On 11/13/2015 03:09 PM, Bruce Ravel wrote:
The dependency on Encoding::FixLatin::XS is a mistake made by me. I
made it a recommendation to quiet a spurious warning that happens on
Windows but not on linux. (No clue about the Mac.) It's not actually
used for anything and I just edite
ks,
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
Software:https://github.com/bruceravel
Demeter:
oblem, it's going to take a lot more
effort to troubleshoot the problem.
Good luck!
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY,
ons for the standards;
in the other one these boxes worked normally and all standards could be
considered.
Some screenshots are attached to this message,
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Gro
-transform k space.
I think that helps put my earlier comment into proper context for you.
Wonderful post, though! It is very pleasant to see a post that doesn't
involve someone complaining about something related to the Mac! :)
Cheers,
B
--
Bruce
also making good progress on Marcelo Alves' observation that
Athena doesn't like files with non-ASCII characters in the file names.
Hopefully, that too will be fixed in the next release.
--
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National Institute of Sta
from so we could know that any translation was
working well.
I'm writing to the mailing list of several reasons:
1) A reviewer explicitly asked to contact Bruce Ravel so that the
new insight could be implemented in ATHENA,
2) I was trying to combine my code with ATHENAs way of
://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-September/012739.html
Apparently setting gnuplot-->terminal to "aqua" works also.
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Buildin
ng back to the parent Brown & Altermott reference or
alternatively can interpolate from Cu and Ni values.
Really excellent point!
Artemis has a few ways of integrating bond valence sums into the workflow:
http://bruceravel.github.io/demeter/artug/extended/bvs.html
B
e would have no idea
what this could be.
Thanks for your comments!
Carolyn Carr
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On 11/09/2015 02:54 PM, Bruce Ravel wrote:
On 11/09/2015 02:29 PM, Robert Gordon wrote:
Ah, yes...special characters...çã...Athena does not seem to like those
in file names
If I replace with Calibração with Calibracao in a test directory of my
own, then the file opens without issue.
-R.
On 11
e path is not a
problem on my linux computer and I guess I have never tested that
properly on Windows.
I'll look into it.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Bui
f there is still trouble, dig deeper.
Zack
(Note, I’ve only used Hephaestus and Athena on El Capitan. But Artemis
worked for me on Yosemite.)
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om the
github repository and replacing the ones installed on your computer.
The files that changed to make this fix are:
lib/Demeter/UI/Athena.pm
lib/Demeter/UI/Athena/Summer.pm
Be sure to download the "raw" file and be sure it is saved with a
".pm" extension.
Regards,
B
the last Athena version?
Yes. No problems here on any of my computers.
Here are some hints on how to ask a question effectively:
http://bruceravel.github.com/demeter/pods/bugs.pod.html
http://bruceravel.github.com/demeter/pods/help.pod.html
B
--
Bruce Ravel
roblem. Without something like a recipe that I can follow, there's not
much I can do to help.
http://bruceravel.github.com/demeter/pods/bugs.pod.html
http://bruceravel.github.com/demeter/pods/help.pod.html
B
--
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N
the behavior you describe.
I am away from my office (and so away from any windows computers) so I
cannot look into it right now. Is there any chance that your anti-virus
software is interrupting gnuplot's operation in some way?
B
--
Bruce Ravel ---
ceravel.github.io/demeter/pods/bugs.pod.html
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
Softwa
ul, actionable bug report would include those error messages,
which tend to be a lot more helpful for me than this sort of
narrative, which is hard for me to understand.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchr
tt
On Wed, Oct 14, 2015 at 5:30 PM, Bruce Ravel mailto:bra...@bnl.gov>> wrote:
On 10/14/2015 05:25 PM, Matt Noerpel wrote:
Thank you for your prompt reply. The Ifeffit.dll file does exist in
that directory. It was last modified on 3/16/2015 and is 753 kb.
Whew!
om: ifeffit-boun...@millenia.cars.aps.anl.gov
[mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel
Sent: 19 October 2015 14:14
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Demeter 0.9.23 in multi-user environments
On 10/19/2015 08:34 AM, Godfrey, Ian wrote:
Hi All,
I'm
stand either of them. As I said, I'll try to
reproduce yours by installing in a system folder.
What happens if you install to, say, C:\DemeterPerl rather than
C:\Program Files\DemeterPerl? I am suspicious that something isn't
happy with that space in the
removal of the prior
installation issue a dialog box so you can opt not to do the removal.
Again, it will take me some time to get there.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
l.gov/pipermail/ifeffit/2015-August/012662.html ?
Umm... no. Thanks for the reminder.
B
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National Institute of Standards and Technology
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Building 535A
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Homepage:
. And tomorrow I will try installing not in the default place on some
computer. Perhaps there is a problem that I simply missed or neglected
B
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National Institute of Standards and Technology
Synchrotron Science Group at
that your anti-virus thing did not intercept
the installation of DLL file?
B
PS: I am close to 100% certain that the XSLoader/DynaLoader thing is a
red herring.
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National Institute of Standards and Technology
Synchrotron S
a way to send me the videos, if you
have them and if it is not much trouble.
Thank you.
Regards
Wuhib
PS: I received a link from Dr. Shu Hayama but as he himself guessed I
am having difficulty playing and downloading the .wmv files due to
probably browser/network related issue
nd Biological Engineering
Northwestern University
Evanston, IL USA
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On 10/07/2015 02:05 PM, Bruce Ravel wrote:
George offers a work-around here:
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-September/012739.html
Also relevant:
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-September/012742.html
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a keyboard shortcut. You will find
yourself typing that A LOT as you use larch in this way. :)
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepag
On 10/02/2015 09:09 AM, Bruce Ravel wrote:
It turns out that, when you use
larch as a python script (as opposed to running it through larch
itself), every damn thing needs the '_larch=mylarch' argument.
Johan,
I explain why this is necessary at
https://bruceravel.gitbooks.io/la
is wrapped inside of
function. This is because that project is an automated testing
framework and, in each case, the fit is called by some other script.
But the structure of the fit is the same as what you are trying to
do. Every call to a larch-y function needs a "_la
g list with any problems, I would be very grateful
for any feedback. If your log-in name meets one of my areas of
concern, I would be doubly grateful for the feedback!
Those who don't want to live near the edge should use 0.9.22 or
0.9.23_pre2 for now.
Thanks!
.
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
Software:https://github.com/bruceravel
Demeter:
, but I am happy to accept patches
or explanations of what to fix. Here's the relevant code:
https://github.com/bruceravel/demeter/blob/master/lib/Demeter/UI/Hephaestus/Formulas.pm
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards
On 09/23/2015 03:44 PM, Pedro F B D Martins wrote:
I would like to thank to Bruce Ravel and Guanghui Zhang for the
suggestions. I've modified the restrictions of Demeter and all items
related to it in Kaspersky, and also installed the new version of
Demeter 0.9.23, which seems to be working
ion with gnuplot. Still, no data is
plotted.
That's not how the communication works. Demeter needs to start its own
instance of gnuplot.
I'm afraid I don't know where to go from there. Perhaps Joe or someone
else can advise.
B
--
Bruce Ravel
t;
Basically, I am wondering if the problem is that gnuplot is not
working or if the problem is that Demeter's communication with gnuplot
is not working.
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Sc
or, but
it would be an adequate way of capturing the 4 data files that Logan
was asking asking about. And it exists as actual code that can be
used today.
B
--
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National Institute of Standards and Technology
Synchrotron Scienc
at the Japanese synchrotrons benefited
greatly by an interested party taking part in the development of those
plugins (thank you Eric! thank you Yohei!). The SSRL plugins could use
some similar TLC.
B
--
Bruce Ravel bra...@bnl.gov
National Institute o
ou intend to use Athena, your best bet
would be to write yourself a little conversion program that leaves the
data in a state that Athena can interpret. Another option is to use
sixpack.
B
--
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National Institute of Standards an
wards transitioning Artemis to use feff85exafs
(https://github.com/xraypy/feff85exafs), but that will take a few months.
This is relevant to the feff6/feff8 discussion:
http://bruceravel.github.io/SCFtests/scf.html
B
--
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Nat
:
https://github.com/bruceravel/demeter/commit/10f9b05539bef286c21a357a0a23c0f93da37eb2
although without the check for the perl executable.
Do the bat files that get generated still seem wrong to you?
B
--
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National Institute of
some testing, but it will, I believe fix the
problem that Martina originally reported and which Robert verified.
Cheers,
B
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
resets to qt when
restarting even though the ini file says wxt.
Ugh! I thought I had fixed that problem.
Top of the to do list for Tuesday morning.
Thanks,
B
--
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National Institute of Standards and Technology
Synchrotron Science
o "wxt". The interaction with the cursor does not work correctly on
some terminals.
If that's not the problem, then I am at a loss. I don't see this
behavior on any of my computers.
B
--
Bruce Ravel bra...@bnl.gov
National Inst
ith deglitching reported by Shoaib, but
the fixes that went into 0.9.22 resolved all of his concerns.
I will need to be able to reproduce this on my own computer in order to
do anything about it:
http://bruceravel.github.io/demeter/pods/bugs.pod.html
B
--
Bruce Ravel -
part of the data. It may help to loosen the
high end spline clamp (which you can read about in the Athena manual).
Since you did not show us what your data looks like, it is hard to say
something more specific than that.
Regards,
B
--
Bruce Ravel bra...@bnl
.14.4, so I have not
yet tested whether PCA works after all this. It's getting kind of
late, so I'll try that in the morning.
Hopefully, this will get you over this hurdle. Presumably, the debian
package did all that
Please report back to the list about what
ift come and go.
Thank you,
George
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the AWS S3 product to host the Windows installer files.
It works for me this morning.
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage
(s) 25.696 bytes
>0 Dir(s) 11.455.164.416 bytes free
>
>
>
>A workaround is:
>- uninstall demeter
>- install demeter to default installation directory "c:\strawberry"
>
>
>
>Kind regards,
>René
>
>
>
st shell with the other metal. For
Au-Cl, try this: http://www.crystallography.net/cod/1510088.html
Thanks for the work around.
Ian
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hopefully your other problem) and put out a new
installer as soon as possible.
B
On 08/04/2015 11:21 AM, Bruce Ravel wrote:
On 08/04/2015 11:14 AM, Godfrey, Ian wrote:
In the preferences, try changing gnuplot-->terminal from "qt" to
"wxt". You might also try "windows
k first shell paths
certainly do not get restored correctly from a project file. I am
currently confused. :( But working on it.
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National Institute of Standards and Technology
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Building
minal from "qt" to
"wxt". You might also try "windows", although I think that one looks
much worse than either qt or wxt.
You might also try changing the font -- gnuplot-->font. It should be
arial. Stick with a fairly normal
es\plot\gnuplot\start.tmpl
Edit line 8 to read
set encoding iso_8859_1
that is, replace "default" with "iso_8859_1".
That's my first thought. No guarantees!
B
--
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National Institute of Standards and
ucl.ac.uk <mailto:i.godf...@ucl.ac.uk> i.godf...@jaist.ac.jp
<mailto:i.godf...@jaist.ac.jp>
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On 07/30/2015 10:49 AM, Bruce Ravel wrote:
1. *Using the FOLP card*: The actual cluster size is about 180 atoms
extending upto 18 A in radial distance from the central cobalt atom. But
there are quite a few instances of Hydrogen atoms that are too close. I
tried the FOLP with the recommendation
that means, but it gives some hints. The source
code corval.f tells us that is "Finds the core-valence separation for
the cluster of atoms." I simply am not knowledgeable enough about the
details of Feff to know why your cluster triggered this warning.
B
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Building 535A
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Homepage:http://bruceravel.github.io/home/
option of using Larch instead of Ifeffit, it
will be easier for me to implement controls to do that, but that is a
future project. The bottom line is that Athena does not currently do
what you are asking for.
B
--
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National Institu
On 07/21/2015 08:52 AM, Bruce Ravel wrote:
That said, "plot this result in norm(E) for a fit in chi(k)" is a good
and useful idea. I'll put it on my to do list.
So is "plot in chi(k) for this fit in norm(E)", for that matter.
B
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l this is because this is a common sort
of problem for those installing Demeter from source code. I wanted to
leave this explanation in the m ailing list archives for the benefit
of anyone in the future who runs into a similar snag.
Cheers,
B
--
Bruce Ravel bra
the autosave file in
~/.horae/stash (it has "autosave in the file name) and see if that is
sufficient to fix the problem.
Basically, I need a way to track down where the problem is actually
happening.
Cheers,
B
Zack
On Dec 10, 2014, at 5:52 AM, Bruce Ravel mailto:bra...@bnl.gov>
effit, Larch, and
Demeter. The different convention would result in phase shifts.
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
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Homepage:
On 07/14/2015 09:41 AM, Bruce Ravel wrote:
The error about Clone.pm not being installed suggests that another
dependency, called PPI, did not install correctly. I would recommend
installing the debian package for that one as well. Doing so should
resolve all of PPI's own dependencies
require at /usr/local/share/perl/5.14.2/PPI.pm
line 19.
BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI.pm
line 19.
Compilation failed in require at Template/Plugin/PerlSyntaxHtml.pm line 5.
BEGIN failed--compilation aborted at Template/Plugin/PerlSyntaxHtml.pm
line 5.
Compilation
erl\site\bin;C:\strawberry\c\bin;C:\strawberry\c\bin\gnuplot\bin;
Hope that helps -- and please let us know!
--Matt
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ere is any other way please let me know.
Thank You ,
Thitipong
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National Institute of Standards and Technology
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Building 535A
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
first bet on over-aggressive anti-virus software.
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
impossible to answer a question like this without a look
at the log file, as explained here:
http://bruceravel.github.io/demeter/pods/bugs.pod.html
B
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National Institute of Standards and Technology
Synchrotron Science
_
>
>
>Someone could help me?
>
>
>Thank you!
>
>
>Best,
>Everton.
>
>
>
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little be confusing.
Good point. It's now fixed at github. You can simply replace the file
or here's the diff:
https://github.com/bruceravel/demeter/commit/0eebb7f926d0028b6797ed38b205a293f52f616a#diff-b7e90e98dcf2bb18b46fe4f3b6297133
Thanks,
B
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aestus.
Thanks
Guanghui
2015-06-18
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N
would likely
select one or a few representative O scatterers. The parameters of
the EXAFS equation would then be parameterized to attempt to capture
the full complexity of the Ti-O partial pair distribution. "Fuzzy
degeneracy over sites" is a tool that attempts to automate that
tedio
fo/ifeffit
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Building 535A
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Software:https://github.com/bruceravel
Demeter
e the
same spectral density?
I think the answer is yes, but I am not sure I understand the
question.
HTH,
B
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the project file correctly. I'll look into it.
Thanks,
B
--
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage:http://bruceravel.github.io
y of your source material. Granted,
it canbe very difficult to obtain rare earth metal samples that are
elementally pure. But if your data range is short because of other
edges, then you need samples that are more pure.
HTH,
B
--
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On 05/27/2015 03:41 PM, Bruce Ravel wrote:
I have a work-around for you while to try I continue to puzzle over
this one. Download a copy of this small text file:
https://raw.githubusercontent.com/bruceravel/demeter/master/lib/Demeter/templates/fit/ifeffit/residual.tmpl
On your computer
.
B
On 05/27/2015 03:41 PM, Bruce Ravel wrote:
Hi Rosalie,
After spending some time with this, I agree that there is something
very wrong that manifests itself when you attempt to save the data+fit
file in k-space.
The executive summary is that there is a problem deep under the hood
with the k
know if this crude fix
works for you.
Cheers,
B
On 05/26/2015 09:18 AM, Bruce Ravel wrote:
On 05/25/2015 08:37 PM, Rosalie Hocking wrote:
If I go to the Artemis data window and go Data “save data and fit as” it
doesn’t seem to match up with the simulations on the window.
Hi Rosalie,
I don&
am not 100% confident that
everything is implemented quite right. I could easily have missed
something...
See the change log at
https://github.com/bruceravel/demeter/blob/master/Changes.org
for the changes that are in this trial version.
Cheers,
B
--
Bruce Ravel --
but ... are you sure that you are saving the data
with the same k-weighting as the plot?
Also, I just want to point out that the k-weighted data are in column 2
of that file and the k-weighted fit is in column 3.
B
--
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Nation
n select "Make VPath"
from the actions menu, then plot in k, R, or q). The intent also is that
the current values for all parameters will be used when the plot is
made. If no fit has been performed, the initial values will be used.
It should not be necessary to change all guesses to
in the latest version.
Still is easy. Well, I think it is. YMMV :)
http://bruceravel.github.io/demeter/artug/plot/vpaths.html
B
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National Institute of Standards and Technology
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Building
n than the work-around I suggested!
:)
B
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National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
Software:htt
-arounds, that's a bit of a pain in backside, but
it will allow to make progress.
Thanks for the bug report. As I often say here on the mailing list,
useful bug reports here on the mailing list help make the software
better for everyone!
Cheers,
B
--
Bruce
On 05/04/2015 09:03 AM, Bruce Ravel wrote:
On 05/03/2015 09:18 PM, Shoaib Muhammad wrote:
Actually plot don't change to scatter by itself when I select the
"Deglitch
and truncate data" from the drop down menu list. I have checked it on
another PC with Win7x32 OS as well and the
his behavior is the same in some of the previous versions of
Athena as well at least on my Windows PC:)
You are absolutely right. I'm not sure why I thought otherwise. Guess
I haven't deglitched any data recently....
B
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?
B
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National Institute of Standards and Technology
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Demeter:
he right tool for the job? Or perhaps you can
figure out something that does what you want using either Ifeffit or
(preferably!) Larch? In that case, let me know and I'll see about
including it in Athena.
B
--
Bruce Ravel bra...@bnl.gov
On 04/20/2015 08:34 AM, Bruce Ravel wrote:
I agree that Athena is not working as advertised for selecting the
norm(E) option in the column selection dialog. I'll look into it.
Happily, Anna and Scott have suggested some work-arounds to keep you
going for now.
I just pushed a fix for
s would be greatly appreciated.
Regards,
Ken Latham
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Bruce Ravel bra...@bnl.gov
National
o get this working in a
proven system, but really would like to get it working on my OS of choice.
Thanks in advance
Ramiro
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-
rviceable. The other is to run your data files through some
kind of filter that changes the end-of-line character. Searching
Google for "convert CR to CRLF" turns up several possibilities.
HTH,
B
--
Bruce Ravel bra...@bnl.gov
National I
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