Dear all, Recently we've measured samples at the DUBBLE Beamline at ESRF for iron and molybdenum (K-edge). After measuring, the DUBBLE software generates a .dat file which must then be translated to other files (depending on the fact whether transmission or fluorescence is measured) using some script in linux. When we try to import some of these transformed files (for transmission measured) into Athena however, the program fails to subtract a background from mu(E), therefore no k and R-space plots are available (see project files MoPEL002 and MoPEL004, the original dat.sample files are included in the zip files). Other files however, work fine (both transmission and fluorescence measured ones). After analyzing the structure of the .dat files, it was discovered which columns are the Io an It data and the correct ln(Io/It) could be manually generated. This manual procedure yields data sets identical to the ones in the dat.sample files, we named them dat.good files. When importing these files into Athena, the background subtraction works fine. It is the exact same data however... Although the problem can be bypassed by processing the data manually, the fact that Athena processes some files correctly and others not seems very strange to us since they all come from the same beamline. We thought it would be interesting to let you all know. Thanks for your time and for making such wonderful software, Alexander Riskin -- Alexander Riskin Universiteit Hasselt IMO - Inorganic and Physical Chemistry Agoralaan – Building D BE-3590 Diepenbeek / Belgium tel. +32.(0)11.26.83.94 fax. +32.(0)11.26.83.23 email: alexander.riskin@uhasselt.be
Hi Alexander, I see two issues with these data files that are probably tripping up Athena: First: the files end with an "END OF DATA" line. This is a fine choice for how to organize a data file, but it's not what Ifeffit is expecting. Second: a bigger issue is that there isn't a column for energy in eV or keV. It looks like the monochromator position is stored in angle (or perhaps I'm misreading the ".dat" files?). Again, this is not what Ifeffit is expecting, and I think this is what is really preventing Athena from processing the data. An Athena plug-in could be made to read these files and do these conversions. There are several example plugins. It would also be pretty easy to write a simple pre-processing script that strips of the last line (the information at the top looks like it would be fine to me) and convert angle to energy. Sorry for the trouble, and hope that helps. --Matt
Alexander, DUBBLE certainly does write out a quirky data file. This was a topic of discussion when I was in Ghent earlier this year. I came up with a solution of the sort that Matt mentioned in his email -- a plugin. It can be found here, where its installation is described in detail. http://cars9.uchicago.edu/ifeffit/BruceRavel/DubbleBeamline I tested one of the data files in your zip file against the plugin and it seemed to work. Speak up on the list if you run into any troubles. I had hoped that the folks who run DUBBLE would point their users at that web page. B On Friday 02 April 2010 04:22:30 am Alexander Riskin wrote:
Dear all,
Recently we've measured samples at the DUBBLE Beamline at ESRF for iron and molybdenum (K-edge). After measuring, the DUBBLE software generates a .dat file which must then be translated to other files (depending on the fact whether transmission or fluorescence is measured) using some script in linux. When we try to import some of these transformed files (for transmission measured) into Athena however, the program fails to subtract a background from mu(E), therefore no k and R-space plots are available (see project files MoPEL002 and MoPEL004, the original dat.sample files are included in the zip files). Other files however, work fine (both transmission and fluorescence measured ones).
After analyzing the structure of the .dat files, it was discovered which columns are the Io an It data and the correct ln(Io/It) could be manually generated. This manual procedure yields data sets identical to the ones in the dat.sample files, we named them dat.good files. When importing these files into Athena, the background subtraction works fine. It is the exact same data however...
Although the problem can be bypassed by processing the data manually, the fact that Athena processes some files correctly and others not seems very strange to us since they all come from the same beamline. We thought it would be interesting to let you all know.
Thanks for your time and for making such wonderful software, Alexander Riskin
-- 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)
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Alexander Riskin -
Bruce Ravel -
Matt Newville