the new baby. > I hope that everything is OK with you and your family. > All the best, Irit. > > Dr. Irit Sagi > Department of structural Biology > The Weizmann Institute of Science > ISRAEL > Tel/Fax 972-8-9342130 > e-mail: irit.sagi(a)weizmann.ac.il > > >>> bunker(a)biocat1.phys.iit.edu 03/13/03 08:38pm >>> > Matt - it might be sensible to just add a new function to do the > rebinning i.e. map mu(E)->mu'(E') on resampled grid (mu data around the > edge could be left unchanged). People could call the function ('rebin"?) > only they needed it; subsequent routines could be kept as they > are now. Anyone who doesn't like the rebinning wouldn't be obligated to > use it. > > thanks - grant > > On Thu, 13 Mar 2003 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > > > 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: Rebinning (Kelly, Shelly D.) > > 2. Rebinning (Bruce Ravel) > > 3. Re: Rebinning (Carlo U. Segre) > > 4. Re: Rebinning (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 12 Mar 2003 13:52:45 -0600 > > From: "Kelly, Shelly D." <SKelly(a)anl.gov> > > Subject: RE: [Ifeffit] Rebinning > > To: "'XAFS Analysis using Ifeffit'" > > <ifeffit(a)millenia.cars.aps.anl.gov> > > Message-ID: > > <DC97518EF1B5E3418A86F59A9A58035D01D9A70A(a)ANLEXCH.CTD.ANL.GOV> > > Content-Type: text/plain; charset="us-ascii" > > > > Hello All, > > > > There seems to be a lot of interest in Rebinning data. I have a perl script > > that > > I've written to do the same thing. I thought it might be of interest. > > > > Shelly > > > > > -----Original Message----- > > > From: Newville, Matthew G. > > > Sent: Tuesday, March 11, 2003 2:08 PM > > > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > > > Subject: Re: [Ifeffit] Rebinning > > > > > > > > > Hi Carlo, > > > > > > Thanks!! That's wonderful. It seems like this should be an > > > option in spline() and bkg_cl(), and possibly in pre_edge(). I > > > admit to being still a little confused by the goal of the > > > rebinning, especially with respect to loss of resolution. It > > > seems like to use this script, you need to do two things: > > > 1. select an E0. The data will be put at energies that > > > will give an even k-grid with this e0. I think it's > > > inevitable that if e0 changes, you might want to re-bin. > > > > > > 2. assume that the k-grid is small enough that the > > > measurements at independent energies are within the > > > acceptable energy resolution that they can be > > > simply summed. > > > > > > Is that right? > > > > > > Would it be OK with you (and everyone else) to have a weighted > > > average replace the boxcar average? For example, at k=12, > > > [E(k+0.05) - E(k)] = 5eV, which is larger than normal energy > > > resolutions, so the boxcar average might wash out the high-k > > > EXAFS, no? It might be better to convolve the spectra with a > > > lorenztian reflecting the incident energy resolution (probably > > > defaulting to 1eV). Does that seem OK or is there something eles > > > going on? > > > > > > Anyway, thanks!! > > > > > > --Matt > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > >

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Artemis document
by Bruce Ravel 14 Mar '03

14 Mar '03

Hi folks, I got mail this afternoon asking me about documentation for Artemis. That has, of course, been a long-standing shortcoming of the code. It turns out that I have spent a decent chunk of time in the last couple weeks working on the Artemis doc. It is only about 25% written, but the portions that I have written are introductory material. It should be useful even in its current, sparse form. Here's the URL: http://leonardo.phys.washington.edu/~ravel/software/exafs/docs.html I am only posting the PDF at this time. I'll be updating it frequently as I work on it, but I probably won't announce updates on this channel until it is a lot closer to finished. So check back often if you are interested. Please be aware that it is nowhere near finished. It is full of gaps, typos, suspicious statements, and dangling trains of thought. It is so far from finished that "documentation" may be too kind of a term. However, it seems that posting the unfinished doc on my web site is well within that open source spirit of "release early, release often" that I have adopted with my codes. If it proves useful to some of you -- super! B P.S. If anyone is interested in helping out with the doc, either by copy editing or by contributing text, let me know -- I'd be jumping- up-and-down happy if that happened. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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A question for Windows users
by Bruce Ravel 14 Mar '03

14 Mar '03

Hi folks, Athena is not always particularly creative about the names it suggests for output files. For example, if you use the feature of saving several marked groups to a single output file, Athena suggests that the names be "marked.space". That is, if you save marked groups as chi(k), the suggested file name is "marked.chi". If you save marked groups as the real part of chi(R), the suggested file name is "marked.chir_re". It is possible to configure Explorer such that it does not display file extensions (i.e. the bit after the dot). That might make it hard to tell different marked group output files apart if the suggested names are used. Is this a problem for anyone? Should I change the suggested names such that the suggestive part is not in the extension? That is, would "chi.marked" and "chir_re.marked" be better names? If no one pipes up, then I'll assume things are ok as they stand. If even one person makes a compelling argument, I'll probably change the suggested names throughout my programs to avoid this situation. Thanks. B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Re: Ifeffit Digest, Vol 1, Issue 121
by Irit Sagi 13 Mar '03

13 Mar '03

Oops, I see that the whole EXAFS community saw this mail.......Oh well, SHALOM from Israel. Irit. Dr. Irit Sagi Department of structural Biology The Weizmann Institute of Science ISRAEL Tel/Fax 972-8-9342130 e-mail: irit.sagi(a)weizmann.ac.il >>> cssagi(a)wisemail.weizmann.ac.il 03/13/03 08:56pm >>> Hi Grant I read your e-mails regarding IFEFFIT and I could not help myself to ask how are you doing and how are things. We are all OK here in Israel, as much as we can of course. I am pregnant with my third child and I am due by the end of the month. Besides this, we are well prepared for the USA-Iraq war. In fact we are expecting it to start on Monday. I was invited to give a talk in the APS workshop this year but I will not be able to make due to the new baby. I hope that everything is OK with you and your family. All the best, Irit. Dr. Irit Sagi Department of structural Biology The Weizmann Institute of Science ISRAEL Tel/Fax 972-8-9342130 e-mail: irit.sagi(a)weizmann.ac.il >>> bunker(a)biocat1.phys.iit.edu 03/13/03 08:38pm >>> Matt - it might be sensible to just add a new function to do the rebinning i.e. map mu(E)->mu'(E') on resampled grid (mu data around the edge could be left unchanged). People could call the function ('rebin"?) only they needed it; subsequent routines could be kept as they are now. Anyone who doesn't like the rebinning wouldn't be obligated to use it. thanks - grant On Thu, 13 Mar 2003 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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: Rebinning (Kelly, Shelly D.) > 2. Rebinning (Bruce Ravel) > 3. Re: Rebinning (Carlo U. Segre) > 4. Re: Rebinning (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Mar 2003 13:52:45 -0600 > From: "Kelly, Shelly D." <SKelly(a)anl.gov> > Subject: RE: [Ifeffit] Rebinning > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <DC97518EF1B5E3418A86F59A9A58035D01D9A70A(a)ANLEXCH.CTD.ANL.GOV> > Content-Type: text/plain; charset="us-ascii" > > Hello All, > > There seems to be a lot of interest in Rebinning data. I have a perl script > that > I've written to do the same thing. I thought it might be of interest. > > Shelly > > > -----Original Message----- > > From: Newville, Matthew G. > > Sent: Tuesday, March 11, 2003 2:08 PM > > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > > Subject: Re: [Ifeffit] Rebinning > > > > > > Hi Carlo, > > > > Thanks!! That's wonderful. It seems like this should be an > > option in spline() and bkg_cl(), and possibly in pre_edge(). I > > admit to being still a little confused by the goal of the > > rebinning, especially with respect to loss of resolution. It > > seems like to use this script, you need to do two things: > > 1. select an E0. The data will be put at energies that > > will give an even k-grid with this e0. I think it's > > inevitable that if e0 changes, you might want to re-bin. > > > > 2. assume that the k-grid is small enough that the > > measurements at independent energies are within the > > acceptable energy resolution that they can be > > simply summed. > > > > Is that right? > > > > Would it be OK with you (and everyone else) to have a weighted > > average replace the boxcar average? For example, at k=12, > > [E(k+0.05) - E(k)] = 5eV, which is larger than normal energy > > resolutions, so the boxcar average might wash out the high-k > > EXAFS, no? It might be better to convolve the spectra with a > > lorenztian reflecting the incident energy resolution (probably > > defaulting to 1eV). Does that seem OK or is there something eles > > going on? > > > > Anyway, thanks!! > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > >

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Re: Ifeffit Digest, Vol 1, Issue 121
by Irit Sagi 13 Mar '03

13 Mar '03

Hi Grant I read your e-mails regarding IFEFFIT and I could not help myself to ask how are you doing and how are things. We are all OK here in Israel, as much as we can of course. I am pregnant with my third child and I am due by the end of the month. Besides this, we are well prepared for the USA-Iraq war. In fact we are expecting it to start on Monday. I was invited to give a talk in the APS workshop this year but I will not be able to make due to the new baby. I hope that everything is OK with you and your family. All the best, Irit. Dr. Irit Sagi Department of structural Biology The Weizmann Institute of Science ISRAEL Tel/Fax 972-8-9342130 e-mail: irit.sagi(a)weizmann.ac.il >>> bunker(a)biocat1.phys.iit.edu 03/13/03 08:38pm >>> Matt - it might be sensible to just add a new function to do the rebinning i.e. map mu(E)->mu'(E') on resampled grid (mu data around the edge could be left unchanged). People could call the function ('rebin"?) only they needed it; subsequent routines could be kept as they are now. Anyone who doesn't like the rebinning wouldn't be obligated to use it. thanks - grant On Thu, 13 Mar 2003 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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: Rebinning (Kelly, Shelly D.) > 2. Rebinning (Bruce Ravel) > 3. Re: Rebinning (Carlo U. Segre) > 4. Re: Rebinning (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Mar 2003 13:52:45 -0600 > From: "Kelly, Shelly D." <SKelly(a)anl.gov> > Subject: RE: [Ifeffit] Rebinning > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <DC97518EF1B5E3418A86F59A9A58035D01D9A70A(a)ANLEXCH.CTD.ANL.GOV> > Content-Type: text/plain; charset="us-ascii" > > Hello All, > > There seems to be a lot of interest in Rebinning data. I have a perl script > that > I've written to do the same thing. I thought it might be of interest. > > Shelly > > > -----Original Message----- > > From: Newville, Matthew G. > > Sent: Tuesday, March 11, 2003 2:08 PM > > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > > Subject: Re: [Ifeffit] Rebinning > > > > > > Hi Carlo, > > > > Thanks!! That's wonderful. It seems like this should be an > > option in spline() and bkg_cl(), and possibly in pre_edge(). I > > admit to being still a little confused by the goal of the > > rebinning, especially with respect to loss of resolution. It > > seems like to use this script, you need to do two things: > > 1. select an E0. The data will be put at energies that > > will give an even k-grid with this e0. I think it's > > inevitable that if e0 changes, you might want to re-bin. > > > > 2. assume that the k-grid is small enough that the > > measurements at independent energies are within the > > acceptable energy resolution that they can be > > simply summed. > > > > Is that right? > > > > Would it be OK with you (and everyone else) to have a weighted > > average replace the boxcar average? For example, at k=12, > > [E(k+0.05) - E(k)] = 5eV, which is larger than normal energy > > resolutions, so the boxcar average might wash out the high-k > > EXAFS, no? It might be better to convolve the spectra with a > > lorenztian reflecting the incident energy resolution (probably > > defaulting to 1eV). Does that seem OK or is there something eles > > going on? > > > > Anyway, thanks!! > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > >

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Re: Ifeffit Digest, Vol 1, Issue 121
by Grant Bunker 13 Mar '03

13 Mar '03

Matt - it might be sensible to just add a new function to do the rebinning i.e. map mu(E)->mu'(E') on resampled grid (mu data around the edge could be left unchanged). People could call the function ('rebin"?) only they needed it; subsequent routines could be kept as they are now. Anyone who doesn't like the rebinning wouldn't be obligated to use it. thanks - grant On Thu, 13 Mar 2003 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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: Rebinning (Kelly, Shelly D.) > 2. Rebinning (Bruce Ravel) > 3. Re: Rebinning (Carlo U. Segre) > 4. Re: Rebinning (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 12 Mar 2003 13:52:45 -0600 > From: "Kelly, Shelly D." <SKelly(a)anl.gov> > Subject: RE: [Ifeffit] Rebinning > To: "'XAFS Analysis using Ifeffit'" > <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <DC97518EF1B5E3418A86F59A9A58035D01D9A70A(a)ANLEXCH.CTD.ANL.GOV> > Content-Type: text/plain; charset="us-ascii" > > Hello All, > > There seems to be a lot of interest in Rebinning data. I have a perl script > that > I've written to do the same thing. I thought it might be of interest. > > Shelly > > > -----Original Message----- > > From: Newville, Matthew G. > > Sent: Tuesday, March 11, 2003 2:08 PM > > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > > Subject: Re: [Ifeffit] Rebinning > > > > > > Hi Carlo, > > > > Thanks!! That's wonderful. It seems like this should be an > > option in spline() and bkg_cl(), and possibly in pre_edge(). I > > admit to being still a little confused by the goal of the > > rebinning, especially with respect to loss of resolution. It > > seems like to use this script, you need to do two things: > > 1. select an E0. The data will be put at energies that > > will give an even k-grid with this e0. I think it's > > inevitable that if e0 changes, you might want to re-bin. > > > > 2. assume that the k-grid is small enough that the > > measurements at independent energies are within the > > acceptable energy resolution that they can be > > simply summed. > > > > Is that right? > > > > Would it be OK with you (and everyone else) to have a weighted > > average replace the boxcar average? For example, at k=12, > > [E(k+0.05) - E(k)] = 5eV, which is larger than normal energy > > resolutions, so the boxcar average might wash out the high-k > > EXAFS, no? It might be better to convolve the spectra with a > > lorenztian reflecting the incident energy resolution (probably > > defaulting to 1eV). Does that seem OK or is there something eles > > going on? > > > > Anyway, thanks!! > > > > --Matt > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > >

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Rebinning
by Carlo U. Segre 12 Mar '03

12 Mar '03

Matt and Bruce: Following our previous discussion of rebinning continuous scan data, I am attaching a python code fragment which we use to perform this function. You are free to use it as you like. It was written by Ken McIvor, a student at IIT as part of a larger project to manipulate and preview MR-CAT XAFS data. We simply pulled out the code and annotated it somewhat. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Research, Armour College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Rebinning
by Bruce Ravel 12 Mar '03

12 Mar '03

Hey folks, As an interface developer, I have to keep a broad perspective. It seems to me that, when Athena gets a rebinning capability, it should give the user a choice between boxcar and convolution (and whatever other technique someone makes a reasonable case for), thus I would want to implement something like what Ken or Shelly wrote as well as an interface to ifeffit's built-in convolution thingie. To address one of Matt's points, I reckon I'll put a flag in Athena's group object that would get set whenever E0 changes. That way Athena could automagically rebin the data before background removal for any data group for which rebinning has been requested. That combined with some of Athena's other automation features should make handling large amounts of qexafs data a breeze. As for which approach is appropriate, Grant pointed out that preserving resolution at high k is not completely necessary. I agree, but only with the caveat that your measurement is of a single edge. One could imagine using quick measurement techniques to measure two different, nearby edges --- perhaps for a dichroism experiment, perhaps simply to measure two exafs spectra. In that case, Matt's concern about boxcar is quite valid. That's not rocket science, but it would be easy to forget at the beamline at 3 in the morning ;-) Regards, B P.S. I really have to insist that everyone (and _especially_ the digest users) respect netiquette quoting guidelines. In the last few days there have been some egregious examples of poor netiquette on our lovely, little mailing list. Here's a nice explanation of how to quote when responding to another person's posting: http://earlydues.hispeed.com/ieel/netiquette.htm#quote -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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RE: [Ifeffit] Rebinning
by Kelly, Shelly D. 12 Mar '03

12 Mar '03

Hello All, There seems to be a lot of interest in Rebinning data. I have a perl script that I've written to do the same thing. I thought it might be of interest. Shelly > -----Original Message----- > From: Newville, Matthew G. > Sent: Tuesday, March 11, 2003 2:08 PM > To: Carlo.Segre(a)iit.edu; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Rebinning > > > Hi Carlo, > > Thanks!! That's wonderful. It seems like this should be an > option in spline() and bkg_cl(), and possibly in pre_edge(). I > admit to being still a little confused by the goal of the > rebinning, especially with respect to loss of resolution. It > seems like to use this script, you need to do two things: > 1. select an E0. The data will be put at energies that > will give an even k-grid with this e0. I think it's > inevitable that if e0 changes, you might want to re-bin. > > 2. assume that the k-grid is small enough that the > measurements at independent energies are within the > acceptable energy resolution that they can be > simply summed. > > Is that right? > > Would it be OK with you (and everyone else) to have a weighted > average replace the boxcar average? For example, at k=12, > [E(k+0.05) - E(k)] = 5eV, which is larger than normal energy > resolutions, so the boxcar average might wash out the high-k > EXAFS, no? It might be better to convolve the spectra with a > lorenztian reflecting the incident energy resolution (probably > defaulting to 1eV). Does that seem OK or is there something eles > going on? > > Anyway, thanks!! > > --Matt > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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rebinning and sampling
by Grant Bunker 12 Mar '03

12 Mar '03

Hi, Matt - I think the essential point is that sampling at 1 eV at k=12 A^(-1) is greatly oversampled. Suppose you want to sample data out to R=10A (just to make sure you get everything). Then the period of those oscillations in k-space is 2 Pi/(2 10A) ~ .3 A^(-1). Nyquist's theorem says you should sample at least twice per cycle, so you need delta K of 0.15 A^(-1) or smaller (you don't want higher frequency noise to alias down to low frequencies0. The 0.05 grid historically used in the UW programs therefore is pretty conservative. Attempting to preserve a 1 eV resolution at k=12 A^(-1) would imply a sampling of about 0.01 A^(-1), which is quite unnecessary. So I think the box-car average is ok when you are far enough above the edge. I implemented something like in my own mathematica programs a couple of years ago and it works fine, and Nick Dimakis built it into the tcl/tk based APEX package last year. thanks - grant On Wed, 12 Mar 2003 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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: fourier transforms and k grids (Matt Newville) > 2. Rebinning (Carlo U. Segre) > 3. Re: Rebinning (Bruce Ravel) > 4. Re: Rebinning (Matt Newville) > 5. Re: Rebinning (Carlo U. Segre) > 6. Re: Rebinning (Carlo U. Segre) > 7. Re: Rebinning (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 11 Mar 2003 12:04:57 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] fourier transforms and k grids > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0303111110060.24069-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Peter, > > Thanks for the report. I've verified your findings that feffit() > is doing the wrong thing for the Fourier transforms for data on > grids other than k-grid of 0.05Ang^-1. Here's what is happening: > > feffit() really is interpolating data internally onto the 0.05 > grid for the fit. The fit _should_ procede correctly for data on > any grid. > > Anyway, at the end of feffit() command it sends the data off to > the fftf() command to make the chir_mag, etc arrays. It is at > this point that the k-array in ***NOT*** being sent to the FFT. > I've verified in my own tests that including the k-array in the > FFT works, giving the right FFT. hopefully I will get a fixed > version posted this week. But currently, the r-space data (data > only, not the fits) from feffit() are wrong when a non-0.05 > k-grid is used. Simply doing > fftf(real=data.chi, k = data.k) > > will give the correct r-space data. > > I also noticed another wart and small inconsistency between > feffit() and fftf() from your example, which has the 'data' over > a smaller range than the FFT window. > > Thanks, and sorry for the trouble, > > --Matt > > > > ------------------------------ > > Message: 2 > Date: Tue, 11 Mar 2003 12:16:24 -0600 (CST) > From: "Carlo U. Segre" <segre(a)iit.edu> > Subject: [Ifeffit] Rebinning > To: IFEFFIT Mailing List <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0303111214010.702-200000(a)boride.phys.iit.edu> > Content-Type: text/plain; charset="us-ascii" > > > Matt and Bruce: > > Following our previous discussion of rebinning continuous scan data, I am > attaching a python code fragment which we use to perform this function. > You are free to use it as you like. It was written by Ken McIvor, a > student at IIT as part of a larger project to manipulate and preview > MR-CAT XAFS data. We simply pulled out the code and annotated it > somewhat. > > Carlo > > -- > Carlo U. Segre -- Professor of Physics > Associate Dean for Research, Armour College > Illinois Institute of Technology > Voice: 312.567.3498 Fax: 312.567.3494 > Carlo.Segre(a)iit.edu http://www.iit.edu/~segre >

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