[Ifeffit] normalization methods
Matthew Marcus
mamarcus at lbl.gov
Wed May 15 17:41:00 CDT 2013
I'm not sure what 'flattening' means. Does that mean dividing by a linear or other polynomial function, fitted to the post-edge?
mam
On 5/15/2013 1:43 PM, George Sterbinsky wrote:
> By standard normalization, I meant subtraction of a linear pre-edge and multiplication by a constant. If this treatment is applied to the XAS spectra before subtraction, one does not obtain an XMCD spectrum that goes to zero in the post edge region for the data I described. As you noted, that is what would be expected given the p-XAS and n-XAS have different slopes in the post-edge region.
>
> On the other hand, standard normalization + flattening does result in pre and post-edge regions that go to zero, again as one might expect. So perhaps, the background modeled by standard normalization + flattening is an accurate representation of the real background in some cases and can be used in quantitative analysis. Is there reason to believe that cannot be the case?
>
> Thanks,
> George
>
>
>
>
> On Wed, May 15, 2013 at 3:04 PM, Matthew Marcus <mamarcus at lbl.gov <mailto:mamarcus at lbl.gov>> wrote:
>
> OK, I guess I don't know what 'standard normalization' is. It looks from the quotient that you'll need some sort of curved post-edge.
> I guess the division didn't work because the electron energy distribution is different pre- and post-edge, so the magnetic effects are
> different and vary across the edge. Thus, the shapes of the MCD peaks will be at least a little corrupted even if the pre- and post-edge
> spectra are taken into account. I don't know what to do about this. Did you try asking Elke?
> mam
>
>
> On 5/15/2013 11:52 AM, George Sterbinsky wrote:
>
> Hi Matthew,
>
>
>
> On Wed, May 15, 2013 at 1:20 PM, Matthew Marcus <mamarcus at lbl.gov <mailto:mamarcus at lbl.gov> <mailto:mamarcus at lbl.gov <mailto:mamarcus at lbl.gov>>> wrote:
>
> You say that the flipping difference (p - n) is 0 in pre-edge and far post-edge regions, which is as it should be, but then say that the
> slopes of p- and n- post-edges, considered separately, are different. I must be misunderstanding because those two statements would seem to be
> inconsistent.
>
>
>
> Sorry, I think my wording wasn't particularly clear here. What I should have said is:
>
> "The goal then is to subtract the /normalized/ XAS measured in a positive field (p-XAS) from /normalized/ XAS measured in a negative field (n-XAS) and get something (the XMCD) that is zero in the pre-edge and post-edge regions. /However, standard normalization does not give this result/"
>
>
> Italics indicate new text.
>
> I wonder if the sensitivity of the TEY changes with magnetic field because of the effect of the field on the trajectories of
> the outgoing electrons, which would explain the differing curves.
>
>
> I would agree, I think the effect of the magnetic field on the electrons is the likely source of the differences in background.
>
> A possibility - if you divide the p-XAS by n-XAS, do you get something
> which is a smooth curve everywhere but where MCD is expected? Does that curve match in pre- and far post-edge regions?
>
>
> No, after division of the p-XAS by the n-XAS (before any normalization), both the pre and post-edge regions are smooth, but one would need a step-like function to connect them. I've attached a plot showing the result of division.
>
>
> If that miracle occurs,
> then perhaps you could fit that to a polynomial, except in the MCD region, then divide the p-XAS by that polynomial, to remove the effect of
> the differing sensitivities.
>
> There are people here at ALS, such as Elke Arenholz <earenholz at lbl.gov <mailto:earenholz at lbl.gov> <mailto:earenholz at lbl.gov <mailto:earenholz at lbl.gov>>>, who do this sort of spectroscopy. I suggest asking her.
>
> mam
>
>
> Thanks for the suggestion and your reply.
>
> George
>
>
>
>
>
>
>
>
> On 5/15/2013 9:58 AM, George Sterbinsky wrote:
>
> The question of whether it is appropriate to use flattened data for quantitative analysis is something I've been thinking about a lot recently. In my specific case, I am analyzing XMCD data at the Co L-edge. To obtain the XMCD, I measure XAS with total electron yield detection using a ~70% left or right circularly polarized beam and flip the magnetic field on the sample at every data point. The goal then, is to subtract the XAS measured in a positive field (p-XAS) from XAS measured in a negative field (n-XAS) and get something (the XMCD) that is zero in the pre-edge and post-edge regions. I often find that after removal of a linear pre-edge, the spectra still have a linearly increasing post edge (with EXAFS oscillations superimposed on it), and the slope of the n-XAS and p-XAS post-edge lines are different. In this case simply multiplying the n-XAS and p-XAS by constants will never give an XMCD spectrum that is zero in the post edge region. There is the
n some
> component of the
>
> XAS background that is not accounted for by linear subtraction and multiplication by a constant. It seems to me that flattening could be a good way to account for such a background. So is flattening a reasonable thing to do in a case such as this, or is there a better way to account for such a background?
>
> Thanks,
> George
>
>
> On Wed, May 15, 2013 at 11:41 AM, Matthew Marcus <mamarcus at lbl.gov <mailto:mamarcus at lbl.gov> <mailto:mamarcus at lbl.gov <mailto:mamarcus at lbl.gov>> <mailto:mamarcus at lbl.gov <mailto:mamarcus at lbl.gov> <mailto:mamarcus at lbl.gov <mailto:mamarcus at lbl.gov>>>> wrote:
>
> The way I commonly do pre-edge is to fit with some form plus a power-law singularity representing the initial rise of the edge, then
> subtract out that "some form". Now, that form can be either linear, linear+E^(-2.7) (for transmission), or linear+ another power-law
> singularity centered at the center passband energy of the fluorescence detector. That latter is for fluorescence data which is affected by
> the tail of the elastic/Compton peak from the incident energy. Whichever form is taken gets subtraccted from the whole data range, resulting
> in data which is pre-edge-subtracted but not yet post-edge normalized. The path then splits; for EXAFS, the usual conversion to k-space, spline
> fitting in the post-edge, subtraction and division is done, all interactively. Tensioned spline is also available due to request of a prominent user.
> For XANES, the post-edge is fit as previously described. Thus, there's no distinction made between data above and below E0 in XANES, whereas
> there is such a distinction in EXAFS.
> mam
>
>
> On 5/15/2013 8:25 AM, Matt Newville wrote:
>
> Hi Matthew,
>
> On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus <mamarcus at lbl.gov <mailto:mamarcus at lbl.gov> <mailto:mamarcus at lbl.gov <mailto:mamarcus at lbl.gov>> <mailto:mamarcus at lbl.gov <mailto:mamarcus at lbl.gov> <mailto:mamarcus at lbl.gov <mailto:mamarcus at lbl.gov>>>> wrote:
>
> What I typically do for XANES is divide mu-mu_pre_edge_line by a linear
> function which goes through the post-edge oscillations.
> This division goes over the whole data range, including pre-edge. If the
> data has obvious curvature in the post-edge, I'll use a higher-order
> polynomial. For transmission data, what sometimes linearizes the background
> is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption
> shape) and change it back afterward. All this is, of course, highly
> subjective and one of the reasons for taking extended XANES data (300eV,
> for instance). For short-range XANES, there isn't enough info to do more
> than divide by a constant. Once this is done, my LCF programs allow
> a slope adjustment as a free parameter, thus muNorm(E) =
> (1+a*(E-E0))*Sum_on_ref{x[ref]______*muNorm[ref](E)}. A sign that this degree of
>
>
> freedom
> may be being abused is if the sum of the x[ref] is far from 1 or if
> a*(Emax-E0) is large. Don't get me started on overabsorption :-)
> mam
>
>
> Thanks -- I should have said that pre_edge() can now do a
> victoreen-ish fit, regressing a line to mu*E^nvict (nvict can be any
> real value).
>
> Still, it seems that the current flattening is somewhere between
> "better" and "worse", which is unsettling... Applying the
> "flattening" polynomial to the pre-edge range definitely seems to give
> poor results, but maybe some energy-dependent compromise is possible.
>
> And, of course, over-absorption is next on the list!
>
> --Matt
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