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) { 918 foreach 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.lawley@psi.chmailto:craig.lawley@psi.ch www.psi.chhttp://www.psi.ch/
Hi Craig, On Wed, May 1, 2019 at 10:51 AM Lawley Craig Richard (PSI) < craig.lawley@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
Dear Matt,
I will take the time to look into this. I saw the previous thread from yourself with the link to the installer and relative information etc.
Many thanks.
Best regards,
Craig
__________________________________________
Paul Scherrer Institut
Craig Lawley
OFLB/U109
Forschungsstrasse 111
5232 Villigen PSI
Schweiz
Telefon: +41 56 310 5054
E-Mail: craig.lawley@psi.chmailto:craig.lawley@psi.ch
www.psi.chhttp://www.psi.ch/
From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville
Sent: Donnerstag, 2. Mai 2019 04:58
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Pseudo Voigt crash Athena
Hi Craig,
On Wed, May 1, 2019 at 10:51 AM Lawley Craig Richard (PSI)
On 05/01/2019 10:57 PM, Matt Newville wrote:
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.
That's not necessary, Matt. I have said before on this mailing list and elsewhere that peak fitting is a very weak part of Athena. While it is true that Ifeffit's capabilities in this area were limited, Athena's implementation was poor. I completely agree that XAS Viewer would be a better choice for this task. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
participants (3)
-
Lawley Craig Richard (PSI) -
Matt Newville -
Ravel, Bruce