[Ifeffit] Bug in Athena?

Zajac, Dariusz A. dariusz.zajac at desy.de
Fri Nov 20 05:36:52 CST 2009

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.

>-----Original Message-----
>From: ifeffit-bounces at millenia.cars.aps.anl.gov 
>[mailto:ifeffit-bounces at 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  
>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
>Ifeffit mailing list
>Ifeffit at millenia.cars.aps.anl.gov 

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