Re: [Ifeffit] Bug report: Athena, multiple data export

[Matt Newville]

Hi Soyoung,

On Fri, Oct 8, 2021 at 5:29 PM Soyoung Kim  wrote:

> I see. Thank you for the quick reply.
>
> But would it be difficult to program it so that it will export properly,
> e.g., with multiple energy axes?
>

Sorry for the slight delay, and I have two answers here:

In general, it depends on what "export properly" means. If you save the
project file, the original, differing energy arrays will be retained.  If
you export to a simple ASCII column file (which is pretty ubiquitous in
scientific data), then each numeric row will be (or perhaps "is likely to
be") interpreted as the same "x" axis (energy or perhaps time - the
independent variable).   So, if you have multiple sets of data with
differing x/energy values, either you have missing values for some data
sets or you have data in rows without a consistent x/energy, and possibly a
different number of rows per column.  Many programs will struggle with such
data files.

But

Because when the data is plotted as a graph, it is hard to tell whether or
> not the x-axes are the same... And if you are processing data from someone
> else, you may not know whether or not they were collected with the same
> energy step settings.
>

That's all true.

And also: it looks to me that the exported data from this project looks
like it is not interpolated as well as it could be. There is a definite
shift in energy in the EXAFS region.

If I read that project into Larch's XAS Viewer and export it as a CSV file
it also interpolates all arrays onto a single energy grid (by default, the
first data set) and it looks better to me (see attached file -- needs
development version of XAS Viewer for this level of details).

I'm not entirely sure where the problem is. It does look like one of the
data sets has two energy points that are very close together as the data
transitions from constant energy steps in the XANES region to wider steps
in the EXAFS region.  That should not cause a problem, but I think that I
do recall that there were some such problems in the past.

We've tried to make XAS Viewer a replacement for Athena and Artemis.   I am
aware of a few missing features, but there are also several features not in
Athena.  I can say that it would be easier for me to fix things with
Larch/XAS Viewer than it is for me to fix things in Athena.

I'm not sure that resolves the issue, but I hope it helps.

--Matt
# 2 files saved Sun Oct 10 23:05:24 2021
# saving x array='energy', y array='norm'
# data1: data1
# data2: data2
#--
# energy data1 data2
4815.00 0.001453 0.001690
4825.00 0.000822 0.000912
4835.00 0.000460 0.000493
4845.00 0.000130 0.96
4855.00 -0.000157 -0.000221
4865.00 -0.000333 -0.000342
4875.00 -0.000527 -0.000602
4885.00 -0.000622 -0.000622
4895.00 -0.000661 -0.000545
4905.00 -0.000571 -0.000717
4915.00 -0.000355 -0.000431
4925.00 -0.000194 -0.000183
4925.25 -0.99 -0.90
4925.50 -0.000137 -0.26
4925.75 -0.35 -0.000216
4926.00 -0.000138 -0.93
4926.25 -0.87 -0.57
4926.50 -0.22 -0.000131
4926.75 -0.73 -0.43
4927.00 -0.54 -0.15
4927.25 -0.77 0.22
4927.50 -0.22 -0.22
4927.75 -0.31 -0.60
4928.00 0.07 -0.000111
4928.25 -0.07 -0.12
4928.50 0.24 0.000120
4928.75 0.000129 0.000133
4929.00 -0.27 -0.31
4929.25 0.21 0.000126
4929.50 0.02 0.000102
4929.75 0.000175 0.000146
4930.00 0.000181 0.98
4930.25 0.000120 0.62
4930.50 0.99 0.000182
4930.75 0.000149 0.000302
4931.00 0.000140 0.000247
4931.25 0.000149 0.000169
4931.50 0.000265 0.52
4931.75 0.000187 0.000186
4932.00 0.000163 0.000254
4932.25 0.000161 0.000328
4932.50 0.000337 0.000265
4932.75 0.000267 0.000309
4933.00 0.000241 0.000317
4933.25 0.000353 0.000428
4933.50 0.000349 0.000468
4933.75 0.000313 0.000472
4934.00 0.000357 0.000432
4934.25 0.000413 0.000417
4934.50 0.000348 0.000373
4934.75 0.000435 0.000430
4935.00 0.000430 0.000403
4935.25 0.000445 0.000549
4935.50 0.000517 0.000485
4935.75 0.000496 0.000453
4936.00 0.000496 0.000410
4936.25 0.000550 0.000529
4936.50 0.000471 0.000627
4936.75 0.000556 0.000605
4937.00 0.000647 0.000682
4937.25 0.000623 0.000636
4937.50 0.000681 0.000806
4937.75 0.000688 0.000709
4938.00 0.000734 0.000610
4938.25 0.000726 0.000498
4938.50 0.000648 0.000657
4938.75 0.000665 0.000524
4939.00 0.000747 0.000738
4939.25 0.000834 0.000892
4939.50 0.000810 0.000900
4939.75 0.000880 0.000767
4940.00 0.000882 0.000733
4940.25 0.000857 0.000880
4940.50 0.000916 0.000922
4940.75 0.000795 0.000897
4941.00 0.000997 0.000900
4941.25 0.000984 0.001074
4941.50 0.000967 0.000955
4941.75 0.001034 0.001153
4942.00 

Re: [Ifeffit] Bug report: Athena, multiple data export

[Anatoly Frenkel]

" But would it be difficult to program it so that it will export properly,
e.g., with multiple energy axes?"
- that is what saving as unique files means.
---
Anatoly I. Frenkel
Professor
Department of Materials Science and Chemical Engineering
Stony Brook University
Stony Brook, NY 11794, Ph: 631-632-2751
Email:  anatoly.fren...@stonybrook.edu

http://you.stonybrook.edu/frenkel

Joint Appointment:
Chemistry Department, Brookhaven National Laboratory
Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494
Email: fren...@bnl.gov
https://www.bnl.gov/staff/frenkel
Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL
http://you.stonybrook.edu/scc2
---


On Fri, Oct 8, 2021 at 6:29 PM Soyoung Kim  wrote:

> I see. Thank you for the quick reply.
>
> But would it be difficult to program it so that it will export properly,
> e.g., with multiple energy axes? Because when the data is plotted as a
> graph, it is hard to tell whether or not the x-axes are the same... And if
> you are processing data from someone else, you may not know whether or not
> they were collected with the same energy step settings.
>
> Best,
> Soyoung
>
> On Fri, Oct 8, 2021 at 3:24 PM Anatoly Frenkel <
> anatoly.fren...@stonybrook.edu> wrote:
>
>> It is not a bug. When groups have unique energy axes they should be saved
>> in different files.
>>
>> Anatoly
>>
>> > On Oct 8, 2021, at 6:19 PM, Soyoung Kim  wrote:
>> >
>> > 
>> > Dear Bruce and IFEFFIT community,
>> >
>> > Hope all is well. I found a bug with Athena's file export function. I
>> had two normalized mu(E) data with very similar spectra but different
>> x-axis values (collected with different energy step settings).
>> > 
>> >
>> > When I batch exported them to a .dat file using the purple E button
>> while "Save next plot to a file" was turned on, the resulting data only had
>> a single x-axis column, which was taken from the first data. Hence, when I
>> plot the two spectra from this .dat file, they now look different:
>> > 
>> >
>> > If I export each data individually to .dat files, then they are correct.
>> > 
>> >
>> >
>> > I'm attaching the Athena project file containing the two data and the
>> .dat files I exported, both together and individually.
>> >
>> > Please let me know if anything is unclear. Thank you in advance for
>> your help.
>> >
>> > Best,
>> > Soyoung Kim
>> >
>> > 
>> > 
>> > 
>> > 
>> > ___
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Re: [Ifeffit] Bug report: Athena, multiple data export

[Soyoung Kim]

I see. Thank you for the quick reply.

But would it be difficult to program it so that it will export properly,
e.g., with multiple energy axes? Because when the data is plotted as a
graph, it is hard to tell whether or not the x-axes are the same... And if
you are processing data from someone else, you may not know whether or not
they were collected with the same energy step settings.

Best,
Soyoung

On Fri, Oct 8, 2021 at 3:24 PM Anatoly Frenkel <
anatoly.fren...@stonybrook.edu> wrote:

> It is not a bug. When groups have unique energy axes they should be saved
> in different files.
>
> Anatoly
>
> > On Oct 8, 2021, at 6:19 PM, Soyoung Kim  wrote:
> >
> > 
> > Dear Bruce and IFEFFIT community,
> >
> > Hope all is well. I found a bug with Athena's file export function. I
> had two normalized mu(E) data with very similar spectra but different
> x-axis values (collected with different energy step settings).
> > 
> >
> > When I batch exported them to a .dat file using the purple E button
> while "Save next plot to a file" was turned on, the resulting data only had
> a single x-axis column, which was taken from the first data. Hence, when I
> plot the two spectra from this .dat file, they now look different:
> > 
> >
> > If I export each data individually to .dat files, then they are correct.
> > 
> >
> >
> > I'm attaching the Athena project file containing the two data and the
> .dat files I exported, both together and individually.
> >
> > Please let me know if anything is unclear. Thank you in advance for your
> help.
> >
> > Best,
> > Soyoung Kim
> >
> > 
> > 
> > 
> > 
> > ___
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Re: [Ifeffit] Bug report: Athena, multiple data export

[Anatoly Frenkel]

It is not a bug. When groups have unique energy axes they should be saved in 
different files. 

Anatoly

> On Oct 8, 2021, at 6:19 PM, Soyoung Kim  wrote:
> 
> 
> Dear Bruce and IFEFFIT community,
> 
> Hope all is well. I found a bug with Athena's file export function. I had two 
> normalized mu(E) data with very similar spectra but different x-axis values 
> (collected with different energy step settings).
> 
> 
> When I batch exported them to a .dat file using the purple E button while 
> "Save next plot to a file" was turned on, the resulting data only had a 
> single x-axis column, which was taken from the first data. Hence, when I plot 
> the two spectra from this .dat file, they now look different:
> 
> 
> If I export each data individually to .dat files, then they are correct.
> 
> 
> 
> I'm attaching the Athena project file containing the two data and the .dat 
> files I exported, both together and individually.
> 
> Please let me know if anything is unclear. Thank you in advance for your help.
> 
> Best,
> Soyoung Kim
> 
> 
> 
> 
> 
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Re: [Ifeffit] Bug Report: incomplete data import in Athena when energy is given in keV

[Matt Newville]

Andreas, Kiril,

On Thu, Oct 25, 2018 at 6:48 AM Kirill Lomachenko 
wrote:

> Dear Bruce and dear all,
> I have the same problem with data import in Athena 0.9.26 that Andreas
> has just described and that, if I am not mistaken has already been
> mentioned in this mailing list before.
> Looking for the possible cause of the problem, in the list of changes
> made for Athena in the latest version of Demeter I found the following:
>
> "Fix a problem processing keV data when using Larch (Thanks to Juan de
> la Figuera) (See issue #42)"
>
> May it be that these modifications are responsible for the observed
> import bug? (just a guess)
>
>
I apologize in advance for repeating myself here, but it really pains me to
see people still using the very out-of-date ifeffit backend.

Larch's XAS Viewer can read the files posted just fine (well, 50 unlabelled
columns is never "fine" -- you really should complain to the folks
generating these files).  It does prompt to convert energies in keV to eV,
and it doesn't lose any data points doing so.  Among other features, it can
read and write Athena project files.  It may not do everything Athena does,
but it does most things, and a few things Athena does not.

--Matt
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Re: [Ifeffit] Bug Report: incomplete data import in Athena when energy is given in keV

[Kirill Lomachenko]

Dear Bruce and dear all,
I have the same problem with data import in Athena 0.9.26 that Andreas 
has just described and that, if I am not mistaken has already been 
mentioned in this mailing list before.
Looking for the possible cause of the problem, in the list of changes 
made for Athena in the latest version of Demeter I found the following:


"Fix a problem processing keV data when using Larch (Thanks to Juan de 
la Figuera) (See issue #42)"


May it be that these modifications are responsible for the observed 
import bug? (just a guess)


Thank you

Kirill


Dr. Kirill A. Lomachenko
Scientist at BM23/ID24 beamlines
European Synchrotron Radiation Facility (ESRF)
71 avenue des Martyrs
CS 40220
38043 Grenoble Cedex 9, France
Tel: +33 438 88 19 14
www.esrf.eu

25.10.2018 11:40, ifeffit-requ...@millenia.cars.aps.anl.gov пишет:

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Today's Topics:

1. Bug Report: incomplete data import in Athena when energy is
   given in keV (Voegelin, Andreas)


--

Message: 1
Date: Thu, 25 Oct 2018 09:39:52 +
From: "Voegelin, Andreas" 
To: XAFS Analysis using Ifeffit 
Subject: [Ifeffit] Bug Report: incomplete data import in Athena when
energy is given in keV
Message-ID:

Content-Type: text/plain; charset="utf-8"

Dear Bruce & Ifeffit Mail-List

Working with Athena (executable Version 0.9.26 with Ifeffit 1.2.12 on Windows 
10), I just noted a problem with data import when energy in the input file is 
given in keV.

Attached an example of recently collected Ce L3 edge data 
(original_format.txt), with the energy in keV in the first column and the 
DT-corrected and normalized fluorescence signal in column 44. The file contains 
2 header rows and 308 lines of data. When this spectrum is loaded into Athena, 
it consists of only 186 instead of 308 datapoints (see information on spectrum 
?original_format,.txt? in Athena project file 
?test_bug_data_import_in_keV.prj?).  The problem also persisted when I reduced 
the input file to only two columns, energy and fluorescence data, and seemed 
not related to file size. The problem occurs on various computers all running 
with the latest version of Athena.

Interestingly, the problem does not occur if the energy in the original file is 
given in eV instead of keV.  From the original file, I created an input file 
?test_energy_in_keV_eV.txt? in which columns 1 and 4 contain the energy in keV 
and columns 2 and 5 the energy in eV. When I import the spectrum using any of 
the columns with energy in eV, the spectrum is loaded correctly and consist of 
308 datapoints.  If I use any of the two columns with energy in keV, the 
imported spectrum again contains only 186 datapoints.

Comparing the mue output files of the spectra read in eV and keV (mue files 
attached), one can see that incomplete data import starts at 5703 eV, i.e., 
where the step size in the scan was changed from 2 eV to 0.5 eV.  Notably, if I 
select column 5 containing the energy in eV, but tell Athena that the energy is 
in keV and needs to be converted to eV, Athena loads all 308 datapoints 
(although with obviously wrong energy scale). This might suggest that the 
problem is related to the absolute difference in energy between datapoints 
rather than to the conversion from keV to eV.

I tested also other data collected at the Mn K and Tl L3 edges and the problem 
is the same.

For the moment, the easiest work-around may be to reprocess all input files by 
adding a column with energy in eV.  If an easy fix could be found for correct 
data import in Athena, however, this would be helpful.

Best regards, Andreas

??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? 
???

Andreas Voegelin, PhD
Eawag - Swiss Federal Institute of Aquatic Science and Technology
Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland
Tel: +41 58 765 54 70
Fax: +41 58 765 52 10
mailto:andreas.voege...@eawag.ch
http://www.eawag.ch/~voegelan





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Re: [Ifeffit] Bug Report importing file.

[Bruce Ravel]

On 07/24/2016 03:55 AM, Samy Ould-Chikh wrote:

I have some issue to import a file in Athena: just a simple x-y column (.txt 
attached with this email).

Ti K-edge.
Data range in the file  : 4916.30 up to 5436.88 eV.
Issue: only data up to 5260 eV are imported (see screenshot: bug-importation).

Version: Demeter 0.9.24
System: Windows 7 Professional SP1

Well, I hope it's just not me not being able to find a proper way to import the 
file...


I have a hard time imagining the need for an XAFS scan with 12000 data 
points.  That will usually provides a point density that about an order 
of magnitude below the core-hole lifetime, maybe 2.  In your case, it 
corresponds to about 0.04 eV steps, which seems silly to me.  While I'm 
quite open to being convinced otherwise, I cannot believe that setting 
up a scan this way is actually necessary.


But, more to the point, I think it is very unprofessional of the 
beamline staff to send you home with data in a format that is so hard to 
use.


Athena does a pretty good job of importing data in all the crazy-ass 
formats that beamlines around the world use.  But it's not really fair 
to expect that she can handle anything you can throw at her.  If a 
beamline presents data in a format that is not easy to interpret, it 
should provide tools for converting the data to a format that can 
reasonably be interpreted.


In your case, the beamline should provide you with a way to rebin the 
data either onto a more coarse grid or onto something like a 
"conventional" EXAFS grid.


So ... what I recommend, if you want to use Athena (*), is that you find 
some way to rebin your data onto a grid that fits within the 8192 limit. 
 Athena's rebinning tool uses a simple box car average -- that would 
suit your data just fine.


If you don't know what a box car average is, a google search for "box 
car average excel", "box car average matlab", "box car average python", 
etc... should provide a hint.  Once you do that, Athena should behave 
without surprises.


B

(*) Or use Athena with Larch.  Larch does not have the 8192 limit.  But 
you should still process the data onto a sensible grid.


B


--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Bug Report importing file.

[Robert Gordon]

According to
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2013-August/006762.html
limit is 8192

It is possible to rebin the data in Athena...in multiple steps...what it 
first imports, then export, then
attach the missing higher E data, re-import, rebin...using a near edge 
step size of 0.2 eV, 0.05 invAng
in the EXAFS and 2 eV in the pre-edge, these two steps were sufficient 
to reduce the data size to 555 points.


The match between original and rebin does show some small differences 
but I didn't deglitch first.




I don't like the steps in the original mu(E) either - rounding off too soon,
or is it there at this level in the raw data?
...discrete noise/quantization error at the 1:800 level versus 
'traditional exafs' 10^6 counts (1:1000)


On 7/24/2016 1:15 AM, Samy Ould-Chikh wrote:

Just a quick idea on why I cannot import the .txt file attached with previous 
email.

I realized that the files contain 11948 points ! (it's QEXAFS data).
Athena might have an hard limit of 8200 points that may be imported in a single 
file.


Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology
Thuwal 23955-6900
Kingdom of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx





-Original Message-
From: Samy Ould-Chikh
Sent: Sunday, July 24, 2016 10:56 AM
To: XAFS Analysis using Ifeffit 
Subject: Bug Report importing file.

Hello,

I have some issue to import a file in Athena: just a simple x-y column (.txt 
attached with this email).

Ti K-edge.
Data range in the file  : 4916.30 up to 5436.88 eV.
Issue: only data up to 5260 eV are imported (see screenshot: bug-importation).

Version: Demeter 0.9.24
System: Windows 7 Professional SP1

Well, I hope it's just not me not being able to find a proper way to import the 
file...


Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom 
of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx





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Re: [Ifeffit] Bug Report importing file.

[Samy Ould-Chikh]

Just a quick idea on why I cannot import the .txt file attached with previous 
email.

I realized that the files contain 11948 points ! (it's QEXAFS data).
Athena might have an hard limit of 8200 points that may be imported in a single 
file.


Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology
Thuwal 23955-6900
Kingdom of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx





-Original Message-
From: Samy Ould-Chikh
Sent: Sunday, July 24, 2016 10:56 AM
To: XAFS Analysis using Ifeffit 
Subject: Bug Report importing file.

Hello,

I have some issue to import a file in Athena: just a simple x-y column (.txt 
attached with this email).

Ti K-edge.
Data range in the file  : 4916.30 up to 5436.88 eV.
Issue: only data up to 5260 eV are imported (see screenshot: bug-importation).

Version: Demeter 0.9.24
System: Windows 7 Professional SP1

Well, I hope it's just not me not being able to find a proper way to import the 
file...


Best Regards,
Samy Ould-Chikh

KAUST Catalysis Center
Bldg.3,Level 4, #4231
4700 King Abdullah University of Science & Technology Thuwal 23955-6900 Kingdom 
of Saudi Arabia

Tel: +966 12 8084486
E-mail: samy.ouldch...@kaust.edu.sa
Website:  http://kcc.kaust.edu.sa/Pages/Home.aspx





This message and its contents including attachments are intended solely for the 
original recipient. If you are not the intended recipient or have received this 
message in error, please notify me immediately and delete this message from 
your computer system. Any unauthorized use or distribution is prohibited. 
Please consider the environment before printing this email.

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Re: [Ifeffit] Bug report ATHENA (Demeter 0.9.24)

[Ravel, Bruce]

Sunil,

You are correct.  Athena does not save settings from the LCF tool.  That's not 
so much a bug as it is a missing feature.

It's on my to do list (there's a link to the to do list on the Demeter home 
page).  I am hoping to make a new release next month ... I will try to address 
this before then.

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
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter


From: Ifeffit [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Patel, 
Sunil [sunil.pa...@honeywell.com]
Sent: Monday, May 16, 2016 5:54 AM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] Bug report ATHENA (Demeter 0.9.24)

Hello All,
I am using the latest version of Demeter (0.9.24) in Windows 7 Enterprise 
(64-bit).
In the process of doing LCF, the fit details (for ex. standards used for 
fitting, fitting range, phase fractions etc.) are not saved into the project 
file. This (very useful!) feature was available in the older version of ATHENA.

Please find attached a project file. To reproduce the problem:

  1.  Open the project file in new ATHENA.
  2.  Do LCF for marked datasets (Data_1 to Data_6) using standards (Standard_1 
and Standard_2), with LCF range= -20 to 40 eV and hitting the “Fit marked 
groups” tab.
  3.  Save the project file and close it.
  4.  Re-open the file and go to the LCF page. The details are not saved. We 
need to re-do the fits to get the values.
  5.  To check, open the ATHENA project file in older version of ATHENA and 
repeat the above steps. LCF details are shown on re-opening the file.

A similar bug report was made last year for an earlier version of Demeter 
(0.9.21).

(http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05057.html )

Thanks & regards,
Sunil Patel

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Re: [Ifeffit] Bug report

[Robert Gordon]

Hi Bruce,

Sorry...should have suggested he back up the directory first. To that 
end, how about adding a statement or two

to the faq along the lines of:

Make a copy of the files in the AppData\Roaming\Demeter directory for 
help in diagnosing what

caused a file corruption.

-R.

On 4/11/2016 8:23 AM, Bruce Ravel wrote:

On 04/11/2016 09:16 AM, Bruce Ravel wrote:

On 04/10/2016 03:38 AM, Lorenzo Stievano wrote:

There must have been something corrupted in the AppData\Roaming\Demeter
directory. It crachesd even with your data file (as for mine), but now
it works fine since I reinstalled it AFTER removing the Roaming
directory.


I don't suppose that you saved the old Roaming folder?  There is no way
for me to identify the cause of this problem if I cannot identify and
inspect the file that triggered the problem.


Lorenzo, Robert,

I added a question to the FAQ related to this thread.

http://bruceravel.github.io/demeter/documents/SinglePage/faq.html#questions-about-windows 



If either of you have a comment on the language of the question or the 
answer, let me know.


Again, it would be a more helpful FAQ entry if could understand the 
origin of the problem.


B



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Re: [Ifeffit] Bug report

[Bruce Ravel]

On 04/11/2016 11:32 AM, Robert Gordon wrote:

how about adding a statement or two
to the faq along the lines of:

Make a copy of the files in the AppData\Roaming\Demeter directory for
help in diagnosing what
caused a file corruption.


Done.  Thanks.
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/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Bug report

[Bruce Ravel]

On 04/10/2016 03:38 AM, Lorenzo Stievano wrote:

There must have been something corrupted in the AppData\Roaming\Demeter
directory. It crachesd even with your data file (as for mine), but now
it works fine since I reinstalled it AFTER removing the Roaming directory.


I don't suppose that you saved the old Roaming folder?  There is no way 
for me to identify the cause of this problem if I cannot identify and 
inspect the file that triggered the problem.


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/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Bug report

[Lorenzo Stievano]

There must have been something corrupted in the AppData\Roaming\Demeter 
directory. It crachesd even with your data file (as for mine), but now 
it works fine since I reinstalled it AFTER removing the Roaming directory.


Thanks for your help,

Lorenzo

Le 10/04/2016 08:20, Robert Gordon a écrit :

The log file was attached, not a data file.
I have attached a datafile that is just text. Try importing it, 
please. It imports without issue for me.


Another thought: When you uninstalled/reinstalled, did you delete the 
AppData\Roaming\Demeter directory?
This may not get removed when an uninstall occurs and if it has a 
corrupted setting somehow, then

deleting it before reinstall may clear that.


On 4/9/2016 11:04 PM, Lorenzo Stievano wrote:

It was actually attached... anyway, now I just paste it in the message:

--

Started at 2016-04-09T21:33:05
Win7Professional (64-bit) Service Pack 1Service Pack 16176012102561

PATH is:
C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program 
Files\DemeterPerl\c\bin;C:\Program 
Files\DemeterPerl\perl\site\bin;C:\Program 
Files\DemeterPerl\perl\bin;C:\Program 
Files\DemeterPerl\c\bin\gnuplot\bin


perl version: v5.18.2
backend: ifeffit

@INC:
C:/Program Files/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread
C:/Program Files/DemeterPerl/perl/site/lib
C:/Program Files/DemeterPerl/perl/vendor/lib
C:/Program Files/DemeterPerl/perl/lib
.
Demeter version 0.9.24

YAML::Tiny failed to classify line ' ' at C:/Program 
Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm line 783.
YAML::Tiny::_error(YAML::Tiny=ARRAY(0x10c7d818), "YAML::Tiny 
failed to classify line 
'\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm 
line 303
YAML::Tiny::_load_string("YAML::Tiny", 
"\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm 
line 37
YAML::Tiny::Load("\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm line 296
Demeter::UI::Athena::IO::_data(Demeter::UI::Athena=HASH(0x4bbae8), 
"C:\\Users\\Utilisateur\\Desktop\\Ge K-edge 
Operando_ROCK\\operando"..., "C:\\Users\\Utilisateur\\Desktop\\Ge 
K-edge Operando_ROCK\\operando"..., 1, 0) called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm line 165
Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x4bbae8)) 
called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 859
Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30), 
Demeter::UI::Athena=HASH(0x4bbae8)) called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 782
Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30)) called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47
eval {...} called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47



--

Le 10/04/2016 07:53, Robert Gordon a écrit :

The data file?

On 4/9/2016 10:19 PM, Lorenzo Stievano wrote:

Here it is.

Le 09/04/2016 23:52, Robert Gordon a écrit :

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

Hi,

I have to report a bug on a computer where Demeter 0.9.24 is 
installed.


Athena worked fine until a few days ago, but from a certain point 
it started to crash when I try to import a simple text data file 
(which worked well before). I have tried reinstalling Demeter (I 
actually did it twice) but the problem persist. The computer 
works under WIndows 7 Professional, SP1, 64 bits.


Can you help me?

Thank you in advance,

Lorenzo

PS: The athena log after the crash is attached.


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Re: [Ifeffit] Bug report

[Robert Gordon]

The log file was attached, not a data file.
I have attached a datafile that is just text. Try importing it, please. 
It imports without issue for me.


Another thought: When you uninstalled/reinstalled, did you delete the 
AppData\Roaming\Demeter directory?
This may not get removed when an uninstall occurs and if it has a 
corrupted setting somehow, then

deleting it before reinstall may clear that.


On 4/9/2016 11:04 PM, Lorenzo Stievano wrote:

It was actually attached... anyway, now I just paste it in the message:

--

Started at 2016-04-09T21:33:05
Win7Professional (64-bit) Service Pack 1Service Pack 16176012102561

PATH is:
C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program 
Files\DemeterPerl\c\bin;C:\Program 
Files\DemeterPerl\perl\site\bin;C:\Program 
Files\DemeterPerl\perl\bin;C:\Program Files\DemeterPerl\c\bin\gnuplot\bin


perl version: v5.18.2
backend: ifeffit

@INC:
C:/Program Files/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread
C:/Program Files/DemeterPerl/perl/site/lib
C:/Program Files/DemeterPerl/perl/vendor/lib
C:/Program Files/DemeterPerl/perl/lib
.
Demeter version 0.9.24

YAML::Tiny failed to classify line ' ' at C:/Program 
Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm line 783.
YAML::Tiny::_error(YAML::Tiny=ARRAY(0x10c7d818), "YAML::Tiny 
failed to classify line 
'\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm 
line 303
YAML::Tiny::_load_string("YAML::Tiny", 
"\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm 
line 37
YAML::Tiny::Load("\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...) 
called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm line 296
Demeter::UI::Athena::IO::_data(Demeter::UI::Athena=HASH(0x4bbae8), 
"C:\\Users\\Utilisateur\\Desktop\\Ge K-edge 
Operando_ROCK\\operando"..., "C:\\Users\\Utilisateur\\Desktop\\Ge 
K-edge Operando_ROCK\\operando"..., 1, 0) called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm line 165
Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x4bbae8)) 
called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 859
Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30), 
Demeter::UI::Athena=HASH(0x4bbae8)) called at C:/Program 
Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 782
Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30)) called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47
eval {...} called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47



--

Le 10/04/2016 07:53, Robert Gordon a écrit :

The data file?

On 4/9/2016 10:19 PM, Lorenzo Stievano wrote:

Here it is.

Le 09/04/2016 23:52, Robert Gordon a écrit :

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

Hi,

I have to report a bug on a computer where Demeter 0.9.24 is 
installed.


Athena worked fine until a few days ago, but from a certain point 
it started to crash when I try to import a simple text data file 
(which worked well before). I have tried reinstalling Demeter (I 
actually did it twice) but the problem persist. The computer works 
under WIndows 7 Professional, SP1, 64 bits.


Can you help me?

Thank you in advance,

Lorenzo

PS: The athena log after the crash is attached.


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Re: [Ifeffit] Bug report

[Lorenzo Stievano]

It crashes with any text data file I try to import. It opens normally 
already saved .prj files.


Le 10/04/2016 07:56, Robert Gordon a écrit :
Another thought: Does this crash happen with other data files, or just 
this one?


On 4/9/2016 10:19 PM, Lorenzo Stievano wrote:

Here it is.

Le 09/04/2016 23:52, Robert Gordon a écrit :

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

Hi,

I have to report a bug on a computer where Demeter 0.9.24 is 
installed.


Athena worked fine until a few days ago, but from a certain point 
it started to crash when I try to import a simple text data file 
(which worked well before). I have tried reinstalling Demeter (I 
actually did it twice) but the problem persist. The computer works 
under WIndows 7 Professional, SP1, 64 bits.


Can you help me?

Thank you in advance,

Lorenzo

PS: The athena log after the crash is attached.


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Re: [Ifeffit] Bug report

[Lorenzo Stievano]

Here it is.

Le 09/04/2016 23:52, Robert Gordon a écrit :

Can you send the text file as well, please?

On 4/9/2016 12:43 PM, Lorenzo Stievano wrote:

Hi,

I have to report a bug on a computer where Demeter 0.9.24 is installed.

Athena worked fine until a few days ago, but from a certain point it 
started to crash when I try to import a simple text data file (which 
worked well before). I have tried reinstalling Demeter (I actually 
did it twice) but the problem persist. The computer works under 
WIndows 7 Professional, SP1, 64 bits.


Can you help me?

Thank you in advance,

Lorenzo

PS: The athena log after the crash is attached.


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Started at 2016-04-09T21:33:05
Win7Professional (64-bit) Service Pack 1Service Pack 16176012102561

PATH is:
C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program 
Files\DemeterPerl\c\bin;C:\Program Files\DemeterPerl\perl\site\bin;C:\Program 
Files\DemeterPerl\perl\bin;C:\Program Files\DemeterPerl\c\bin\gnuplot\bin

perl version: v5.18.2
backend: ifeffit

@INC:
C:/Program Files/DemeterPerl/perl/site/lib/MSWin32-x64-multi-thread
C:/Program Files/DemeterPerl/perl/site/lib
C:/Program Files/DemeterPerl/perl/vendor/lib
C:/Program Files/DemeterPerl/perl/lib
.
Demeter version 0.9.24

YAML::Tiny failed to classify line 
''
 at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm line 783.
YAML::Tiny::_error(YAML::Tiny=ARRAY(0x10c7d818), "YAML::Tiny failed to 
classify line 
'\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...)
 called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm line 303
YAML::Tiny::_load_string("YAML::Tiny", 
"\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...)
 called at C:/Program Files/DemeterPerl/perl/vendor/lib/YAML/Tiny.pm line 37

YAML::Tiny::Load("\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}\x{0}"...)
 called at C:/Program Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm 
line 296
Demeter::UI::Athena::IO::_data(Demeter::UI::Athena=HASH(0x4bbae8), 
"C:\\Users\\Utilisateur\\Desktop\\Ge K-edge Operando_ROCK\\operando"..., 
"C:\\Users\\Utilisateur\\Desktop\\Ge K-edge Operando_ROCK\\operando"..., 1, 0) 
called at C:/Program Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena/IO.pm 
line 165
Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x4bbae8)) 
called at C:/Program Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 
859
Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30), Demeter::UI::Athena=HASH(0x4bbae8)) called 
at C:/Program Files/DemeterPerl/perl/site/lib/Demeter/UI/Athena.pm line 782
Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0x456260), 
Wx::CommandEvent=SCALAR(0x10c7bc30)) called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47
eval {...} called at C:\Program 
Files\DemeterPerl\perl\site\bin\dathena.bat line 47
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[Ifeffit] Bug report

[Lorenzo Stievano]

Hi,

I have to report a bug on a computer where Demeter 0.9.24 is installed.

Athena worked fine until a few days ago, but from a certain point it 
started to crash when I try to import a simple text data file (which 
worked well before). I have tried reinstalling Demeter (I actually did 
it twice) but the problem persist. The computer works under WIndows 7 
Professional, SP1, 64 bits.


Can you help me?

Thank you in advance,

Lorenzo

PS: The athena log after the crash is attached.


dathena.log
Description: Binary data
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Re: [Ifeffit] Bug report - autosave on mac

[Zack Gainsforth]

If it helps, I saw this also on Artemis (OS X 10.10.3).  When I opened Artermis 
it asked to restore from an autosave, and then hung.  This continued until I 
deleted ~/.horae and now it is fine.  

Zack


 On Dec 10, 2014, at 5:52 AM, Bruce Ravel bra...@bnl.gov wrote:
 
 Jean-Baptiste,
 
 I still don't have a clear idea what the problem is, but I gave it some 
 thought yesterday while sitting on a train.
 
 I would suggest simply deleting the $HOME/.horae directory and letting Athena 
 start from scratch.  You'll lose your list of recently accessed files and any 
 modifications to the configuration you may have made.  But I can think of at 
 least one recent situation where Athena got confused by a corrupted file in 
 that folder.  Maybe that's the problem?
 
 B
 
 
 On 12/09/2014 04:46 AM, Jean-Baptiste ABBE wrote:
 Hi everybody,
 
 I wanted to report a really annoying problem for mac users. I’m running
 Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to
 install also quartzX11 to be able to plot data (without it, it couldn’t
 find the DISPLAY value), but otherwise evrything went smoothly for a few
 days.
 Then the first bug occured. I wasn’t able anymore to select any point on
 the plotting area to do normalization, I had to set the value in the
 boxes instead. It was annoying, but I could manage that. But now I have
 a much more disturbing issue.
 Athena once crashed, (in the terminal, it was sait « Terminated 15 »),
 and every time I tried to launch it again, the same thing happens :
 1) athena launch, a little bit longer than usual
 2) a box appear to give me choice to recover data by importing it from
 autosave or not
 3) I can’t select anaything and the rainbow wheel of death appears.
 After a few hours, nothing changes… and I have to terminate the programm
 manually.
 
 So I do some search on the internet and found thoses topics on the
 mailing list, and I tried thoses solutions :
 https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html
 https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.html
 https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html
  
 https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html
 
 I tried to find the autosave file : nothing
 I tried to uninstall and reinstall macports : nothing
 I tried to uninstall macports and install the demeter-devel : nothing
 In demeter-devel, i tried to modify the athena.demeter_config file, by
 changing the autosave prompt box value from true to false, and despite
 being admin on ma mac, I’m not able to change antything in the file. So
 nothing works at this moment.
 
 I will try again other solutions, but I will gladly accept any kind of
 help to solve my issues.
 
 
 Thank you
 
 ABBE J-Baptiste
 
 
 ___
 Ifeffit mailing list
 Ifeffit@millenia.cars.aps.anl.gov
 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
 
 
 
 -- 
 Bruce Ravel   bra...@bnl.gov 
 mailto: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/ 
 http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/ 
 http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Bug report - autosave on mac

[Bruce Ravel]

On 07/15/2015 01:52 PM, Zack Gainsforth wrote:

If it helps, I saw this also on Artemis (OS X 10.10.3).  When I opened
Artermis it asked to restore from an autosave, and then hung.  This
continued until I deleted ~/.horae and now it is fine.


If either of you see this again, try just deleting 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 bra...@bnl.gov
mailto:bra...@bnl.gov wrote:

Jean-Baptiste,

I still don't have a clear idea what the problem is, but I gave it
some thought yesterday while sitting on a train.

I would suggest simply deleting the $HOME/.horae directory and letting
Athena start from scratch.  You'll lose your list of recently accessed
files and any modifications to the configuration you may have made.
 But I can think of at least one recent situation where Athena got
confused by a corrupted file in that folder.  Maybe that's the
problem?

B


On 12/09/2014 04:46 AM, Jean-Baptiste ABBE wrote:

Hi everybody,

I wanted to report a really annoying problem for mac users. I’m running
Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to
install also quartzX11 to be able to plot data (without it, it couldn’t
find the DISPLAY value), but otherwise evrything went smoothly for a few
days.
Then the first bug occured. I wasn’t able anymore to select any point on
the plotting area to do normalization, I had to set the value in the
boxes instead. It was annoying, but I could manage that. But now I have
a much more disturbing issue.
Athena once crashed, (in the terminal, it was sait « Terminated 15 »),
and every time I tried to launch it again, the same thing happens :
1) athena launch, a little bit longer than usual
2) a box appear to give me choice to recover data by importing it from
autosave or not
3) I can’t select anaything and the rainbow wheel of death appears.
After a few hours, nothing changes… and I have to terminate the programm
manually.

So I do some search on the internet and found thoses topics on the
mailing list, and I tried thoses solutions :
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html
https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.html
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html

I tried to find the autosave file : nothing
I tried to uninstall and reinstall macports : nothing
I tried to uninstall macports and install the demeter-devel : nothing
In demeter-devel, i tried to modify the athena.demeter_config file, by
changing the autosave prompt box value from true to false, and despite
being admin on ma mac, I’m not able to change antything in the file. So
nothing works at this moment.

I will try again other solutions, but I will gladly accept any kind of
help to solve my issues.


Thank you

ABBE J-Baptiste


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--
Bruce Ravel  bra...@bnl.gov
mailto: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/
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
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--
 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/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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[Ifeffit] Bug report - freezing changes plots

[Zack Gainsforth]

Hi Bruce,

I notice the following bug in Artemis on a Mac.

Normal: right click k to plot three k-weighted spectra in k-space, offset 
vertically and scaled to be the same height.

Then check the freeze button and right click k and you get a plot where the 
three k-weights are not offset and despite the legend saying they are scaled, 
they really don’t look it.

I can send screenshots if desired.

Zack

 On Jul 15, 2015, at 11:03 AM, Bruce Ravel bra...@bnl.gov wrote:
 
 On 07/15/2015 01:52 PM, Zack Gainsforth wrote:
 If it helps, I saw this also on Artemis (OS X 10.10.3).  When I opened
 Artermis it asked to restore from an autosave, and then hung.  This
 continued until I deleted ~/.horae and now it is fine.
 
 If either of you see this again, try just deleting 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 bra...@bnl.gov 
 mailto:bra...@bnl.gov
 mailto:bra...@bnl.gov mailto:bra...@bnl.gov wrote:
 
 Jean-Baptiste,
 
 I still don't have a clear idea what the problem is, but I gave it
 some thought yesterday while sitting on a train.
 
 I would suggest simply deleting the $HOME/.horae directory and letting
 Athena start from scratch.  You'll lose your list of recently accessed
 files and any modifications to the configuration you may have made.
 But I can think of at least one recent situation where Athena got
 confused by a corrupted file in that folder.  Maybe that's the
 problem?
 
 B
 
 
 On 12/09/2014 04:46 AM, Jean-Baptiste ABBE wrote:
 Hi everybody,
 
 I wanted to report a really annoying problem for mac users. I’m running
 Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to
 install also quartzX11 to be able to plot data (without it, it couldn’t
 find the DISPLAY value), but otherwise evrything went smoothly for a few
 days.
 Then the first bug occured. I wasn’t able anymore to select any point on
 the plotting area to do normalization, I had to set the value in the
 boxes instead. It was annoying, but I could manage that. But now I have
 a much more disturbing issue.
 Athena once crashed, (in the terminal, it was sait « Terminated 15 »),
 and every time I tried to launch it again, the same thing happens :
 1) athena launch, a little bit longer than usual
 2) a box appear to give me choice to recover data by importing it from
 autosave or not
 3) I can’t select anaything and the rainbow wheel of death appears.
 After a few hours, nothing changes… and I have to terminate the programm
 manually.
 
 So I do some search on the internet and found thoses topics on the
 mailing list, and I tried thoses solutions :
 https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html
 https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.html
 https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html
 
 I tried to find the autosave file : nothing
 I tried to uninstall and reinstall macports : nothing
 I tried to uninstall macports and install the demeter-devel : nothing
 In demeter-devel, i tried to modify the athena.demeter_config file, by
 changing the autosave prompt box value from true to false, and despite
 being admin on ma mac, I’m not able to change antything in the file. So
 nothing works at this moment.
 
 I will try again other solutions, but I will gladly accept any kind of
 help to solve my issues.
 
 
 Thank you
 
 ABBE J-Baptiste
 
 
 ___
 Ifeffit mailing list
 Ifeffit@millenia.cars.aps.anl.gov
 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
 
 
 
 --
 Bruce Ravel  bra...@bnl.gov 
 mailto:bra...@bnl.gov
 mailto:bra...@bnl.gov mailto: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/ 
 http://bruceravel.github.io/home/
 Software: https://github.com/bruceravel https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/ 
 http://bruceravel.github.io/demeter/
 ___
 Ifeffit mailing list
 Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov
 mailto:Ifeffit@millenia.cars.aps.anl.gov 
 mailto:Ifeffit@millenia.cars.aps.anl.gov
 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit 
 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
 
 
 
 ___
 Ifeffit mailing list
 Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov
 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit 
 http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
 
 
 
 -- 
 Bruce Ravel   bra...@bnl.gov 
 mailto:bra...@bnl.gov
 

Re: [Ifeffit] Bug report - autosave on mac

[Bruce Ravel]

Jean-Baptiste,

I still don't have a clear idea what the problem is, but I gave it some 
thought yesterday while sitting on a train.


I would suggest simply deleting the $HOME/.horae directory and letting 
Athena start from scratch.  You'll lose your list of recently accessed 
files and any modifications to the configuration you may have made.  But 
I can think of at least one recent situation where Athena got confused 
by a corrupted file in that folder.  Maybe that's the problem?


B


On 12/09/2014 04:46 AM, Jean-Baptiste ABBE wrote:

Hi everybody,

I wanted to report a really annoying problem for mac users. I’m running
Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to
install also quartzX11 to be able to plot data (without it, it couldn’t
find the DISPLAY value), but otherwise evrything went smoothly for a few
days.
Then the first bug occured. I wasn’t able anymore to select any point on
the plotting area to do normalization, I had to set the value in the
boxes instead. It was annoying, but I could manage that. But now I have
a much more disturbing issue.
Athena once crashed, (in the terminal, it was sait « Terminated 15 »),
and every time I tried to launch it again, the same thing happens :
1) athena launch, a little bit longer than usual
2) a box appear to give me choice to recover data by importing it from
autosave or not
3) I can’t select anaything and the rainbow wheel of death appears.
After a few hours, nothing changes… and I have to terminate the programm
manually.

So I do some search on the internet and found thoses topics on the
mailing list, and I tried thoses solutions :
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html
https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.html
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html

I tried to find the autosave file : nothing
I tried to uninstall and reinstall macports : nothing
I tried to uninstall macports and install the demeter-devel : nothing
In demeter-devel, i tried to modify the athena.demeter_config file, by
changing the autosave prompt box value from true to false, and despite
being admin on ma mac, I’m not able to change antything in the file. So
nothing works at this moment.

I will try again other solutions, but I will gladly accept any kind of
help to solve my issues.


Thank you

ABBE J-Baptiste


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--
 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/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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[Ifeffit] Bug report - autosave on mac

[Jean-Baptiste ABBE]

Hi everybody,

I wanted to report a really annoying problem for mac users. I’m running Athena 
on my laptop, on OSX 10.10 (Yosemite) with macports. I had to install also 
quartzX11 to be able to plot data (without it, it couldn’t find the DISPLAY 
value), but otherwise evrything went smoothly for a few days.
Then the first bug occured. I wasn’t able anymore to select any point on the 
plotting area to do normalization, I had to set the value in the boxes instead. 
It was annoying, but I could manage that. But now I have a much more disturbing 
issue.
Athena once crashed, (in the terminal, it was sait « Terminated 15 »), and 
every time I tried to launch it again, the same thing happens :
1) athena launch, a little bit longer than usual
2) a box appear to give me choice to recover data by importing it from autosave 
or not
3) I can’t select anaything and the rainbow wheel of death appears.
After a few hours, nothing changes… and I have to terminate the programm 
manually.

So I do some search on the internet and found thoses topics on the mailing 
list, and I tried thoses solutions :
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html 
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html
https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.html 
https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html

I tried to find the autosave file : nothing
I tried to uninstall and reinstall macports : nothing
I tried to uninstall macports and install the demeter-devel : nothing
In demeter-devel, i tried to modify the athena.demeter_config file, by changing 
the autosave prompt box value from true to false, and despite being admin on ma 
mac, I’m not able to change antything in the file. So nothing works at this 
moment.

I will try again other solutions, but I will gladly accept any kind of help to 
solve my issues.


Thank you

ABBE J-Baptiste___
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Re: [Ifeffit] Bug report - autosave on mac

[Bruce Ravel]

On 12/09/2014 04:46 AM, Jean-Baptiste ABBE wrote:

Athena once crashed, (in the terminal, it was sait « Terminated 15 »)


Is that the only thing it said?  Were there no further error messages?

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/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7

[Chris Patridge]

What system are working on?  It might be system specific. 

Thanks

Chris

Sent from my iPhone

 On Jul 7, 2014, at 5:45 AM, Badari Rao badari@gmail.com wrote:
 
 Dear Sir,
 I am facing two problems while handling files in Athena.
 
 First of all, when I freshly open Athena and import a file, it gives some 
 kind of warning, which says can't locate Encoding/FixLatin/XS.pm in @NIC.. 
 etc. I have attached a screenshot of the warning message. However, I could 
 continue with my work without any problem, and importing more files did not 
 give this warning.
 
 The second problem, which is a major one is that I am not able to use the 
 align data option. Whenever I select my data and click on align data, the 
 software crashes and closes. kindly look into this issue. I would also like 
 to mention that both these bugs were not present in the earlier version: 
 Demeter 0.9.20_pre5.
 
 Thanking You,
 -- Yours Sincerely,
 Badari Narayana. A. R.
 Ph.D Student, Nanoscience and Nanotechnology,
 c/o Prof Rajeev Ranjan,
 Electroceramics Lab,
 Department of Materials Engineering,
 Indian Institute of Science.
 Athena_Error.JPG
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Re: [Ifeffit] Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7

[Matt Newville]

Send a file for which this happens (for each of these two almost certainly
separate problems).

--Matt
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Re: [Ifeffit] Bug Report: Error while handling files in Athena in the latest version, Demeter 0.9.20_pre7

[Bruce Ravel]

On 07/07/2014 05:45 AM, Badari Rao wrote:

First of all, when I freshly open Athena and import a file, it gives
some kind of warning, which says can't locate Encoding/FixLatin/XS.pm in
@NIC.. etc. I have attached a screenshot of the warning message.
However, I could continue with my work without any problem, and
importing more files did not give this warning.


I am aware of this problem, which began with the most recent trial 
release for 0.9.20.  As you say, it is not serious as you can simply 
click OK and carry on.  But it is distracting.  It will be fixed in 
the next trial release.


 The second problem, which is a major one is that I am not able to use
 the align data option. Whenever I select my data and click on
 align data, the software crashes and closes. kindly look into this
 issue. I would also like to mention that both these bugs were not
 present in the earlier version: Demeter 0.9.20_pre5.

This is actually the same problem that George reported on the Mac late 
last week.  I believe that I fixed it last week.  I will build a new 
trial release later today and let you know when it is available.


Thanks for the feedback.
B



--
 Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Bruce Ravel]

On 06/25/2014 02:31 AM, Badari Rao wrote:

The new release is working fine in windows 7 64 bit. I was able to
re-open a saved file. Thank you very much.


Great!


However, there is one more problem happening. When I re-open a previous
file and simply press on save and then close it (I did not do anything
else at all), all the data is lost. My file size which was 179KB,
reduced to 1KB and when I re-opened it, there was nothing stored in it.
There is no problem if I do more fitting and then save the data. This is
a minor problem but a dangerous as one might lose all his hard-work done
in fitting the data.


Well, you are correct saying that it is surprising behavior for imported 
data to be lost if you save before having done a fit.  I'll look into 
it.  However, if you have done a lot of hard work, you have probably 
hit the fit button at least once.


B

--
 Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Bruce Ravel]

On 06/25/2014 04:03 PM, Bruce Ravel wrote:

However, there is one more problem happening. When I re-open a previous
file and simply press on save and then close it (I did not do anything
else at all), all the data is lost. My file size which was 179KB,
reduced to 1KB and when I re-opened it, there was nothing stored in it.
There is no problem if I do more fitting and then save the data. This is
a minor problem but a dangerous as one might lose all his hard-work done
in fitting the data.


Well, you are correct saying that it is surprising behavior for imported
data to be lost if you save before having done a fit.  I'll look into
it.  However, if you have done a lot of hard work, you have probably
hit the fit button at least once.


The situation where the data is lost if you save a project before doing 
a fit will be fixed in the next release.


This afternoon, I have been working on setting up a computer to make a 
32-bit build of Demeter.  Once that is ready and tested, I will properly 
release 0.9.20.


B


--
 Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Matt Newville]

I'd guess that the empty  fits/ folder is causing the  restore_fit()
function in Demeter/UI/Artemis/Project.pm to fail to restore any fits.

It's easy enough to reproduce:   Start Artemis, open any Feff input file,
run feff, load no data.   Save the project, and quit.  The project cannot
be reopened.

Don't know what the best solution is

--Matt


On Tue, Jun 24, 2014 at 11:21 AM, Badari Rao badari@gmail.com wrote:

 Hello Sir,
 I wanted to report that I am facing the same problem as the one faced by
 Mengling Stuckman (dated: Wed, 19 Mar 2014 11:53:10 -0700.)
 It does not appear to be problem with the operating system because I am
 facing the same problem in systems with windows 7 as well as windows xp.
 I have tried a fresh install on a new system with windows 7 os, and the
 same problem occurred. Even a simple artemis file in which I have just
 imported and saved the processed file from athena cannot be re-opened in
 artemis.
 Kindly sort out the problem.
 I have attached one sample artemis file which is giving the problem and
 also the demeter log file from %APPDATA%\demeter.

 https://www.mail-archive.com/search?l=ifeffit%40millenia.cars.aps.anl.govq=from:%22Mengling+Stuckman%22o=newest

 Thanking You,
 -- Yours Sincerely,
 Badari Narayana. A. R.
 Ph.D Student, Nanoscience and Nanotechnology,
 c/o Prof Rajeev Ranjan,
 Electroceramics Lab,
 Department of Materials Engineering,
 Indian Institute of Science.


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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Bruce Ravel]

On 06/24/2014 12:21 PM, Badari Rao wrote:

I wanted to report that I am facing the same problem as the one faced by
Mengling Stuckman (dated: Wed, 19 Mar 2014 11:53:10 -0700.)
It does not appear to be problem with the operating system because I am
facing the same problem in systems with windows 7 as well as windows xp.
I have tried a fresh install on a new system with windows 7 os, and the
same problem occurred. Even a simple artemis file in which I have just
imported and saved the processed file from athena cannot be re-opened in
artemis.
Kindly sort out the problem.
I have attached one sample artemis file which is giving the problem and
also the demeter log file from %APPDATA%\demeter.



Here is an early look at the next release.  Could you give it a try and 
let me know if it solves the problem for you.  (It works for me on your 
example project file.)


https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_pre5.exe

B

--
 Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Matt Newville]

 Here is an early look at the next release.  Could you give it a try and
let me know if it
 solves the problem for you.  (It works for me on your example project
file.)


https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_pre5.exe
https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_pre5.exe



On a 32-bit Windows 7 system, this isn't working for me.With a fresh
install I get


   C:\strawberry\perlbin\perl5.16.3.exe
   This version of C:\strawberry\perl\bin\perl5.16.3.exe is not compatible
with the version of
   Windows you're running. Check your computer's system information to see
whether you
   need a x86 (32-bit) or x64 (64-bit) version of the program, and then
contact the software
   publisher.


--Matt
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Bruce Ravel]

On 06/24/2014 02:28 PM, Matt Newville wrote:

  Here is an early look at the next release.  Could you give it a try
and let me know if it
  solves the problem for you.  (It works for me on your example project
file.)
 
 
https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_pre5.exe
https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9.20_pre5.exe
 


On a 32-bit Windows 7 system, this isn't working for me.With a fresh
install I get


Good point.  The thing on the other end of that link will only work on a 
64 bit system.


I am going to build a 32-bit version as well, but haven't gotten around 
to it yet.


B

--
 Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Shoaib Muhammad]

Dear all,

Just want to add, on a 64bit Windows 8 it installed without any problem.

 (If I have understood the problem being discussed here correctly), I have
performed following steps:

1- Opened Artemis
2- Imported Atoms file and run Feff Calculation
3- Saved the project
4- Opened the saved project file, it opens with previous Feff Calculations
along with a nice message It seems that you have not actually performed a
fit in this fitting project

Regards,
/Shoaib 


-Original Message-
From: ifeffit-boun...@millenia.cars.aps.anl.gov
[mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel
Sent: Wednesday, June 25, 2014 3:33 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

On 06/24/2014 02:28 PM, Matt Newville wrote:
   Here is an early look at the next release.  Could you give it a try 
 and let me know if it   solves the problem for you.  (It works for me 
 on your example project
 file.)
  
  
 https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.9
 .20_pre5.exe 
 https://s3.amazonaws.com/demeter4xas/Demeter_Installer_for_Windows_0.
 9.20_pre5.exe
  


 On a 32-bit Windows 7 system, this isn't working for me.With a fresh
 install I get

Good point.  The thing on the other end of that link will only work on a
64 bit system.

I am going to build a 32-bit version as well, but haven't gotten around to
it yet.

B

--
  Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Bruce Ravel]

On 03/20/2014 09:29 AM, Bruce Ravel wrote:

On 03/20/2014 09:22 AM, Mengling Stuckman wrote:


I'm sending a couple. One is new that I didn't do any fit. The other is
old that contained my fitting. Both of them can't open in my Artemis.


I'll take a look.

B



Mengling,

I haven't forgotten about your problem, but I also haven't yet found a 
free moment to take a look.


B


--
 Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Bruce Ravel]

On 03/20/2014 09:22 AM, Mengling Stuckman wrote:


I'm sending a couple. One is new that I didn't do any fit. The other is
old that contained my fitting. Both of them can't open in my Artemis.


I'll take a look.

B

--
 Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Bruce Ravel]

On 03/20/2014 09:33 AM, Mengling Yi Stuckman wrote:

Sorry I think my attachment didn't go through. Maybe the zip file will work.


They did.  You can stop sending things now ;)

I see the same problem on my computer with your AZTCLP file.

*That's* why you send an example.  Now I have a fighting chance of 
figuring out the problem.


B


--
 Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Bruce Ravel]

On 03/19/2014 04:19 PM, Mengling Stuckman wrote:


Again, the message showing in the log file is:
Can't call method workspace without a package or object reference at
C:/strawberry/perl/site/lib/Demeter/Fit.pm line 1550.

or sometimes:

Can't call method group on an undefined value at
C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 466.



Are you quite sure that is the only text in the log file?

Demeter first writes several lines about the environment in which
Demeter is operating.  The error message is almost always followed by
several lines of backtrace.  All of that provides context for me to
understand the proximal cause of the problem.  If you extract a part
of the log file, then that context is lost to me.


Demeter also seemed to work fine last week and only stopped working
yesterday. I didn't update anything on my work computer, so I don't
know what is causing the problem.


Artemis worked on that computer last week and does not work this week?
And you did nothing to change the computer?  Something doesn't add up.

Did your anti virus software update?  Did your institution's system
administrators perform an update?  Did you install any new software?
Anything?  It's hard for me to understand how the behavior of the
program can change simply by walking away for a few days.

Without being able to watch this on one of my computers, I can only
guess what the problem might be by examining the two lines of code you
cite.

My best guess is that something is preventing you from unpacking the
project file.  An .fpj file is nothing more than a zip file with a
different file extension.  It gets unpacked in %APPDATA%\stash (where
%APPDATA% is the location of the log file).  That means that you have
to have permission to write files to that location.  So, my best guess
is that something is preventing you from writing to that space.  I
have no guess for what the cause of that is.

So, check the permission of that folder.  Try making a file in that
folder by hand.  Try extracting a zip file buy hand into that folder.

If not that, then I'm afraid I'm out of ideas.

B


--
 Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Mengling Stuckman]

Thank you, Bruce,

This is the complete log file:

Started at 2014-03-19T14:26:09
Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561

PATH:
C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0\;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\strawberry1\perl\bin;C:\strawberry1\perl\site\bin;C:\strawberry1\c\bin;\\
admin.netl.doe.gov\it\Oracle11g\product\11.2.0\client_1\bin;

perl version: v5.12.3

@INC:
C:/strawberry/perl/site/lib
C:/strawberry/perl/vendor/lib
C:/strawberry/perl/lib
.

Can't call method workspace without a package or object reference at
C:/strawberry/perl/site/lib/Demeter/Fit.pm line 1550.

 or this very last sentence will change to

Can't call method group on an undefined value at
C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 466.
if I open a different .fpj file.

Because the first few lines were similar to what I saw in Athena log file
when Athena is working, I didn't cite these.

Thank you very much for double-checking it!

I did try to check the permission of that folder by adding a file into that
folder and extracting a zip file into that folder. Neither had any problem.
I do have permission of that folder.

I also tried to open my files in Artemis installed on several other
computers in my workplace. Other computers didn't work as well. I guess it
might be a problem with the operating system/software conflict in my
workplace? I didn't install any other software by myself. All the other
updates for antivirus or Windows 7 are automatic through workplace system
management that I don't have control. I might be able to call IT support
tomorrow to see if they know anything about the system that might have
conflict with Demeter.

Without being able to watch this on one of my computers, I can only
guess what the problem might be by examining the two lines of code you
cite.

I am wondering how to examine the two lines of code I cited. Maybe I could
talk to IT support about the code and see if there is anything they or we
can do to fix that.

Really appreciated for your replies! I know this is a very personalized
computer problem, not related to your software, which might be beyond your
duty to fix. So really thankful for your help!

Mengling


On Wed, Mar 19, 2014 at 4:44 PM, Bruce Ravel bra...@bnl.gov wrote:

 On 03/19/2014 04:19 PM, Mengling Stuckman wrote:


 Again, the message showing in the log file is:
 Can't call method workspace without a package or object reference at
 C:/strawberry/perl/site/lib/Demeter/Fit.pm line 1550.

 or sometimes:

 Can't call method group on an undefined value at
 C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 466.


 Are you quite sure that is the only text in the log file?

 Demeter first writes several lines about the environment in which
 Demeter is operating.  The error message is almost always followed by
 several lines of backtrace.  All of that provides context for me to
 understand the proximal cause of the problem.  If you extract a part
 of the log file, then that context is lost to me.


  Demeter also seemed to work fine last week and only stopped working
 yesterday. I didn't update anything on my work computer, so I don't
 know what is causing the problem.


 Artemis worked on that computer last week and does not work this week?
 And you did nothing to change the computer?  Something doesn't add up.

 Did your anti virus software update?  Did your institution's system
 administrators perform an update?  Did you install any new software?
 Anything?  It's hard for me to understand how the behavior of the
 program can change simply by walking away for a few days.

 Without being able to watch this on one of my computers, I can only
 guess what the problem might be by examining the two lines of code you
 cite.

 My best guess is that something is preventing you from unpacking the
 project file.  An .fpj file is nothing more than a zip file with a
 different file extension.  It gets unpacked in %APPDATA%\stash (where
 %APPDATA% is the location of the log file).  That means that you have
 to have permission to write files to that location.  So, my best guess
 is that something is preventing you from writing to that space.  I
 have no guess for what the cause of that is.

 So, check the permission of that folder.  Try making a file in that
 folder by hand.  Try extracting a zip file buy hand into that folder.

 If not that, then I'm afraid I'm out of ideas.


 B


 --
  Bruce Ravel   bra...@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
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Re: [Ifeffit] Bug report: Artemis cannot re-open saved projects

[Bruce Ravel]

Can you humor me and send me one of your .fpj files?  I would like to 
examine its contents.


B

On 03/19/2014 05:36 PM, Mengling Stuckman wrote:

Thank you, Bruce,

This is the complete log file:

Started at 2014-03-19T14:26:09
Win7Enterprise (64-bit) Service Pack 1Service Pack 16176012102561

PATH:
C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0\;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\strawberry1\perl\bin;C:\strawberry1\perl\site\bin;C:\strawberry1\c\bin;\\admin.netl.doe.gov
http://admin.netl.doe.gov\it\Oracle11g\product\11.2.0\client_1\bin;

perl version: v5.12.3

@INC:
C:/strawberry/perl/site/lib
C:/strawberry/perl/vendor/lib
C:/strawberry/perl/lib
.

Can't call method workspace without a package or object reference at
C:/strawberry/perl/site/lib/Demeter/Fit.pm line 1550.

  or this very last sentence will change to

Can't call method group on an undefined value at
C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 466.
if I open a different .fpj file.

Because the first few lines were similar to what I saw in Athena log
file when Athena is working, I didn't cite these.

Thank you very much for double-checking it!

I did try to check the permission of that folder by adding a file into
that folder and extracting a zip file into that folder. Neither had any
problem. I do have permission of that folder.

I also tried to open my files in Artemis installed on several other
computers in my workplace. Other computers didn't work as well. I guess
it might be a problem with the operating system/software conflict in my
workplace? I didn't install any other software by myself. All the other
updates for antivirus or Windows 7 are automatic through workplace
system management that I don't have control. I might be able to call IT
support tomorrow to see if they know anything about the system that
might have conflict with Demeter.

Without being able to watch this on one of my computers, I can only
guess what the problem might be by examining the two lines of code you
cite.

I am wondering how to examine the two lines of code I cited. Maybe I
could talk to IT support about the code and see if there is anything
they or we can do to fix that.

Really appreciated for your replies! I know this is a very personalized
computer problem, not related to your software, which might be beyond
your duty to fix. So really thankful for your help!

Mengling


On Wed, Mar 19, 2014 at 4:44 PM, Bruce Ravel bra...@bnl.gov
mailto:bra...@bnl.gov wrote:

On 03/19/2014 04:19 PM, Mengling Stuckman wrote:


Again, the message showing in the log file is:
Can't call method workspace without a package or object
reference at
C:/strawberry/perl/site/lib/__Demeter/Fit.pm line 1550.

or sometimes:

Can't call method group on an undefined value at
C:/strawberry/perl/site/lib/__Demeter/UI/Artemis/Project.pm line
466.


Are you quite sure that is the only text in the log file?

Demeter first writes several lines about the environment in which
Demeter is operating.  The error message is almost always followed by
several lines of backtrace.  All of that provides context for me to
understand the proximal cause of the problem.  If you extract a part
of the log file, then that context is lost to me.


Demeter also seemed to work fine last week and only stopped working
yesterday. I didn't update anything on my work computer, so I don't
know what is causing the problem.


Artemis worked on that computer last week and does not work this week?
And you did nothing to change the computer?  Something doesn't add up.

Did your anti virus software update?  Did your institution's system
administrators perform an update?  Did you install any new software?
Anything?  It's hard for me to understand how the behavior of the
program can change simply by walking away for a few days.

Without being able to watch this on one of my computers, I can only
guess what the problem might be by examining the two lines of code you
cite.

My best guess is that something is preventing you from unpacking the
project file.  An .fpj file is nothing more than a zip file with a
different file extension.  It gets unpacked in %APPDATA%\stash (where
%APPDATA% is the location of the log file).  That means that you have
to have permission to write files to that location.  So, my best guess
is that something is preventing you from writing to that space.  I
have no guess for what the cause of that is.

So, check the permission of that folder.  Try making a file in that
folder by hand.  Try extracting a zip file buy hand into that folder.

If not that, then I'm afraid I'm out of ideas.


B


--
  Bruce Ravel  --__-- bra...@bnl.gov
mailto:bra...@bnl.gov

  

[Ifeffit] Bug Report - (D)Athena Doesn't Open

[Rodriguez, Roberto]

I'm currently having trouble opening both (D)Athena and (D)Artemis.  When I 
first installed Demeter a couple months ago, the programs worked properly 
without any issue until recently.  In both cases, the command prompt and the 
splash screen appear momentarily, disappears, and then nothing happens - the 
program never opens. To my knowledge, no settings have been changed that would 
prevent Athena/Artemis from opening. In contrast, (D)Hephaestus and (D)Atoms 
open and appear to function properly. I've tried uninstalling/reinstalling 
Demeter 0.9.13.1 in addition to installing the Updater 0.9.17, but I keep 
having the same issue. Any suggestions would be most helpful. Operating system 
is Windows 7 Enterprise.

Regards,
Roberto

Roberto Rodriguez
Development Engineer
UOP LLC, A Honeywell Company
25 E Algonquin Rd., Des Plaines, IL 60017
Office: Bldg. 2, 350-B
Office Phone: (847)391-2582
Cell: (815) 351-4481
Email: roberto.rodrig...@uop.commailto:roberto.rodrig...@uop.com



dathena.log
Description: dathena.log


dartemis.log
Description: dartemis.log
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Re: [Ifeffit] Bug Report - (D)Athena Doesn't Open

[Bruce Ravel]

This turned out to be due to a corrupted %APPDATA%\demeter\demeter.mru
file.

That file is used by AA to populate the Recently used submenu under
the File menu in each program.  Somehow, Roberto's .mru file had
become filled with lots of null characters.  The part of Demeter that
opens and reads the mru file got confused by the corrupted file.

I have no ida how the corruption happened.  If anyone else observes
this, please report so that we can identify the cause and leave a
searchable record here on the mailing list.

Roberto was able to resolve the issue by deleting the .mru file.  The
only loss was the record of recently visited files.

Note that this is the sort of problem that is impossible for me to
diagnose without the log files, which Roberto happily included in his
posting to the mailing list.  So let this be a reminder of the
importance of useful, actionable bug reports.

  http://bruceravel.github.io/demeter/pods/bugs.pod.html

B


On Wednesday, May 29, 2013 05:57:04 PM Rodriguez, Roberto wrote:
 I'm currently having trouble opening both (D)Athena and (D)Artemis.  When I
 first installed Demeter a couple months ago, the programs worked properly
 without any issue until recently.  In both cases, the command prompt and
 the splash screen appear momentarily, disappears, and then nothing happens
 - the program never opens. To my knowledge, no settings have been changed
 that would prevent Athena/Artemis from opening. In contrast, (D)Hephaestus
 and (D)Atoms open and appear to function properly. I've tried
 uninstalling/reinstalling Demeter 0.9.13.1 in addition to installing the
 Updater 0.9.17, but I keep having the same issue. Any suggestions would be
 most helpful. Operating system is Windows 7 Enterprise.
 
 Regards,
 Roberto
 
 Roberto Rodriguez
 Development Engineer
 UOP LLC, A Honeywell Company
 25 E Algonquin Rd., Des Plaines, IL 60017
 Office: Bldg. 2, 350-B
 Office Phone: (847)391-2582
 Cell: (815) 351-4481
 Email: roberto.rodrig...@uop.commailto:roberto.rodrig...@uop.com


-- 

 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
 Building 535A
 Upton NY, 11973

 Homepage:http://xafs.org/BruceRavel
 Software:https://github.com/bruceravel
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Re: [Ifeffit] Bug Report - (D)Athena Doesn't Open

[abansode]

Hi Roberto,
Since uninstalling and installing didn’t helped, you could give a try by doing 
a System Restore to the restore point when it was working.
Try to Run as administrator if you haven't tried.
cheers
Atul


From: Rodriguez, Roberto 
Sent: Wednesday, May 29, 2013 7:57 PM
To: ifeffit@millenia.cars.aps.anl.gov 
Subject: [Ifeffit] Bug Report - (D)Athena Doesn't Open

I’m currently having trouble opening both (D)Athena and (D)Artemis.  When I 
first installed Demeter a couple months ago, the programs worked properly 
without any issue until recently.  In both cases, the command prompt and the 
splash screen appear momentarily, disappears, and then nothing happens - the 
program never opens. To my knowledge, no settings have been changed that would 
prevent Athena/Artemis from opening. In contrast, (D)Hephaestus and (D)Atoms 
open and appear to function properly. I’ve tried uninstalling/reinstalling 
Demeter 0.9.13.1 in addition to installing the Updater 0.9.17, but I keep 
having the same issue. Any suggestions would be most helpful. Operating system 
is Windows 7 Enterprise.

 

Regards,

Roberto

 

Roberto Rodriguez

Development Engineer 

UOP LLC, A Honeywell Company

25 E Algonquin Rd., Des Plaines, IL 60017

Office: Bldg. 2, 350-B

Office Phone: (847)391-2582

Cell: (815) 351-4481

Email: roberto.rodrig...@uop.com

 




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