Thank you, Bruce and Scott. Actually, I replotted all my figures using EXCEL except this one. It worked well for individual spectrum and linear combination fitting, but in least-squares peak fitting, I couldn't find the data for Gaussian and arctangent step peaks. Could you please let me know where I can find those data? Thanks again.
Jenny
________________________________
From: Bruce Ravel
I submitted a manuscript where XANES least-squares peak fitting was used. A figure (attached with this email) was copied from Athena. The problem is that the reviewer asked me to change the color peaks to black and white with diferent types of lines. I was trying to figure it out by myself, but failed. Could anyone help me out? Thank you in advance!
Jenny, The figures from Ifeffit and friends are not really intended to be of sufficient quality for a publication. See questions 10 and 11 at http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions You may find Richard Mayes' suggestion in the answer to question 10 helpful. Athena gives you quite enough information to replicate your plot in other plotting software. The line shapes are all standard line shapes and the parameters are reported after the fit. 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/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ________________________________ Now with a new friend-happy design! Try the new Yahoo! Canada Messenger __________________________________________________________________ Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your favourite sites. Download it now at http://ca.toolbar.yahoo.com.
On Monday 16 March 2009 01:22:01 pm Jenny Cai wrote:
Thank you, Bruce and Scott. Actually, I replotted all my figures using EXCEL except this one. It worked well for individual spectrum and linear combination fitting, but in least-squares peak fitting, I couldn't find the data for Gaussian and arctangent step peaks. Could you please let me know where I can find those data? Thanks again.
Hi Jenny, I have admitted many times on this mailing list that the peak fitting dialog is one of the least polished parts of Athena. There currently is no way to get Athena to write out a file with columns for the individual line shapes. :( You can make a data group out of the fit and export that in the normal manner. For the individual line shapes, you have to reconstruct them from the fitted values. Here are the functional forms of the step functions used in Athena. In each case, A is the amplitude term, E is the centroid term, W is the width term, and e is the value on the energy axis: atan: f(e) = A * atan( (e - E)/W ) / pi + 0.5 erfc: f(e) = A * erfc( (e - E)/W ) + 1.0 For the peak functions, Athena uses Ifeffit definitions as they are given at http://cars9.uchicago.edu/~ifeffit/refman/node16.html gaussian: f(e) = A/(W * sqrt(2*pi)) * exp( -(e-E)^2 / 2*W^2 ) lorentzian: f(E) = A*W / ( 2 * pi * ( (e-E)^2 + (W/2) ^2 ) ) All of these formulas are included in the little log file that gets written out by the peak fitting dialog and are included there specifically to help the user reconstruct the lineshapes in another plotting program. HTH, 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 (2)
-
Bruce Ravel -
Jenny Cai