Athena 0.9.24 (64-bit) on Windows: Problems with Alignment and with plotting window
Dear Bruce After upgrading from Demeter 0.9.22 to Demeter 0.9.24 (64-bit) on two PCs with Windows 7 Enterprise, I now encounter two problems that I did not observe before: 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. 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. Furthermore, within the plotting window, the zoom function does not seem to work anymore. Best regards, Andreas °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° Andreas Voegelin, PhD Eawag - Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland Tel: +41 58 765 54 70 mailto:andreas.voegelin@eawag.ch http://www.eawag.ch/~voegelan
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. Work-around: 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. B -- Bruce Ravel ------------------------------------ bravel@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/
Dear Bruce 1) Thank you for the explanation regarding the alignment function. My selection of E0 for the standard Fe foil indeed did not make much sense for alignment purposes. It was inherited from another project file in which I used the Fe foil spectrum for LCF with an E0 consistent with other (non-metallic) reference spectra. It is clear that a reasonable (and similar) E0 for all reference foils is the easiest solution. Maybe a hint popping up when e0_standard - e0_sample exceeds some threshold (~5 eV?) might help the user to realize that an unreasonable selection of E0 may affect the functioning of the auto align algorithm. 2) The attached printscreen image shows the Athena GUI snapped to the left half of the screen, the plotting window snapped to the right half. In earlier versions, the plotting window kept this size over an entire session. With the installation of the most recent release (0.9.24) of Demeter, whenever I selected a new plot or used one of the buttons within the plotting window, the plotting window was resized to its (small) size at startup. In the meantime, I figured out that this behavior can be changed in the "terminal configuration menu" (see attached printscreen; menu opened with wrench button in plotting window) in which the first option ("Put the window at the top of your desktop after each plot") must be deselected to prevent resizing with each new plot. Since I never used this terminal configuration menu before, I assume that this option was by default deselected in earlier versions of Demeter, but by default selected in the most recent release. Once this option is deselected again, it appears to remain deselected after a restart of Athena. (With respect to the zoom function in the plotting window: thank you for reminding me how to use it properly ...). Best regards, Andreas
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit- bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: Freitag, 11. Dezember 2015 15:40 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Athena 0.9.24 (64-bit) on Windows: Problems with Alignment and with plotting window
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.
Work-around: 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.
B
-- Bruce Ravel ------------------------------------ bravel@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/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
participants (2)
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Bruce Ravel -
Voegelin, Andreas