[Ifeffit] Athena 0.9.24 (64-bit) on Windows: Problems with Alignment and with plotting window

Bruce Ravel bravel at bnl.gov
Fri Dec 11 08:40:06 CST 2015

On 12/11/2015 03:36 AM, Voegelin, Andreas wrote:
> 1)  In Athena, auto-align does not seem to work properly: In the
> attached project file, the first spectrum is a reference Fe foil
> spectrum. Trying to align the reference spectra linked with the
> sample spectra to this reference foil, the "auto-align" function
> results in an obviously wrong alignment (see jpg file).  Even if I
> first manually correctly align the reference spectra, "auto align"
> again shifts the spectrum to a wrong place.

Hi Andreas,

In your following email, you noticed that changing the E0 from 7128 to
7112 in your reference foil made Athena behave as expected.

The reason that the e0 of the reference matters is that it is used for
the initial guess for the energy shift.  In the auto-alignment fit,
there are two parameters, the e0 shift and an over all scaling
factor.  The fit minimizes

    mu_standard(e) - SCALE * mu_data(e+ESHIFT)

by optimizing SCALE and ESHIFT.  The initial guess for SCALE is 1, the
initial guess for ESHIFT is (e0_standard - e0_data).

By that choice of the initial guess for ESHIFT, Athena is making some
assumptions about your data, your choices for e0, and the scan-to-scan
size of the energy shifts.  When those assumptions are ok, this
starting value of ESHIFT gives the fit a hint about what value it's
looking for.

In your case, it seems that was a bad assumption.  Athena was surprised
by your choice of e0 for the standard.  ESHIFT started off so wrong
that the minimization never found the proper solution.

   Probably the simplest practical solution is to mark all of the
   reference foils, select your alignment standard, right click on e0,
   choose "set marked groups to this value of e0".

   That will make e0 for all the reference foils the same as your
   standard, i.e. 7128.  With that, ESHIFT will use 0 as its initial
   guess and the auto-alignment will work.

Long term solution:
   A possible solution to this problem is to add a new control to the
   alignment tool.  Radio buttons could be provided to let the user
   choose to have ESHIFT be 0 or (e0_standard - e0_data).  I could also
   provide some feedback about initial value and final value of ESHIFT,
   which could provide a hint to the user about changing that choice
   for ESHIFT.

> 2) Plotting window is always set to small size when plotting a graph
> and zooming does not work: Working with Athena, I normally used the
> left half of the screen to display the GUI and the right half to
> display the plotting window.  After I installed Demeter 0.9.24, the
> plotting window is always reduced  in size and moved to the left part
> of the screen when I try to plot a graph from Athena.

I don't really understand this description.  On the Windows machine
here in my office, the plot window is the same size it always was.

Are you saying that, in the past, the plot window somehow sparng into
life occupying the right half of the screen and with a size of 1/2 the
screen size?  That's not something I did!

I have never understood how Windows decides where on the screen to
first place the window.  It always seems to decide that the plot
window belongs *underneath* the Athena window regardless of where on
screen I put Athena.  F%^&*n' Windows!

There are ways to set window size and position every time a plot is
made.  That's not a very good solution, though, because it doesn't
respect when the window has been moved or resized by hand.

There's probably a way to configure the plotting program to start in
the configuration you want, but I don't know how to do that on Windows
off the top of my head.

> Furthermore, within the plotting window, the zoom function does not
> seem to work anymore.

That is not a problem for me here in my office.

At the risk of telling you something you already know, zooming is done
with the right mouse button (click-right + drag) in the wxt window
shown in your screenshot.


  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 535A
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/

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