[Ifeffit] Import Error
Ravel, Bruce
bravel at bnl.gov
Sat Apr 6 09:16:35 CDT 2019
I did not remember when you asked the other day, but it occurred to me
that your data-in-keV problem was reported a few months ago.
https://millenia.cars.aps.anl.gov/pipermail/ifeffit/2019-January/009688.html
I have not yet made a new Windows release with the fix. However, it is
not too hard to apply the fix by editing a small amount of Athena's
source code.
I think this is the easiest way to explain the small changes. Find the
file "lib/Demeter/Data.pm" underneath the location on your computer that
the software was installed. Look at this link:
https://github.com/bruceravel/demeter/commit/1b586b88d36336cad00b13d73913ebdb48b1d132#diff-74dd62af0fb82fb27595c1edcf73041f
Make the indicated change at line 22 (i.e. add $EPSILON6 to the argument
list of qw().)
Make the indicated changes around 885 (i.e. add the two lines before the
while block and alter the argument of the greater-than comparison in the
first line of the while block).
The change at line 871 is irrelevant and has no impact on Athena's
operations.
That should do it. You can then drop the edited file into place on any
other computer.
B
On 04/05/2019 10:33 AM, Clark Adam Hugh (PSI) wrote:
> Dear Bruce and Lucy
>
> Thanks for your work around Lucy, it works perfectly but still doesn't explain the behavior I am observing.
>
> Bruce what other information would be useful to diagnose the problem I am currently having? I have attached two figures, one showing the import window with the setting I have been using, specifically that I am not using the rebin feature. The second figure shows the difference in the pre-edge region between importing the data with eV and keV units for the energy column to demonstrate clearly that resampling is occurring when importing with data that has an energy column of KeV.
>
> Many Thanks
> Adam Clark
>
> __________________________________________
> Paul Scherrer Institut
> Adam Hugh Clark
> WLGA/129
> Forschungsstrasse 111
> 5232 Villigen PSI
> Schweiz
>
> Telefon: +41 56 310 41 51
> E-Mail: adam.clark at psi.ch
> -----Original Message-----
> From: Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request at millenia.cars.aps.anl.gov
> Sent: Freitag, 5. April 2019 15:20
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Ifeffit Digest, Vol 194, Issue 4
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> Today's Topics:
>
> 1. Data Import Bug (Athena 0.9.26) (Clark Adam Hugh (PSI))
> 2. Re: Data Import Bug (Athena 0.9.26) (Ravel, Bruce)
> 3. Re: Data Import Bug (Athena 0.9.26) (Lucy M Mottram)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 5 Apr 2019 11:33:13 +0000
> From: "Clark Adam Hugh (PSI)" <adam.clark at psi.ch>
> To: "ifeffit at millenia.cars.aps.anl.gov"
> <ifeffit at millenia.cars.aps.anl.gov>
> Subject: [Ifeffit] Data Import Bug (Athena 0.9.26)
> Message-ID:
> <BDFF4FC62383D24DA3EF530480A33EA70B616536 at MBX214.d.ethz.ch>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Mailing List
>
> I have recently come across a data import error when using Athena version 0.9.26. When importing data there appears to be a resampling which significantly reduces the resolution of the data. Attached is an example dataset with an energy step of 0.5 eV on the Cu K edge. When importing with Athena 0.9.26 this data is significantly resampled resulting in an energy resolution on the edge of 1.5 eV which can either be seen by plotting or by exporting and inspecting the datafile. Using version 0.9.25 resolves this issue entirely. The data itself appears to actually be visible correctly during the import process (the import tab shows the data listed correctly when choosing which columns to import).
>
> Is there a setting somewhere within Athena 0.9.26 that sets the default behavior to resample the imported data?
>
> Thanks
> Adam Clark
>
> __________________________________________
> Paul Scherrer Institut
> Adam Hugh Clark
> WLGA/129
> Forschungsstrasse 111
> 5232 Villigen PSI
> Schweiz
>
> Telefon: +41 56 310 41 51
> E-Mail: adam.clark at psi.ch
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> ------------------------------
>
> Message: 2
> Date: Fri, 5 Apr 2019 12:18:01 +0000
> From: "Ravel, Bruce" <bravel at bnl.gov>
> To: "ifeffit at millenia.cars.aps.anl.gov"
> <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Data Import Bug (Athena 0.9.26)
> Message-ID: <83c1d066-e0dc-9c37-6d9c-ca806d641c7d at bnl.gov>
> Content-Type: text/plain; charset="Windows-1252"
>
>
> Unfortunately, I don't observe what you are describing.
>
> Grasping at straws here, but are you inadvertently using this import feature?
>
>
> http://bruceravel.github.io/demeter/documents/Athena/import/preproc.html#rebinning-quick-scan-data
>
> B
>
> On 04/05/2019 07:33 AM, Clark Adam Hugh (PSI) wrote:
>> Dear Mailing List
>>
>> I have recently come across a data import error when using Athena
>> version 0.9.26. When importing data there appears to be a resampling
>> which significantly reduces the resolution of the data. Attached is an
>> example dataset with an energy step of 0.5 eV on the Cu K edge. When
>> importing with Athena 0.9.26 this data is significantly resampled
>> resulting in an energy resolution on the edge of 1.5 eV which can
>> either be seen by plotting or by exporting and inspecting the
>> datafile. Using version 0.9.25 resolves this issue entirely. The data
>> itself appears to actually be visible correctly during the import
>> process (the import tab shows the data listed correctly when choosing which columns to import).
>>
>> Is there a setting somewhere within Athena 0.9.26 that sets the
>> default behavior to resample the imported data?
>>
>> Thanks
>>
>> Adam Clark
>>
>> __________________________________________
>> Paul Scherrer Institut
>> Adam Hugh Clark
>> WLGA/129
>> Forschungsstrasse 111
>> 5232 Villigen PSI
>> Schweiz
>>
>> Telefon: +41 56 310 41 51
>> E-Mail: adam.clark at psi.ch
>>
>>
>>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>>
>
>
> --
> Bruce Ravel ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology
> Synchrotron Science Group at NSLS-II
> Lead Beamline Scientist, 6BM (BMM)
> Building 743, Room 114
> Upton NY, 11973
>
> Homepage: http://bruceravel.github.io/home/
> Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
> Software: https://github.com/bruceravel
> Demeter: http://bruceravel.github.io/demeter/
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 5 Apr 2019 14:18:58 +0100
> From: Lucy M Mottram <lmmottram1 at sheffield.ac.uk>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Data Import Bug (Athena 0.9.26)
> Message-ID:
> <CAJ7D-QF6+DZ8QjXG-4L1Gj4NrzuEoVauTkT0AnLERJkymrMZ-w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Adam and Mailing List,
>
> I've checked and found some of my data has a similar problem, I don't know how to solve this using settings in Athena, however as a workaround I have found that if I convert the energy in my raw data file from KeV to Ev before importing it into Athena (using excel) it appears that re-sampling issue does not occur. Hopefully that helps in the short term and gives a clue to what is going wrong with the import.
>
> All the best
> Lucy Mottram
>
> On Fri, 5 Apr 2019 at 12:35, Clark Adam Hugh (PSI) <adam.clark at psi.ch>
> wrote:
>
>> Dear Mailing List
>>
>>
>>
>> I have recently come across a data import error when using Athena
>> version 0.9.26. When importing data there appears to be a resampling
>> which significantly reduces the resolution of the data. Attached is an
>> example dataset with an energy step of 0.5 eV on the Cu K edge. When
>> importing with Athena 0.9.26 this data is significantly resampled
>> resulting in an energy resolution on the edge of 1.5 eV which can
>> either be seen by plotting or by exporting and inspecting the
>> datafile. Using version 0.9.25 resolves this issue entirely. The data
>> itself appears to actually be visible correctly during the import
>> process (the import tab shows the data listed correctly when choosing which columns to import).
>>
>>
>>
>> Is there a setting somewhere within Athena 0.9.26 that sets the
>> default behavior to resample the imported data?
>>
>>
>>
>> Thanks
>>
>> Adam Clark
>>
>>
>>
>> __________________________________________
>> Paul Scherrer Institut
>> Adam Hugh Clark
>> WLGA/129
>> Forschungsstrasse 111
>> 5232 Villigen PSI
>> Schweiz
>>
>> Telefon: +41 56 310 41 51
>> E-Mail: adam.clark at psi.ch
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>>
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--
Bruce Ravel ------------------------------------ bravel at bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Lead Beamline Scientist, 6BM (BMM)
Building 743, Room 114
Upton NY, 11973
Homepage: http://bruceravel.github.io/home/
Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
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