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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