[Ifeffit] [External] Re: XAS viewer unit detection during data reading
Edmund Welter
edmund.welter at desy.de
Thu Mar 2 07:41:43 CST 2023
Dear Mary,
fortunately HDF5/NEXUS and ASCII would not be mutually exclusive. If we
start to use HDF5/NEXUS at the beamline, and I think we have to soon, we
can always store an ASCII file with the most important data (energy
axis, I0, I1, FluoData etc.) and meta data in parallel. Alternatively,
any user could write a short Python (or whatever) script that extracts
the important data into an ASCII file.
There will be a whole session dedicated to the topic of "*Sharing and
re-using XAS data"*, where data formats but also meta data (which data,
which label etc.) at the Q2XAFS workshop in Melbourne in August this
year. Info can be found here:
https://xrayabsorption.org/q2xafs-2023/
So, if anyone is interested in this or related topics concerning the
broad field of "Quality Assurance" for XAFS spectroscopy, the Q2XAFS
will be the place to present and discuss ideas!
Best regards,
Edmund
On 01.03.23 21:25, Shultz, Mary Jane wrote:
>
> Chiming in from left field here.
>
> Strong bias to keep the data in ASCII. ASCII will be robust long after
> all other formats have passed into electronic oblivion. I insist that
> my students keep all original data in ASKII form, so am a bit biased.
>
> Thanks
>
> Mary
>
> *From:* Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov> *On Behalf
> Of *Matt Newville
> *Sent:* Wednesday, March 1, 2023 1:24 PM
> *To:* XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> *Subject:* [External] Re: [Ifeffit] XAS viewer unit detection during
> data reading
>
> Hi Edmund, Mauro,
>
> I think that maybe relaxing the test to be "if it starts with
> the letter E or e" and then also apply the current tests of the
> numerical data (sort of like: are the numbers increasing? is the
> minimum value between about 100 and 150,000? is the average step size
> somewhere between 0.01 and 10?).
>
> But also, if you or anyone else has a "typical beamline file" -- and
> especially if there is a positive identifier for a beamline say the
> name of the beamline in the first couple of lines of the file -- we
> can add that to the files identified as XAFS data files.
>
> OK, slight diversion:
>
> I "almost agree" with Mauro's recommendation to distribute data in
> HDF5/NeXus format instead of ASCII files. ;).
>
> I am probably biased, but I think XDI (Ravel, et al J Synch Rad. 2012
> https://doi.org/10.1107/S0909049512036886and also Ravel and Newville,
> J. Phys Conference, 2015
> https://doi.org/10.1088/1742-6596/712/1/012148) would be the preferred
> way to exchange XAFS data. The 2012 paper actually discusses HDF5 as
> well.
>
> For HDF5/NeXus, I have a few slightly incompatible opinions that I
> think we should resolve:
>
> a) for many facilities, HDF5/NeXus is the preferred method for making
> all data available especially to comply with F.A.I.R. guidelines (or
> mandates).
>
> b) I use HDF5 every day. It is the right tool for some jobs, but it
> has some limitations.
>
> c) The current NeXus definition for XAS data is actually not very good
> and does not really comply with XDI or the discussion summarized in
> the J Synch Rad paper. I am not aware of anyone actually using this.
> I am willing to work on trying to get the NeXus XAS schema improved.
>
> d) We in the XAFS community should have a defined schema for NeXus
> that better complies with the 2012 paper and XDI.
>
> If anyone *is* collecting data into HDF5 or NeXus-like files, please
> send examples -- we want to support them in Larch, but also we want to
> get to a standard that is feasible. If anyone is interested in
> participating in discussions about "NeXus and/or HDF5 and/or similar
> for XAS", please contact me.
>
> --Matt
>
> On Wed, Mar 1, 2023 at 7:33 AM Edmund Welter <edmund.welter at desy.de>
> wrote:
>
> Dear Maurizio, Matt,
>
> I just checked why some older files from my beamline work
> correctly while the newer ones are not identified as xas data.
> After your explanation the reason is quite simple. In the old
> format the last line of the header was
>
> #enc_energy mono_energy mono_bragg Step_Pos mono_X1vert....
>
> After rewriting major parts of the beamline software among other
> things the last line of the header changed to:
>
> # E_enc E_step Bragg_enc Bragg_step...
>
> Once I replace E_enc with something like energy_enc or enc_energy
> the data is correctly identified as xas data.
>
> So, the easiest solution for data taken at P65 is that I will
> change the header in the data file so that the first column has a
> name that contains "energy". I think i remember that Athena was
> looking for the first column were the value of every point n+1 is
> larger than the value of point n. it then usually correctly
> identified that column to be the energy axis. However, I think
> labeling the columns correctly, that means following common
> accepted conventions, is much easier than programming a bunch of
> complicated fail safe energy axis recognising procedures.
>
> Cheers,
>
> Edmund
>
> On 28.02.23 18:16, Matt Newville wrote:
>
> Hi Siebe,
>
> Just to agree with Edmund and Mauro: selecting "energy" and
> changing data type from "raw" to "XAS" should help. But, you
> would have to do this for every file, which is not ideal.
>
> The file reader is trying to guess whether data is in energy
> (and if so, what units are used) and whether it is really XAS
> data or some other kind of data. I suspect that it is
> defaulting to "raw" because the energy column is not labeled
> "energy", but "col1" -- it sort of looks like the reader is
> not doing a good job of guessing what the columns mean.
>
> Posting a file would help diagnose why it is guessing wrong.
> The file reading does try to guess what beamline a data file
> came from, so if you send a file, maybe we can add enough
> hints for files from that beamline to work more reliably.
>
> On Tue, Feb 28, 2023 at 6:37 AM Welter, Edmund
> <edmund.welter at desy.de> wrote:
>
> Dear Siebe,
>
> did you try to change the data type from "raw" to XAS. If
> you click on the small arrow on the right you should have
> the choice between xas and raw. On my computer that works
> and after that I can choose the unit for the X-axis. For
> some reason "raw" seems to be the preset choice. Maybe
> Matt could change that, I fell into this trap several times.
>
> Cheers,
>
> Edmund
>
> ------------------------------------------------------------------------
>
> *From: *"van der Veer, Siebe" <s.van.der.veer at rug.nl>
> *To: *"XAFS Analysis using Ifeffit"
> <ifeffit at millenia.cars.aps.anl.gov>
> *Sent: *Tuesday, 28 February, 2023 13:16:18
> *Subject: *[Ifeffit] XAS viewer unit detection during data
> reading
>
> Dear all,
>
> I am not sure if this mailing list is the correct medium
> for this question. Apologies, if not.
>
> I am looking to import files in XAS viewer, which worked
> fine in ATHENA, but in XAS viewer the correct units of the
> data are not detected and I cannot manually change them. I
> can get a plot of the data, but the data is not recognized
> by the software as XAS data, i.e. a lot of
> plotting/conversion options do not show.
>
> I hope the following screenshots provide sufficient
> information to illustrate my issue.
>
> Reading in a .dat file of fluorescence data. I can't
> change the units in the marked area.
>
> The data can be read into the XAS viewer, but I don't have
> the regular plotting options in these dropdown menus.
>
> Any advice would be much appreciated.
>
> Kind regards,
>
>
>
> --
>
> *Siebe van der Veer* | *PhD student*
>
> Nanostructures of Functional Oxides | Zernike Institute
> for Advanced Materials
>
> University of Groningen | Nijenborgh 4, 9747 AG Groningen
> | The Netherlands
>
> Email: s.van.der.veer at rug.nl |
>
>
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> --
>
> --Matt Newville <newville at cars.uchicago.edu
> <http://cars.uchicago.edu>> 630-327-7411
>
>
>
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> --
>
> --Matt Newville <newville at cars.uchicago.edu
> <http://cars.uchicago.edu>> 630-327-7411
>
>
>
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