should we break symmetry? ;) darek

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Carlo Segre Sent: Thursday, November 19, 2009 3:35 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Bug in Athena?

symmetry? ;)

Carlo

On Thu, 19 Nov 2009, Zajac, Dariusz A. wrote:

...

Dear Bruce, Dear All, maybe it is a naïve question but I want to ask and to point this problem...

Windows XP. Athena 0.8.059 Sc.Linux. Athena 0.8.060

I have a set of data with refernces (one sample, many scans). I have marked sample's groups and do "merge marked data in mu(E)" then I get merged data together with reference (2 groups: merge - sample, and Ref merge - reference). But... ...if I have marked reference sample's groups and do "merge" then I get 2 groups: merge - which is merged data of reference, and Ref merge - which is marged data of sample. Oposite to that I did in first example!

Is any hidden idea, I can not see, why it should be that way? If you don't know about that, can confuse and surprise... cheers darek _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org

Hi Matt: I agree. It is useful to have the reference channel from the first of the merged data pulled over as reference for the merged data but this actuallly only makes sense if the user first aligned using the reference. carlo On Thu, 19 Nov 2009, Matt Newville wrote:

Is there ever a case where a merged reference channel is useful?

I thought the only possible use for a reference channel was for comparing individual scans. That is, prior to merging.

--Matt

On Thu, Nov 19, 2009 at 6:45 AM, Zajac, Dariusz A. wrote:

...

Dear Bruce, Dear All, maybe it is a naïve question but I want to ask and to point this problem...

Windows XP. Athena 0.8.059 Sc.Linux. Athena 0.8.060

I have a set of data with refernces  (one sample, many scans). I have marked sample's groups and do "merge marked data in mu(E)" then I get merged data together with reference (2 groups: merge - sample, and Ref merge - reference). But... ...if I have marked reference sample's groups and do "merge" then I get 2 groups: merge - which is merged data of reference, and Ref merge - which is marged data of sample. Oposite to that I did in first example!

Is any hidden idea, I can not see, why it should be that way? If you don't know about that, can confuse and surprise... cheers darek _______________________________________________ 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

-- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://www.iit.edu/~segre segre@debian.org

Hi Scott On Thu, Nov 19, 2009 at 9:50 AM, Scott Calvin wrote:

Hi Matt,

I'm the one who requested the merged reference channel.

If the data is ideal, of course only one reference scan is needed. But there are two common ways it can be nonideal that are relevant:

1) The monochromator does not hold calibration; i.e. there is an energy shift between scans

2) The reference channel is very noisy, perhaps because of an inherently thick sample

If  1) is a significant problem and 2) is not, then it makes sense to align the scans using the reference, at which point any reference scan will do for determination of the chemical shift of the merged data from the sample.

If 2) is a significant problem and 1) is not, then it makes sense to merge the references along with the sample data, because that will make it easier to determine the chemical shift.

For this case, wouldn't it be better to measure the reference separately to determine the chemical shift, and not rely on the reference channel for this purpose? How often is the reference channel both noisy AND improved by merging? That would imply a transmission measurement that was poor due to low flux. But if this is because the sample is thick as you suggest, the x-rays hitting the reference could be dominated by harmonics, and the reference data may just be bad, not noisy due to counting statistics. --Matt PS: I think that means I agree with Anatoly!

--Matt

PS: I think that means I agree with Anatoly!

Me too! :-) I like the side-effect of merging the reference when the spectra are merged. However, it is the spectra that I merge rather than the refs. The refs can be cleaner for alignment though for samples with small edges. Adam _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Hi All, I am a little bit surprised how my post had made a nice discussion ;) I didn't want to discuss about reference spectra and their usefulness. I only wanted to point that when you merge data with marked reference groups you get inversed merged groups - in "merge" group reference and in "Ref merge" your real data. Let users decide if it is useful or not. For me it is! Especially when I work with many repeats, like e.g. in QEXAFS, when the signal from sample and from reference in single scan is to noisy. cheers darek

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Friday, November 20, 2009 12:48 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Bug in Athena?

On Nov 19, 2009, at 2:59 PM, Matt Newville wrote:

...

For this case, wouldn't it be better to measure the reference separately to determine the chemical shift, and not rely on the reference channel for this purpose?

How often is the reference channel both noisy AND improved by merging? That would imply a transmission measurement that was poor due to low flux. But if this is because the sample is thick as you suggest, the x-rays hitting the reference could be dominated by harmonics, and the reference data may just be bad, not noisy due to counting statistics.

It's a good point. But pick your poison. When I am trying to be careful about chemical shift, I don't trust that the mono won't just happen to skip a step between measuring the standard separately and measuring the sample. So I do both. I measure a standard in the sample channel, with a reference in the reference channel. I then leave the reference in the reference channel, and put my sample in. If the sample is a "reasonable" thickness for transmission, but a bit on the high side (say 2.3 absorption lengths), the photon count is down pretty far by the time it gets to the reference. The reference is also often the worst detector and amplifier that a line has, as the good stuff is used for I0, It, and If. So the reference channel may well have a considerable amount of random noise which can be improved by merging.

If that's the case, and if my sample appears to be suffering no beam damage (scans when aligned, lie on top of each other), then I align used the sample data. I then merge the sample data and the reference data. By comparing the sample to the reference and the previous scans where I measured the standard to the reference, I can see if there's been any energy shift between scans. As far as harmonics, this procedure should detect them. If the merged reference looks different from sample to sample (including the case where a standard was also in the sample channel), that suggests that there are issues with harmonics. If those issues move the first peak of the first derivative, I know they're going to affect my determination of chemical shift. Also, if I get a nonzero chemical shift from this procedure for the standard, I know there's an issue. If not, they're not a problem.

The net result is that I have good confidence that I'm getting accurate chemical shifts, as loss of energy calibration, harmonics, and noise should all become evident by this procedure.

I'm not recommending this procedure over others; it's just what I do in some cases. But it doesn't seem like an unreasonable procedure to me.

--Scott Calvin Sarah Lawrence College

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Dear Bruce, Dear All, maybe it is a naïve question but I want to ask and to point this

There are a few questions all mixed together here. Why does Athena make a merge of references? As Matt points out, that is an odd thing to do. I decided I wanted some kind of reference channel tied to the merged spectrum so that I could take merged data from different project files and figure out how to align them in a consistent manner. The easiest way to do this was to tie something to the merged spectrum as its reference channel. I decided to make a merge of the reference spectra to serve this purpose. That was just a decision -- I could just as well have made a copy of the reference of the first spectrum in the merge list. So what explains the behavior Darek is asking about? Well, Athena doesn't actually make a serious distinction between data and its reference. They are both treated normal dtaa groups internally. The sense in which the reference is somehow special is that you, the user, tend not to look at it after you have done data alignment. So, when you make a merge, Athena sums up all the marked groups. Then, if ach one has a reference tied to it, it sums up the references and then ties together these two merged spectra. However, the reference tying runs both ways. If you change the energy shift for one, the other's energy shift changes the same way. In that sense, there is *no* difference between data and a reference. So, if you make a merge of data, ther references get merged into a merged reference. If you make a merge of references, the data get merged as well. The data groups that are maked get called "merge". The merge of the tied groups gets called " Ref merge". If you do the merge of the reference channels, these two merged groups get labeled backwards. I think that explains everything.... B On Thursday 19 November 2009 07:45:14 am Zajac, Dariusz A. wrote: problem...

Windows XP. Athena 0.8.059 Sc.Linux. Athena 0.8.060

I have a set of data with refernces (one sample, many scans). I have marked sample's groups and do "merge marked data in mu(E)" then I get merged data together with reference (2 groups: merge - sample, and Ref merge - reference). But... ...if I have marked reference sample's groups and do "merge" then I

get 2

groups: merge - which is merged data of reference, and Ref merge - which is marged data of sample. Oposite to that I did in first example!

Is any hidden idea, I can not see, why it should be that way? If you don't know about that, can confuse and surprise... cheers darek ___________l____________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Bruce Ravel ----------------------------------- bravel@bnl.gov National Institute of Standards and Technology Synchrotron Measurements Group, Beamlines X23A2, X24A, U7A Building 535A, Room M7 Brookhaven National Laboratory Upton NY, 11973, USA My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

My 2 cents, It seems reasonable to me as well. The current behaviour of not making a strong distinction of what is data and what is reference is a good one in my opinion. Athena should just work and let me, the user, interpret the results and apply the labels. Cheers, Adam Scott Calvin wrote:

Hi Bruce,

On Nov 19, 2009, at 11:48 AM, Bruce Ravel wrote:

...

Why does Athena make a merge of references? As Matt points out, that is an odd thing to do.

I may be confused as to what we're talking about. Why is this an odd thing to do? It seems perfectly normal to me to want the reference scans merged as well as the sample scans, in order to get a clean measure of chemical shift.

--Scott Calvin Sarah Lawrence College

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--

On Thursday 19 November 2009 01:48:49 pm Scott Calvin wrote:

...

Why does Athena make a merge of references? As Matt points out, that is an odd thing to do.

I may be confused as to what we're talking about. Why is this an odd thing to do? It seems perfectly normal to me to want the reference scans merged as well as the sample scans, in order to get a clean measure of chemical shift.

Ummm... ok.... "could" be seen as an odd thing to do... B -- Bruce Ravel ----------------------------------- bravel@bnl.gov National Institute of Standards and Technology Synchrotron Measurements Group, Beamlines X23A2, X24A, U7A Building 535A, Room M7 Brookhaven National Laboratory Upton NY, 11973, USA My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/