Xanes peaks fitting with Athena: no data on output
Hi dears, I was using Athena (Ifeffit version 1.2.11) to fit XANES peaks and it worked very well. But, at the end when I try to "save fit as data group" the output is empty (or almost). The only thing that I get when I save the group data as "norm(E)" is the following: # Athena multicolumn data file -- Athena version 0.8.056 # This file contains normalized mu(E) from: # Peak hnvp (column 2) #------------------------ # energy Peak_hnvp I have no data in the output! Also, when I click the "save fit as data group" button, the plot window becomes blank/white, without plots! I have to have the fits to put them on a high-quality figure for publication. Interestingly, the fits appear in the plot window but I can not get the data corresponding to the fits. I can just save the window as GIF or PS files, and it works well. I use Athena on windows XP and Vista and the problem is the same for both. I´ve attached my data file in case someone would like to have a look on it. For sure I´m doing something stupid and I don´t see where is the fail! All the best, Ismael. -- Ismael Leandro Graff Departamento de Física - UFPR Centro Politécnico, CP 19044 81531-990, Curitiba, Brazil. Tel: +55 41 3361 3427 Fax: +55 41 3361 3418
Hi Ismael, I'm using Athena 0.8.058 (IFEFFIT 1.2.11c) with windows XP. If you select the tick box next to your file in Athena then select "file - save marked groups to file as" then select the type of plot you want e.g. norm(E) or chi(k)^3 (I've attached the exported examples) etc the data is saved. Using the import ASCII option in e.g. Origin allows you to open your file and produce a publication quality figure. I'm not sure if this is what you've tried already or not but if it is, then you may need to check your installation. Hope this helps, Steve Stephen Price Russell Group Department of Chemistry University of Southampton Highfield Southampton SO17 1BJ Ext: 24104 Tel: 02380 594104 -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Ismael Graff Sent: 10 June 2009 02:55 To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Xanes peaks fitting with Athena: no data on output Hi dears, I was using Athena (Ifeffit version 1.2.11) to fit XANES peaks and it worked very well. But, at the end when I try to "save fit as data group" the output is empty (or almost). The only thing that I get when I save the group data as "norm(E)" is the following: # Athena multicolumn data file -- Athena version 0.8.056 # This file contains normalized mu(E) from: # Peak hnvp (column 2) #------------------------ # energy Peak_hnvp I have no data in the output! Also, when I click the "save fit as data group" button, the plot window becomes blank/white, without plots! I have to have the fits to put them on a high-quality figure for publication. Interestingly, the fits appear in the plot window but I can not get the data corresponding to the fits. I can just save the window as GIF or PS files, and it works well. I use Athena on windows XP and Vista and the problem is the same for both. I´ve attached my data file in case someone would like to have a look on it. For sure I´m doing something stupid and I don´t see where is the fail! All the best, Ismael. -- Ismael Leandro Graff Departamento de Física - UFPR Centro Politécnico, CP 19044 81531-990, Curitiba, Brazil. Tel: +55 41 3361 3427 Fax: +55 41 3361 3418
Ismael, OK! With a bit of further explanation from Adam, I was able to understand the issue. You are certainly correct -- the button labeled "Save fit as a data group" certainly does not do what it says! There is no work around in the current version of Athena -- that button is simply broken. I am planning to make a new release of my software some time in the next three weeks or so -- before the APS XAFS Summer School next month. This problem, along with a few others that have come to my attention recently, will be fixed in the next release. Thank you for the bug report. As always -- the software benefits enormously from the feedback I receive in this forum. Regards, B On Tuesday 09 June 2009 09:55:08 pm Ismael Graff wrote:
Hi dears,
I was using Athena (Ifeffit version 1.2.11) to fit XANES peaks and it worked very well. But, at the end when I try to "save fit as data group" the output is empty (or almost). The only thing that I get when I save the group data as "norm(E)" is the following:
# Athena multicolumn data file -- Athena version 0.8.056 # This file contains normalized mu(E) from: # Peak hnvp (column 2) #------------------------ # energy Peak_hnvp
I have no data in the output! Also, when I click the "save fit as data group" button, the plot window becomes blank/white, without plots! I have to have the fits to put them on a high-quality figure for publication. Interestingly, the fits appear in the plot window but I can not get the data corresponding to the fits. I can just save the window as GIF or PS files, and it works well. I use Athena on windows XP and Vista and the problem is the same for both. I´ve attached my data file in case someone would like to have a look on it. For sure I´m doing something stupid and I don´t see where is the fail!
All the best, Ismael.
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Dear Bruce, thank you very much for your prompt answer. An user of Athena that participates in the mailing list gave me a way to get the data of the fitted curves. Shortly, I use the log file to get the functions parameters and, with the definition of the functions, I go to Origin and generate the curves. So, I can plot the fitted curves with the experimental data. Kind regards, Ismael.
Ismael,
OK! With a bit of further explanation from Adam, I was able to understand the issue. You are certainly correct -- the button labeled "Save fit as a data group" certainly does not do what it says!
There is no work around in the current version of Athena -- that button is simply broken. I am planning to make a new release of my software some time in the next three weeks or so -- before the APS XAFS Summer School next month. This problem, along with a few others that have come to my attention recently, will be fixed in the next release.
Thank you for the bug report. As always -- the software benefits enormously from the feedback I receive in this forum.
Regards, B
On Tuesday 09 June 2009 09:55:08 pm Ismael Graff wrote:
Hi dears,
I was using Athena (Ifeffit version 1.2.11) to fit XANES peaks and it worked very well. But, at the end when I try to "save fit as data group" the output is empty (or almost). The only thing that I get when I save the group data as "norm(E)" is the following:
# Athena multicolumn data file -- Athena version 0.8.056 # This file contains normalized mu(E) from: # Peak hnvp (column 2) #------------------------ # energy Peak_hnvp
I have no data in the output! Also, when I click the "save fit as data group" button, the plot window becomes blank/white, without plots! I have to have the fits to put them on a high-quality figure for publication. Interestingly, the fits appear in the plot window but I can not get the data corresponding to the fits. I can just save the window as GIF or PS files, and it works well. I use Athena on windows XP and Vista and the problem is the same for both. I´ve attached my data file in case someone would like to have a look on it. For sure I´m doing something stupid and I don´t see where is the fail!
All the best, Ismael.
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973
My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Ismael Leandro Graff Departamento de Física - UFPR Centro Politécnico, CP 19044 81531-990, Curitiba, Brazil. Tel: +55 41 3361 3427 Fax: +55 41 3361 3418
On Wednesday 10 June 2009 10:21:58 am you wrote:
thank you very much for your prompt answer. An user of Athena that participates in the mailing list gave me a way to get the data of the fitted curves. Shortly, I use the log file to get the functions parameters and, with the definition of the functions, I go to Origin and generate the curves. So, I can plot the fitted curves with the experimental data.
See? Once again, the mailing list proves to the killer feature of the Ifeffit software! ;-) B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
On Wednesday 10 June 2009 09:47:22 am Bruce Ravel wrote:
There is no work around in the current version of Athena -- that button is simply broken. I am planning to make a new release of my software some time in the next three weeks or so -- before the APS XAFS Summer School next month. This problem, along with a few others that have come to my attention recently, will be fixed in the next release.
I was poking around at the peak fitting dialog this morning after fixing the bug that Ismael reported and decided that I didn't like the log file that gets written by the peak fitting utility. The next version will have a much improved peak fit log file. The header of the new log file will contain the same information as the old log file. The rest of the log will will be columns of data containing the energy axis, the data, the fit, each component, and the residual. Thus the log file will be trivial to import into an external polotting program. As I said before, all this should be available by the beginning of July. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
participants (3)
-
Bruce Ravel -
Ismael Graff -
Price S.W.T.