Re: [Ifeffit] Pseudo Voigt crash Athena
Hi Craig, On Wed, May 1, 2019 at 10:51 AM Lawley Craig Richard (PSI) < craig.law...@psi.ch> wrote: > Dear Mailing list, > > > > I have run into an issue with the peak fitting section included in Athena. > If I include a peak that is a Pseudo-Voigt and then save the project file. > Upon trying to reopen the same project file, Athena becomes non responsive > with the error message “PV is not yet implemented”. > This may sound like a broken record, but I strongly encourage you to try Larch and the XAS Viewer application for peak fitting of XAS spectra. The ifeffit library is really old (has not been updated in 5 years), not supported, and its interface to peak fitting is primitive. Larch (and the lmfit library it uses) and the XAS Viewer GUI are all supported. Peak-fitting of XANES is one feature which I am confident to say is definitely better than Athena. I'm willing to take 100% of the blame for this, but peak-fitting does not work well in Athena. XAS Viewer has more lineshapes including both PseudoVoigt and (true!) Voigt lineshape functions. It also supports better mechanisms for applying mathematical constraints and for applying bounds on parameters which can be important for modeling XANES with multiple peaks.lmfit/Larch also provides more and better fit statistics, such as reporting FWHM (and its uncertainty) for each peak, and (for XANES) the centroid of the pre-edge peaks. Though not supported directly in the GUI, lmfit/Larch does allow one to do a more thorough estimate of uncertainties and to use minimization methods other than Levenberg-Marquardt. My experience is that these seem to be not so important for peak-fitting of XANES data, but I don't know that this is always the case (and to be clear, there are certain classes of "line shape fitting" where these are important). Like Athena, XAS Viewer records all the code actually run making it easy to turn a GUI session into a Larch script or Python program to do more detailed analysis or to help write analysis scripts for batch processing. Hope that helps, --Matt ___ 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
[Ifeffit] Pseudo Voigt crash Athena
Dear Mailing list,
I have run into an issue with the peak fitting section included in Athena. If I
include a peak that is a Pseudo-Voigt and then save the project file. Upon
trying to reopen the same project file, Athena becomes non responsive with the
error message "PV is not yet implemented".
The log file for the crash is as follows:
Started at 2019-05-01T17:37:06
Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561
PATH is:
C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\perl\site\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\perl\bin;C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\bin\gnuplot\bin
DEMETER_BASE is:
C:\Users\lawley_c\AppData\Roaming\DemeterPerl
IFEFFIT_DIR is:
C:\Users\lawley_c\AppData\Roaming\DemeterPerl\c\share\ifeffit\
perl version: v5.24.0
backend: ifeffit
@INC:
C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread
C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib
C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/vendor/lib
C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/lib
.
Demeter version 0.9.26
Can't call method "SetValue" on an undefined value at
C:/Users/lawley_c/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena/PeakFit.pm
line 916.
Where lines 910-920 in the PeakFit.pm file readout as:
910 if ($result == wxID_NO) {
911 $::app->{main}->status("Not deleting lineshape.");
912 return 0;
913 };
914 ## demolish the LineShape object, if it exists
915 $this->{'lineshape'.$n}->DEMOLISH if exists $this->{'lineshape'.$n};
916 ## dig through the hierarchy of the StaticBox and Remove/Destroy each
element
917 foreach my $s ($this->{'func'.$n}->GetChildren) {
918foreach my $w ($s->GetSizer->GetChildren) {
919$w->GetWindow->Destroy if defined($w->GetWindow);
I couldnt find any previous thread regarding this issue. If anyone knows a
solution or could link me to a pre existing thread I would much appreciate it.
Thanks in advance
Craig
___
Paul Scherrer Institut
Craig Lawley
OFLB/U109
Forschungsstrasse 111
5232 Villigen PSI
Schweiz
Telefon: +41 56 310 5054
E-Mail: craig.law...@psi.ch
www.psi.ch
[Ifeffit] Larch 0.9.43
Hi Folks, Larch 0.9.43 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/installation.html If you already have installed Larch, you should be able to update to the latest version with ~> conda update -c gsecars xraylarch from a terminal on Linux or Mac OSX. On Windows, you may have to specify the full path with something like: C:\Users\\AppData\Local\Continuum\xraylarch\Scripts\conda.exe -c gsecars xraylarch If you have any trouble upgrading, you can simply remove the xraylarch installation folder and reinstall. If you would like to install Larch into a different Python environment, please read https://xraypy.github.io/xraylarch/installation.html Version 0.9.43 has several improvements to the XAS Viewer GUI application, including: - better handling of read/write cycles of multiple Athena project files. - better default normalization and better control over normalization, especially for XANES data. - improved PCA analysis (in part from the recent discussion here with Joselaine Cáceres Gonzalez), so that it now reports IND values to help determine the number of components and reports eigenvalues from simple matrix inversion (not SVD) so that they more closely match those in the XAFS literature. - addition of Partial Least Squares and LASSO regression analysis for selection and prediction of external quantities (valence, for example) based on training sets of XANES data with known values for these quantities. This machine-learning approach is based on work of M Dyar, et al in a series of papers over the past several years. I encourage and request anyone interested, and especially MacOS users, to try out the XAS Viewer app and let us know what needs improvement. For people interested in using Larch from Python, Version 0.9.43 includes a complete refactoring of the code to make Larch work better as a "normal" Python library. Specifically, the previous code organization with most of the real analysis code in "plugins" has been replaced with all code now placed within the main larch module, still organized by topic. This improves packaging -- `pip install xraylarch` can now work. This code reorganization also means that the python programmer can use more normal imports to get at the Larch library so that one can simply do >>> from larch.xafs import pre_edge, autobk, xftf We also fixed a serious and deep flaw that selected a matplotlib plotting library too early, making larch difficult to use with Jupyter, Spyder, or other Qt-based GUIs. This is now fixed, and import statements like the one above can be seamlessly used in Jupyter notebooks. I should note that the documentation and examples are definitely lagging behind the code especially regarding the most recent developments, but this will be worked on. If you having any questions, trouble, or suggestions on any part of Larch, please let us know. --Matt Newville ___ 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
