[Ifeffit] normalization methods

Matthew Marcus mamarcus at lbl.gov
Thu May 16 11:37:36 CDT 2013

That 'flattening' function seems over-complicated to me and makes an artificial discontinuity, at least in slope, at E0 which is
a somewhat arbitrary quantity.  Why not simply divide by the post-edge quadratic (norm(E) = (mu(E)-pre_edge_line(E))/quadratic(E))?
In some cases, where there's a big curvature, it may make sense to divide mu(E) by the quadratic, then subtract a pre-edge.  What I've never
solved satisfactorily is the case in which the extrapolation of the pre-edge line crosses the post-edge, so mu(E)-pre_edge_line(E)<0 for
some part of the range.  I've never understood why this happens.

On 5/16/2013 4:47 AM, Matt Newville wrote:
> Hi Matthew, George, Zach,
> Thanks for the discussion!
> On Wed, May 15, 2013 at 5:41 PM, Matthew Marcus <mamarcus at lbl.gov> wrote:
>> I'm not sure what 'flattening' means.  Does that mean dividing by a linear
>> or other polynomial function, fitted to the post-edge?
>>          mam
> Sorry, I should have been clearer.  "Standard Athena/Ifeffit" is to
>    a) regress a pre-edge line to mu(E) (no power laws)
>    b) regress a post-edge quadratic
>    c) set edge_step = post_edge_quadratic(E0) - pre_edge_line(E0)
>    b) set  norm(E)  = (mu(E) - pre_edge_line(E)) / edge_step.
> Flattening (Athena only, now backported to larch) fits a quadratic to
> the post-edge range (typcically E0+100 to end of data) of norm(E), and
> then sets
>    flattened(E) =  norm(E) for E<= E0
>                       =  norm(E) - quadratic(E) + quadratic(E0)   for E > E0
> I think this was originally meant for display purposes only.
> Hopefully Bruce can correct me if I'm wrong on any of the details here.
> I think it's fair to say that the "Standard Athena/Ifeffit" approach
> to normalization is simple-minded.  It was designed for EXAFS in an
> era when accessing databases seemed like a challenge, so even for
> EXAFS it is simple-minded.
> Flattening might be better at removing instrumental backgrounds, and
> be better for linear analysis of XANES.  The main concern I would have
> is the potential for a slight discontinuity at E0, or the potential
> strong dependence from the choice of E0.
> Using something like bkg_cl() (which matched mu(E) to the data from
> the Cromer-Liberman tables) or MBACK (which I believe is similar, but
> also accounts for  "elastic/Compton leakage" into the pre-edge part of
> fluorescence spectra).
>>From my point of view, the question is: what's the best way to do
> this?    The pre_edge() function in Larch does include an energy
> exponent term, and now writes out the "flattened" array, as above.
> It does not include the scaling MAM described, but that would not be
> hard.      Reimplementing bkg_cl() would not be too hard, but perhaps
> trying to port MBACK would be better.     Perhaps all of the above is
> best?
> --Matt
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