Re: [Ifeffit] Bug Report: incomplete data import in Athena when energy is given in keV

Dear Bruce and dear all, I have the same problem with data import in Athena 0.9.26 that Andreas has just described and that, if I am not mistaken has already been mentioned in this mailing list before. Looking for the possible cause of the problem, in the list of changes made for Athena in the latest version of Demeter I found the following: "Fix a problem processing keV data when using Larch (Thanks to Juan de la Figuera) (See issue #42)" May it be that these modifications are responsible for the observed import bug? (just a guess) Thank you Kirill Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu 25.10.2018 11:40, ifeffit-request@millenia.cars.aps.anl.gov пишет:

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1. Bug Report: incomplete data import in Athena when energy is given in keV (Voegelin, Andreas)

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Message: 1 Date: Thu, 25 Oct 2018 09:39:52 +0000 From: "Voegelin, Andreas" To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Bug Report: incomplete data import in Athena when energy is given in keV Message-ID: Content-Type: text/plain; charset="utf-8"

Dear Bruce & Ifeffit Mail-List

Working with Athena (executable Version 0.9.26 with Ifeffit 1.2.12 on Windows 10), I just noted a problem with data import when energy in the input file is given in keV.

Attached an example of recently collected Ce L3 edge data (original_format.txt), with the energy in keV in the first column and the DT-corrected and normalized fluorescence signal in column 44. The file contains 2 header rows and 308 lines of data. When this spectrum is loaded into Athena, it consists of only 186 instead of 308 datapoints (see information on spectrum ?original_format,.txt? in Athena project file ?test_bug_data_import_in_keV.prj?). The problem also persisted when I reduced the input file to only two columns, energy and fluorescence data, and seemed not related to file size. The problem occurs on various computers all running with the latest version of Athena.

Interestingly, the problem does not occur if the energy in the original file is given in eV instead of keV. From the original file, I created an input file ?test_energy_in_keV_eV.txt? in which columns 1 and 4 contain the energy in keV and columns 2 and 5 the energy in eV. When I import the spectrum using any of the columns with energy in eV, the spectrum is loaded correctly and consist of 308 datapoints. If I use any of the two columns with energy in keV, the imported spectrum again contains only 186 datapoints.

Comparing the mue output files of the spectra read in eV and keV (mue files attached), one can see that incomplete data import starts at 5703 eV, i.e., where the step size in the scan was changed from 2 eV to 0.5 eV. Notably, if I select column 5 containing the energy in eV, but tell Athena that the energy is in keV and needs to be converted to eV, Athena loads all 308 datapoints (although with obviously wrong energy scale). This might suggest that the problem is related to the absolute difference in energy between datapoints rather than to the conversion from keV to eV.

I tested also other data collected at the Mn K and Tl L3 edges and the problem is the same.

For the moment, the easiest work-around may be to reprocess all input files by adding a column with energy in eV. If an easy fix could be found for correct data import in Athena, however, this would be helpful.

Best regards, Andreas

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Andreas Voegelin, PhD Eawag - Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland Tel: +41 58 765 54 70 Fax: +41 58 765 52 10 mailto:andreas.voegelin@eawag.ch http://www.eawag.ch/~voegelan