[Ifeffit] Problem with XAS Viewer

[Xinyue Wang]

Hi Matt,

Thanks for your detailed instructions. I am just trying to follow the steps
and see how it works. I am not trying to do complicated things.
My issue is I would expect the grey vertical lines after press the "Fit
Baseline" button, but nothing shows up. I tried to select a
larger region(which was not pre-peak), also nothing happened. So I am
confused.
Besides, can I use the XAS Viewer to do main peak fitting?
I know that Larch has its own language based on python. I am wondering can
I use larch function, like fitting peaks in Jupiter Notebook?
Thanks for your help.

Thank,
Xinyue

On Sat, May 2, 2020 at 6:36 AM Matt Newville <newville at cars.uchicago.edu>
wrote:

> Hi Xinyue,
>
> On Fri, May 1, 2020 at 9:16 PM Xinyue Wang <xyw0719 at gmail.com> wrote:
>
>> Hi,
>>
>> I am Xinyue, a student who interested in using XAS Viewer. My issue is
>> when I tried baseline fitting, I followed the document. But there was no
>> region, no centroid, and no fitting line shown. Here is a screenshot of my
>> work. Could you please help me with this?
>> Thanks for your help.
>>
>
> It's hard to tell from the screenshot alone.  Just to clarify, the idea
> for the panel is to fit pre-edge peaks to known lineshapes (Gaussian,
> Lorentzian, Voigt, etc).  The interface could probably be used for
> general-purpose curve-fitting of many kinds of spectra, but right now it
> definitely skews to pre-edge peak fitting.
>
> Because of that emphasis, the idea is to first press the "Fit Baseline"
> button -- this will do a crude fit of a Lorentzian + Line that are meant to
> represent any residual background and the main absorption edge.  The fit
> for this baseline is done over the energy range defined by "Fit Energy
> Range" but ignoring the "Pre-edge Peak Range", which is meant to be the
> portion of the XAS spectra where the pre-edge peaks are. That is, this
> baseline fit should
> look something like Figure 5.4.2 at
> https://xraypy.github.io/xraylarch/xasviewer/index.html#pre-edge-peak-fitting.
> In that figure, the black dots show the ends of the Pre-edge Peak Range
> that is ignored in this baseline fit.   For sure, the initial guess for
> this range may not be very good.  But it is easy to refine this ignored
> range.  It is also not actually critical to get this baseline fit perfect -
> it's just a place to start the fits of the peaks themselves, and the
> remaining fits will refine the baseline as well as the peaks over the full
> energy range.     After a baseline fit is done, you can add peaks and then
> use the "Fit Model", which fits over the whole "Fit Energy Range",
> ignoring the "Pre-edge Peak Range".
>
> From your screenshot, I don't see much of a pre-edge and not many obvious
> peaks.  The result is that the actual fit energy range for the baseline
> (that is
> "Fit Energy Range" - "Pre-edge Peak Range") is very short.  I can believe
> the fit will fail under those conditions.  But I sort of think that failure
> really comes because your data doesn't have pre-edge peaks.
>
> Maybe you are trying to do something more complicated?
>
> --Matt
>
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