[Ifeffit] Change in fixed baseline after fit in XAS Viewer

Mon May 4 23:07:18 CDT 2020

Hi Matt,

Thanks for the reply.

On Mon, May 4, 2020 at 3:04 PM Matt Newville <newville at cars.uchicago.edu>
wrote:

> Hi George,
>
>
>
> On Mon, May 4, 2020 at 12:25 PM George Sterbinsky <
> GeorgeSterbinsky at u.northwestern.edu> wrote:
>
>> Hello,
>>
>> I have observed changes in fixed parameters while running a pre-edge peak
>> fit in XAS Viewer. I first run a baseline fit. This provides a good match
>> to the data in the baseline fitting region. I would like to subtract the
>> baseline from the data and then numerically integrate the data. In order to
>> export the baseline fit and data, I fix all of the fitting parameters for
>> bline and bpeak and then click "fit model". This generates a baseline and
>> fit that no longer match the data well in the baseline fitting region.
>> Additionally, in the "Fit Results" window, the reported best-fit values of
>> the fixed parameters are slightly different from the values reported in the
>> "Value" field after the baseline fit, to which they were fixed. This
>> appears to be the result of rounding of the baseline fit parameters at some
>> point after the baseline fit. For example bline_slope was fixed to
>> "-0.0024752483" but the best-fit value is "-0.00247500". I realize I am
>> using XAS Viewer in a way that it was not exactly designed for, and perhaps
>> no one anticipated someone fixing a parameter out to 10 decimal places.
>> However, what I am doing still seems reasonable, and I would greatly
>> appreciate it if XAS Viewer could be updated so that all digits entered in
>> the Value field for a fixed parameter will be maintained for the fit. I am
>> happy to provide a project file and instructions to reproduce my
>> observation if they would be helpful.
>>
>>
> When you do "Fit Model", the fit will not ignore the "pre-edge peak
> range".   So, if you just have a baseline, that could definitely change the
> resulting baseline "Lorentzian + Line". Could that be what you're seeing?
>

I have fixed all fit parameters after the baseline fit was carried out, so
nothing is actually getting fit when I hit the "fit model" button. I just
want to export the baseline fit. By fixing all of the parameters and then
running "fit model", I'm just getting the "Fit Results" window to open.
>From there, I can then export the "fit" as an xdi file.

> FWIW, it should definitely be possible to fix the baseline (even if that
> might not always be ideal) parameters after just fitting the baseline.  It
> seems like that works to me, but I only tried for one test case.
>

Yes, it seems to work except for the loss of precision.

> I can definitely believe that there is some loss of precision when copy
> parameters from "best fit" values.
>

The loss of precision occurs when the numbers from the baseline fit are
transferred to the best fit. In other words, when copying the values to the
best fit, rather than from the best fit. To illustrate this, I have
attached a screenshot of the main larch GUI after the baseline fit that
shows the precision of bline_slope and bline_intercept. I have also
attached a screenshot of the plot window showing the baseline matches the
data well in fit region. After fixing all bline and bpeak parameters and
pressing "fit model", the values of bline_slope and bline_intercept (as
well as those of the bpeak parameters) lose precision, as shown in the
attached screenshot of the "fit results" window. The effect of this is also
evident in the attached data plot after the fit model button was pressed.
The baseline no longer matches the data well. Again, all fit parameters
were fixed, so the baseline before the fit should look identical to the
baseline after the fit.

> It might be helpful to extract the extra-verbose Larch script (Ctrl-l to
> bring up the Larch buffer, the Ctrl-s to save the session history) and send
> that.
>

I have saved the history and attached it as "history.lar".

> --Matt
>
> PS: I can also see that it would be nice to report things like
>
>    Area of data, Area of data - baseline, Area of Peaks (other than
> baseline)
>

Yes, that would be nice. But if one wanted only a baseline fit and the area
of data - baseline, I think the precision issue I am encountering now might
still present a problem. Actually my goal here is to get the centroid of
the data minus the baseline so that I can compare it with the centroids of
various fit models that I have tried, which are different enough to make me
wonder which one is 'correct.' Since the baseline is fit along with the
peaks, I didn't really want to use the baseline from one of the pre-edge
peak fits for this. I want to use the baseline from the baseline fit.

>
> in addition to Peak centroid.   The Area of the Peaks is just the sum of
> the peak amplitudes (as the peak functions are all unit normalized), but it
> would be nicer to do that in a way that included the propagation or
> uncertainties (including correlations).
>

Yes, I actually noticed that when looking at the forms of the fit functions
at https://xraypy.github.io/xraylarch/fitting/lineshapes.html and have been
taking advantage of it.

Thanks for your help,

George

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