A trick I've used when the fluorescence data are good but affected by overabsorption, and the transmission data are noisy is to reduce both data sets to post-edge normalized form (0 in pre-edge, oscillating about 1 post-edge), then apply a simple overabsorption model to 'correct' the fluorescence so it matches the transmission. This is a bit risky in that some of the same samples which exhibit overabsorption will also show hole (thickness) effect, which looks enough like overabsorption so that you under-correct the fluorescence. Otherwise, if the goal is to reduce noise, perhaps the best way is to reduce both to post-edge normalized form, then do a weighted sum. What weights? Look at the noise level on each and weight it accordingly. One way to do that is to fit a polynomial and look at the magnitude of the residuals and ask "how many counts/point would an ideal Poissonian counter need to get the residual this low?". The "2-column Editor" program available from the ALS Beamline 10.3.2 website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm -> Utilities has that as a capability. If you want to use it, download the program and reply to me off-line for an explanation of how to use the noise analysis; the on-line doc is outdated and doesn't include that feature. mam ----- Original Message ----- From: "Bruce Ravel" To: "XAFS Analysis using Ifeffit" Sent: Monday, August 10, 2009 3:20 PM Subject: Re: [Ifeffit] Is it legitimate to merge transmission data withfluorescence data?

On Monday 10 August 2009 06:13:32 pm jrkizews@ncsu.edu wrote:

...

Dear XAFS community members, I have a question concerning data merge. We normally collect XAFS data in both transmission mode and fluorescence mode. We normally have to merge a few scans to enhance signal-to-noise ratio. For one particular sample, I want to know if it is legitimate to merge its transmission scans with its fluorescence scans to improve data quality?

Hi Fiona,

There is no a priori reason not to do so and certainly not a numerical reason. From a numerical perspective, you can merge anything with anything!

My one concern is that the fluorescence and transmission data are really equivalent. That is, if the fluo data are affected by significant self-absorption attenuation or if the transmission data suffer from significant pin-hole effects, then you run the risk of degrading the entire data set by doing the merge. But if the data are merely noisy, then I think you are safe doing so.

Think about it this way: when you use a multi-element detector, you are making several measurements which are presumed to be identical. We routinely merge the channels of an MED. You situation is, from a measurement theory perspective, analogous. Assuming your data do not suffer from the problems mentioned above, it seems all right to me.

B

--

Bruce Ravel ------------------------------------ bravel@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/~ravel/software/exafs/

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Good point. That depends on the penetration depth of the fluorescence signal and the takeoff angle. You can calculate this if you know the composition using tools like Hephaestus. mam ----- Original Message ----- From: "Zajac, Dariusz A." To: "XAFS Analysis using Ifeffit" Sent: Tuesday, August 11, 2009 12:17 AM Subject: Re: [Ifeffit] Is it legitimate to merge transmissiondatawithfluorescence data?

Hi all, there is one point of discussion missing for me - does the signal from transmision and fluorescence is the same? The fluorescence signal is "more sensitive" to the surface in some situations, thus if you expect some changes (e.g. oxidation) of the surface of your sample you should be more carefull with data merging. Otherwise as it is written in previuos posts. greetings darek

...

-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matthew Sent: Tuesday, August 11, 2009 12:55 AM To: Bruce Ravel; XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Is it legitimate to merge transmission datawithfluorescence data?

A trick I've used when the fluorescence data are good but affected by overabsorption, and the transmission data are noisy is to reduce both data sets to post-edge normalized form (0 in pre-edge, oscillating about 1 post-edge), then apply a simple overabsorption model to 'correct' the fluorescence so it matches the transmission. This is a bit risky in that some of the same samples which exhibit overabsorption will also show hole (thickness) effect, which looks enough like overabsorption so that you under-correct the fluorescence.

Otherwise, if the goal is to reduce noise, perhaps the best way is to reduce both to post-edge normalized form, then do a weighted sum. What weights? Look at the noise level on each and weight it accordingly. One way to do that is to fit a polynomial and look at the magnitude of the residuals and ask "how many counts/point would an ideal Poissonian counter need to get the residual this low?". The "2-column Editor" program available from the ALS Beamline 10.3.2 website http://xraysweb.lbl.gov/uxas/Beamline/Software/Software.htm -> Utilities has that as a capability. If you want to use it, download the program and reply to me off-line for an explanation of how to use the noise analysis; the on-line doc is outdated and doesn't include that feature. mam ----- Original Message ----- From: "Bruce Ravel" To: "XAFS Analysis using Ifeffit" Sent: Monday, August 10, 2009 3:20 PM Subject: Re: [Ifeffit] Is it legitimate to merge transmission data withfluorescence data?

...

On Monday 10 August 2009 06:13:32 pm jrkizews@ncsu.edu wrote:

...

Dear XAFS community members, I have a question concerning data merge. We normally collect XAFS data in both transmission mode and fluorescence mode. We normally have to merge a few scans to enhance signal-to-noise ratio. For one particular sample, I want to know if it is legitimate to merge its transmission scans with its fluorescence scans to improve data quality?

Hi Fiona,

There is no a priori reason not to do so and certainly not a numerical reason. From a numerical perspective, you can merge anything with anything!

My one concern is that the fluorescence and transmission data are really equivalent. That is, if the fluo data are affected by significant self-absorption attenuation or if the transmission data suffer from significant pin-hole effects, then you run the risk of degrading the entire data set by doing the merge. But if the data are merely noisy, then I think you are safe doing so.

Think about it this way: when you use a multi-element detector, you are making several measurements which are presumed to be identical. We routinely merge the channels of an MED. You situation is, from a measurement theory perspective, analogous. Assuming your data do not suffer from the problems mentioned above, it seems all right to me.

B

--

Bruce Ravel ------------------------------------ bravel@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/~ravel/software/exafs/

_______________________________________________ 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