Re: Ifeffit Digest, Vol 40, Issue 10
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Today's Topics:
1. data file format (emmanuelle montarges-pelletier) 2. Re: data file format (Matthew) 3. Re: data file format (Bruce Ravel) 4. The most important fitting parameters (Bridget Ingham)
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Message: 1 Date: Wed, 21 Jun 2006 10:25:47 +0200 From: emmanuelle montarges-pelletier
Subject: [Ifeffit] data file format To: ifeffit@millenia.cars.aps.anl.gov Message-ID: <1F268809-6D80-4EE8-996D-209DFF3FEE07@ensg.inpl-nancy.fr> Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Hello I have some problems with data file format as I try to import exafs files in Artemis or in Athena. I am working on a powerbook G4, with OSX 10.4.6. I installed the ifeffit package, including Athena and Artemis. Athena could open any XAS "raw" file from fluorescence or transmission measurements. However, if I perform any modifications on these raw files with exterior programs (Michalowicz programs, Kaleidagraph) and try to import the new files , saved as text files, Athena or Arthemis can not open them. I guess it may come from the encoding of the text file. Do you have any clue on this encoding issue? Do you know any program which would allow me to transform these text files in readable files for Artemis? Thank you for your answer sincerely Emmanuelle
There are two types of encodings which may differ among text files from different countries and OSs. I don't know how Athena&Co. handle either of them. One is that numbers and decimals can differ per country. If Kgraph is using a local encoding other than the American standard, say, using commas instead of periods, it's possible that Artemis won't understand it. I have the same problem with my analysis programs. Every so often I get a panicky email from a user whose files won't open. The other variation is in what constitutes the end of a line, which is OS-dependent. It could be carriage return, linefeed, or CR-LF. mam
Salut Emmanuelle,
Matthew's suggestion of floats with commas is a good suggestion. A&A make no attempt at respecting localization. (That is, a number between one and two might be written as 1,234 -- which would confuse A&A -- rather than 1.234.) If that is the case, your best bet is to go back to the exterior program and ask it nicely to write out points instead of commas. Or you might need to edit the file by hand.
I thought that the end-of-line issue (Matthew's other suggestion) was one that was solved in A&A years ago. If that proves not to be the case, please let me know.
Another possibility is that the exterior program added other text to the file that is confusing A&A. Here is my explanation of how Athena reads ascii data files
http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions
and here is the explanation of the file-reading function in Ifeffit which Athena uses:
http://cars9.uchicago.edu/~ifeffit/refman/node24.html
The situation in Artemis is similar, although restricted in the sense that Artemis is expecting its data to be chi(k).
If none of that clarifies the issue for you, I'll need to see an example of the data file which is causing the problem.
The easiest way to move data from Athena to Artemis is to have Artemis import its data directly from the Athena project file.
If there is some data processing feature that Athena does not do but which you require before moving on to data analysis, you should consider making a feature request here on the mailing list. Athena will never get the features that you need if I am not aware that they are needed!
B
Just an additional point: take care to save the file as unix file and not standard Mac (use a free text editor as TextWrangler to do this kind of manipulation). Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen@univ-poitiers.fr __________________________________________
On Wednesday 21 June 2006 12:40, Michel Jaouen wrote:
Just an additional point: take care to save the file as unix file and not standard Mac (use a free text editor as TextWrangler to do this kind of manipulation).
Actually, the opposite was my point. I thought that the whole end of line problem was long ago solved in A&A. It is my intention that A&A will work transparently with any of the three end-of-line conventions. That way, you don't need to worry about Wrangling your Text. If that's not your experience, let me know and I'll work on it. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Hi Everyone, I have a question about Artemis log file. I noticed that two r-factors are reported in the log file. One is in the fifth line and it is called 'R-factor' and the other one is under the data set fitting conditions and it is called 'r-factor for this data set'. They have in general different values. What does it mean? Which is the difference between the two? Lisa
At 02:13 PM 6/21/2006, Bruce wrote:
Actually, the opposite was my point. I thought that the whole end of line problem was long ago solved in A&A. It is my intention that A&A will work transparently with any of the three end-of-line conventions. That way, you don't need to worry about Wrangling your Text.
If that's not your experience, let me know and I'll work on it.
I thought the CRLF problem was solved, but at least in one case it's not. I used FEFF 8.28 to generate a set of paths on a Mac (OS 10.4.7). (The FEFF 8.28 I have might have been slightly modified to increase the number of paths allowed or something like that; I don't recall. But there were no changes to file handling.) Under Artemis 0.8.007 on either the Mac or the PC, choosing theory -> New Feff input template -> Import Feff.inp doesn't quite work. The Mac version doesn't give an error message, but only the headers seem to get read in--the interpretation lists no paths. On the PC (under Windows XP), errors are generated; they begin: Use of uninitialized value in pattern match (m//) at ?PerlApp/Chemistry/Elements.pm line 527. main::_ANON_('Use of uninitialized value in pattern match (m//) at /PerlApp/Ch...') called at /PerlApp/Chemistry/Elemenmts.pm line 527 Chemistry:Elements::_is_Z(undef) called at /PerlApp/Chemistry/Elements.pm line 355 Again, only headers are read in. Changing the LF generated by the Mac to a CRLF in all the text files in the folder solves the problem. --Scott Calvin Sarah Lawrence College
participants (4)
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Bruce Ravel
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Lisa Giachini
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Michel Jaouen
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Scott Calvin