[Ifeffit] Demeter-devel MacPorts Athena issues & work-around

Margaret Hinkle mhinkle at eps.wustl.edu
Sat Jul 5 14:49:22 CDT 2014


Dear Bruce,
Your fix worked beautifully -- thank you for your clear instructions!
Athena & I are both very happy. The data loads in perfectly.

And I do apologize for my poor wording with my initial e-mail --  my
statement about the MacPort version of Athena not being able to load in
data files with 'headers of any sort' was really a reflection on the fact
that I had attempted to load in data files from 4 different beamlines at
the APS, so I did not think at the time that my problem was
header-type-specific. However, I did not specifically say that in my email
(going for brevity). If I run across a problem in the future, I will be
sure to include example files and all the pertinent information upfront.

Thank you again for all your help!

Best,
Margaret Anne

------------------------------------
Margaret Anne G. Hinkle
Ph.D. Candidate
Earth and Planetary Sciences
Washington University in St. Louis
Rudolph Hall
Campus Box 1169
1 Brookings Drive
St. Louis, MO 63130
email: mhinkle at eps.wustl.edu
website: aqgeochem.wustl.edu


On Sat, Jul 5, 2014 at 2:06 PM, Bruce Ravel <bravel at bnl.gov> wrote:

> On 07/04/2014 12:11 PM, Margaret Hinkle wrote:
>
>> Thanks for your help & your quick reply. I did not expect my altering
>> one character in the code to fix the problem -- I had just hoped it
>> would tell me if the Tip of the Day was indeed the culprit. I did as you
>> suggested, and the problem is completely fixed. Thanks!
>>
>> Per your comment regarding Issue 2 -- I have attached two files, one
>> with the header removed (filename: '...NoHeader_exafsscan.dat'), and the
>> other with the header left in with #s commenting it out (filename:
>> '...Header_exafsscan.dat'). Note that these are transmission samples,
>> with I0 in column 56, and I1 in column 57.
>>
>>
> Margaret Anne,
>
> By the end of this email, I am going to thoroughly solve your problem.
> But, first, I am going to step up on my soapbox and pontificate.  It's
> kinda what I do on this mailing list....
>
>
>
> You started this by writing "I can only load data files into Athena if
> there are no headers of any sort".  That is a demonstrably untrue
> statement, and easily so.  Were it true, this mailing list would be either
> (a) filled with nothing but posts about people complaining that they cannot
> import their data, or (b) silent because no one would use software so
> completely fucked up and useless.
>
> A true statement might have been that you had examples of data files that
> could not be imported into Athena.  But you did not include an example of
> the troublesome data file -- I had to ask for it.
>
> When you ask a question, you should try to put yourself in the shoes of
> the person answering.  I am not in the same room as you, I am not looking
> at your computer, and I do not have the example that triggers the problem
> here in front of me.  And I do not possess telepathy.  When you ask a
> question, you have to give the person who wants to help a fighting chance
> of being able to help.
>
>
>
> All right.  Enough of that.  Let's solve your problem.
>
> Find the installation location of Demeter on your computer.  If you do not
> know where that is, then open a command terminal and enter the following
> command:
>
>    perl -e 'use Demeter; print $INC{"Demeter.pm"}, $/'
>
> The thing that gets printed is the folder containing the main Demeter
> module file.  Everything else is beneath that folder.
>
> Download this file:
>
>    https://s3.amazonaws.com/demeter4xas/SpecFileLongLine.pm
>
> and save it as
>
>    Demeter/Plugins/SpecFileLongLine.pm
>
> where "Demeter/" is a folder inside the folder we identified above.
>
> Make sure that the file is called "SpecFileLongLines.pm" -- exactly as
> written there -- and that your web browser does not "help you out" by
> changing the extension of the file to ".txt" or any other such shenanigans.
>
> Now fire up Athena and select "Plugin Registry" from the main menu. This
> will display the view shown here:
>
>
> http://bruceravel.github.io/demeter/aug/other/plugin.html#
> athena%27spluginregistry
>
> There should be an row that says "SpecFileLongLine".  Click it on.
>
> You should now be able to import your files without needing to edit the
> header.
>
> Note that if you attempt to import one of your data files *without*
> enabling the "SpecFileLongLine" plugin, Athena will continue to crash. The
> mere presence of the SpecFileLongLine.pm file is not enough -- you *must*
> enable in the plugin registry.
>
>
>
> So, what was the problem?
>
> Well, Ifeffit -- which is the math and XAS engine underneath the hood of
> Athena -- is written in Fortran.  Fortran does not have dynamic memory
> allocation.  Thus there are some hardwired limits to things in Ifeffit, not
> all of which get handled gracefully when exceeded.
>
> The line in your data file causing the problem is the one that starts with
> "#L".  It contains the column labels and is about 330 characters long.  As
> one point, Ifeffit attempts to stuff those 330 characters in a variable
> configured to be 256 characters long.  That is the cause and location of
> the error message you cited.
>
> The plugin does the simplest possible thing.  It makes a copy of the data
> file, copying every line except the one beginning with #L.  Athena then
> reads the copy.  The original data is untouched, the copy is deleted once
> Athena reads it in.  Athena is happy and so, I hope, are you!
>
>
>
> Let me know if you have any problems with the plugin.  It worked for me on
> my linux computer.  I suspect it'll work for you as well, but one never
> knows....
>
>
> B
>
>
>
>
> --
>  Bruce Ravel  ------------------------------------ bravel at bnl.gov
>
>  National Institute of Standards and Technology
>  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
>  Building 535A
>  Upton NY, 11973
>
>  Homepage:    http://xafs.org/BruceRavel
>  Software:    https://github.com/bruceravel
> _______________________________________________
> Ifeffit mailing list
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>
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