New subject: Sudden Difficulty with Importing Data into Athena

3 Feb 2012

      This will make me seem pretty dense, but I'm still trying to figure
out how to reply to specific threads in the list-serve from my gmail,
and I keep seeming to create new threads... for which I wholeheartedly
apologize if it's becoming annoying.  But I really do thank everyone
for their help and patience thus far.

What I've attempted since earlier today:
1.  Completely reinstalling from older versions and newer versions of
IFEFFIT onto the Mac.  Didn't work.
2.  I went to two other Macs, did a clean install of the newest iXAFS
software and it worked fine... which can only mean something really
crazy is going on with the Mac I am trying to use for my work.  I'd
like to mention again that I was able to import data just fine last
night, and it was only this morning that things started breaking.
3.  I've reinstalled X11 and XQuartz.
4.  I've checked the data files on the other Mac machines (and Dr.
Zając checked them) and the files were fine.
5.  I attempted to run from the command line and found some errors
that weren't there at one time.
6.  I then checked my version of perl, and it is version 5

bash-3.2$ perl -v

This is perl, v5.10.0 built for darwin-thread-multi-2level
(with 2 registered patches, see perl -V for more detail)

6.  Something that MAY shed light on the situation... when I open
iXAFS from the Application menu in the Dock (I'll try attaching an
image), it seems that iXAFS is "broken" or not installing correctly.
However, I can then open iXAFS up in the FINDER window, it looks
"okay" and can be opened... it just doesn't function correctly.  What
I don't understand is why a clean install doesn't fit the problem...
are there hidden files I should remove as well that aren't removed
when I uninstall iXAFS from the application directory with (rm -rf ) ?

7.  George mentions that his build is different than my own, so now I
am looking at my structure (modified for more pleasant viewing), but
the directory does seem to exist.:

bash-3.2$ ls /Applications/iXAFS.app/
Contents

ls /Applications/iXAFS.app/Contents/
Info.plist      MacOS           PkgInfo         Resources

ls /Applications/iXAFS.app/Contents/Resources/
Artemis.icns            Athena.icns             English.lproj
Hephaestus.icns         Horae                   iXAFS Shell.icns
iXAFS Shell.sh          iXAFS.icns

ls /Applications/iXAFS.app/Contents/Resources/Horae/bin/
Aquaterm.app            atoms                   crc32
 feffit
ifeffit                 libpng-config           perlindex               tkpod
artemis                 autobk                  diffkk
 findatp
ifeffit_shell.pl        libpng12-config         rdaj
athena                  chartex                 feff6
hephaestus              ixafs-env               lsprj                   tkmore

Tony Kelly, M.Sc.
DTRA PhD Student
Air Force Institute of Technology
Nuclear Physics and Engineering

On Thu, Feb 2, 2012 at 5:15 PM,
 wrote:
...
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Today's Topics:
  1. Re: Sudden Difficulty with Importing Data into Athena
     (Dr. Dariusz A. Zaj?c)
  2.  Sudden Difficulty with Importing Data into Athena (Tony Kelly)
  3. Re: Sudden Difficulty with Importing Data into Athena
     (Bruce Ravel)
  4. Re: Sudden Difficulty with Importing Data into Athena (Tony Kelly)
  5. Re: Sudden Difficulty with Importing Data into Athena
     (Dr. Dariusz A. Zaj?c)
  6. Re: Sudden Difficulty with Importing Data into Athena
     (Dr. Dariusz A. Zaj?c)
----------------------------------------------------------------------
Message: 1
Date: Thu, 02 Feb 2012 19:07:32 +0100
From: "Dr. Dariusz A. Zaj?c" 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
       Athena
Message-ID: <4F2AD0E4.3010107@ifj.edu.pl>
Content-Type: text/plain; charset=UTF-8; format=flowed
check the data, if at the end of  files are some zeros or strange
numbers or even empty line(maybe). That what you described can be
exactly caused by problem with the data in file, eg. injection during
measurements
W dniu 12-02-02 18:22, Tony Kelly pisze:
...
Hopefully this is not long winded, but I want to be as detailed with
the problem as I can be.  In the past, I have never had difficulty
importing data into Athena, given it was formatted properly.  It was
working as recently as last night, but suddenly I have a problem
today.
1.  I open Athena
2.  I go to File->Open Files
3.  I click on the data file to bring me to the window where I choose
Energy, Numerator, Denominator for the data and any reference spectra,
etc
4.  I choose the Energy, Numerator and Denominator
This is when the first moment of "oddness" happens... I don't get a
plot.  Normally, I would get a plot of the spectra I am about to
import to know if I selected the correct columns with the correct sign
(and whether a Log is needed).
5.  Confused, I continue anyway and import my choices.
6.  I then get the following error from Athena:
The following problems were found for group "Fe.060"
  1  : The edge energy is unset
  2  : The kmin for the forward transfer is negative (-2)
You should fix these values before continuing analysis of these data.
Note 1: I was trying with some old data that I have analyzed in the
past from Athena through Artemis and know to be okay for analysis.
Note 2: I then tried studying some MnO spectra by importing that data
taken during the 2011 XAFS Summer School in Chicago taken from APS.  I
know these text files to work, as we looked at them AT the summer
school.
Note 3:  As a last resort, I tried downloading the Fe example from the
Athena website (as you can see above from Fe.060), but it can't even
read this in.
Note 4: Athena CAN open old projects where the data was already
imported without problems... it just seems I can't start a new project
and import data into it successfully.  I have tried searching all
through the internet for anyone who had the error above or my
difficulties to no avail.  I have tried making sure the line breaks
were correct by resaving data into new files through textwrangler and
even going through vim in a terminal, to no avail.
Note 5: As a last resort, I reinstalled iXAFS, but this hasn't fixed
the problem.
Anyone have any suggestions?  Am I suddenly forgetting a step in the
data import process?
Thanks,
Tony Kelly
Air Force Institute of Technology
Nuclear Physics and Engineering
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------------------------------
Message: 2
Date: Thu, 2 Feb 2012 13:18:14 -0500
From: Tony Kelly 
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit]  Sudden Difficulty with Importing Data into Athena
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1
Hi Bruce,
Thank you for the quick reply.  I tried uninstalling and reinstalling
twice, though I suppose I could try a different version.  I have also
made sure that my x11/xquartz software was up to date, though I have
not changed or added software or updates between the last time it
worked and now.
It literally worked last night, then it no longer worked this morning.
I've never had antivirus software on my macs, but I could download one
and do a scan to see what that gives me.
If I find a clear solution to what may have happened, I'll be sure to
reply again to share the answer.
Tony Kelly
Air Force Institute of Technology
Nuclear Physics and Engineering
------------------------------
Message: 3
Date: Thu, 2 Feb 2012 13:27:37 -0500
From: Bruce Ravel 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
       Athena
Message-ID: <201202021327.38153.bravel@bnl.gov>
Content-Type: Text/Plain;  charset="iso-8859-1"
On Thursday, February 02, 2012 01:18:14 pm Tony Kelly wrote:
...
Thank you for the quick reply.  I tried uninstalling and reinstalling
twice, though I suppose I could try a different version.  I have also
made sure that my x11/xquartz software was up to date, though I have
not changed or added software or updates between the last time it
worked and now.
I have to ask the obvious questions ... :)
...
It literally worked last night, then it no longer worked this morning.
I've never had antivirus software on my macs, but I could download one
and do a scan to see what that gives me.
I am not suggesting that.  I was suspicious that AV software had
deleted something as a false positive.
You might have mentioned in your original email that you were using
the Mac.  In this case, I don't see yet how it matters, but it
certainly is awfully big omission.
...
If I find a clear solution to what may have happened, I'll be sure to
reply again to share the answer.
Try opening a terminal and running athena from the command line.  The
advantage of this is that you will get to see whatever error messages
get issued when Athena runs into her problems.
Also Darek's suggestion of checking to make sure the input data has not
been somehow corrupted is a good one.
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/ifeffit/Demeter
------------------------------
Message: 4
Date: Thu, 2 Feb 2012 14:23:07 -0500
From: Tony Kelly 
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
       Athena
Message-ID:

Content-Type: text/plain; charset=ISO-8859-1
1.  I made sure to check the data files for strange behavior,
definitely a good idea.  I know when I use other software such as
ROOT, file structure and pat names can become problems.  This didn't
fix the problem, however :-/
2.  I then ran Athena from the command line as was suggested, and it
seems that there is a major problem there:
bash-3.2$ athena
Can't load '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle'
for module Ifeffit:
dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle,
1): Library not loaded: libifeffit.so
 Referenced from:
/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle
 Reason: image not found at
/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm
line 204.
 at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67
Compilation failed in require at
/Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
BEGIN failed--compilation aborted at
/Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
3.  Then I became more curious and attempted ifeffit itself:
bash-3.2$ ifeffit
dyld: Library not loaded: libpgplot.dylib
 Referenced from: /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit
 Reason: image not found
Trace/BPT trap
I am using Max OSX 10.6.8.
Intel Core i5.
Any other Mac users out there have ideas?
Thanks much,
Tony Kelly
Air Force Institute of Technology
Nuclear Physics and Engineering
------------------------------
Message: 5
Date: Thu, 02 Feb 2012 20:56:44 +0100
From: "Dr. Dariusz A. Zaj?c" 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
       Athena
Message-ID: <4F2AEA7C.8070400@ifj.edu.pl>
Content-Type: text/plain; charset=UTF-8; format=flowed
can you send me this file you can not open?
W dniu 12-02-02 20:23, Tony Kelly pisze:
...
1.  I made sure to check the data files for strange behavior,
definitely a good idea.  I know when I use other software such as
ROOT, file structure and pat names can become problems.  This didn't
fix the problem, however :-/
2.  I then ran Athena from the command line as was suggested, and it
seems that there is a major problem there:
bash-3.2$ athena
Can't load '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle'
for module Ifeffit:
dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle,
1): Library not loaded: libifeffit.so
  Referenced from:
/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle
  Reason: image not found at
/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm
line 204.
  at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67
Compilation failed in require at
/Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
BEGIN failed--compilation aborted at
/Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
3.  Then I became more curious and attempted ifeffit itself:
bash-3.2$ ifeffit
dyld: Library not loaded: libpgplot.dylib
   Referenced from: /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit
   Reason: image not found
Trace/BPT trap
I am using Max OSX 10.6.8.
Intel Core i5.
Any other Mac users out there have ideas?
Thanks much,
Tony Kelly
Air Force Institute of Technology
Nuclear Physics and Engineering
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Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
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------------------------------
Message: 6
Date: Thu, 02 Feb 2012 23:15:48 +0100
From: "Dr. Dariusz A. Zaj?c" 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] Sudden Difficulty with Importing Data into
       Athena
Message-ID: <4F2B0B14.2070807@ifj.edu.pl>
Content-Type: text/plain; charset=UTF-8; format=flowed
Hmm,
under Win XP I had no problems to open files, together with the
reference. For Tony's data as well as downloaded from internet's one.
I'm just thinking - this maybe is some problem with the settings in open
window, or with compilation of Athena.
About second case I have not to much to say,
About first - maybe some option for opening file and processing data? I
tried to see each counter separately and I had no problems, also with
negate function...
any ideas?
darek
W dniu 12-02-02 20:23, Tony Kelly pisze:
...
1.  I made sure to check the data files for strange behavior,
definitely a good idea.  I know when I use other software such as
ROOT, file structure and pat names can become problems.  This didn't
fix the problem, however :-/
2.  I then ran Athena from the command line as was suggested, and it
seems that there is a major problem there:
bash-3.2$ athena
Can't load '/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle'
for module Ifeffit:
dlopen(/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle,
1): Library not loaded: libifeffit.so
  Referenced from:
/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/site_perl/5.12.1/darwin-multi-2level/auto/Ifeffit/Ifeffit.bundle
  Reason: image not found at
/Applications/iXAFS.app/Contents/Resources/local/lib/perl5/5.12.1/darwin-multi-2level/DynaLoader.pm
line 204.
  at /Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67
Compilation failed in require at
/Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
BEGIN failed--compilation aborted at
/Applications/iXAFS.app/Contents/Resources/local/bin/athena line 67.
3.  Then I became more curious and attempted ifeffit itself:
bash-3.2$ ifeffit
dyld: Library not loaded: libpgplot.dylib
   Referenced from: /Applications/iXAFS.app/Contents/Resources/Horae/bin/ifeffit
   Reason: image not found
Trace/BPT trap
I am using Max OSX 10.6.8.
Intel Core i5.
Any other Mac users out there have ideas?
Thanks much,
Tony Kelly
Air Force Institute of Technology
Nuclear Physics and Engineering
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Ifeffit@millenia.cars.aps.anl.gov
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***************************************

Re: [Ifeffit] Sudden Difficulty with Importing Data into Athena

Tony Kelly

George Sterbinsky

Tony Kelly

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