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/S0909049512036886 and 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 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 > 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 sever
Re: [Ifeffit] XAS viewer unit detection during data reading
Dear Edmund,
That's great that you have find why the ASCII data parser in Larch was
not detecting automatically the energy column from the labels in the
header. The current choice is to look for "energy" or "ene" in the
header to identify a data column as energy array.
Please, if you are willing to publicly share and example data file from
P65, we could include it in the xafsdata examples here:
https://github.com/xraypy/xraylarch/tree/master/examples/xafsdata/beamlines
Those files are used for running the automatic tests and permit us
improving the quality of Larch's code.
This is valid for any beamline who wants to contribute, even if I
strongly encourage distributing data in HDF5/NeXus format instead of
ASCII files.
Best,
Mauro
On 01/03/2023 14:31, Edmund Welter 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
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"
*To: *"XAFS Analysis using Ifeffit"
*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.
image.png
The data can be read into the XAS viewer, but I don't have the
regular plotting options in these dropdown menus.
image.png
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.v...@rug.nl|
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
h
Re: [Ifeffit] XAS viewer unit detection during data reading
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
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"
*To: *"XAFS Analysis using Ifeffit"
*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.
image.png
The data can be read into the XAS viewer, but I don't have the
regular plotting options in these dropdown menus.
image.png
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.v...@rug.nl|
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--
--Matt Newville <http://cars.uchicago.edu>> 630-327-7411
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Re: [Ifeffit] XAS viewer unit detection during data reading
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 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" > *To: *"XAFS Analysis using Ifeffit" > *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. > > [image: image.png] > > The data can be read into the XAS viewer, but I don't have the regular > plotting options in these dropdown menus. > > [image: image.png] > > 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.v...@rug.nl | > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > -- --Matt Newville 630-327-7411 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] XAS viewer unit detection during data reading
Dear Siebe, In addition to the quick workaround suggested by Edmund, if you could send your data file to me (here or by private email), I could have a look why xas_viewer is not detecting the energy scale automatically. @Edmund, usually the "xas" file type is setted automatically when the x-axis is identified as energy scale in the `read_ascii` function. If you have data files that are not detected correctly as XAS data files, please, do not hesitate to send them to us. Best, Mauro On 28/02/2023 13:37, Welter, Edmund 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" *To: *"XAFS Analysis using Ifeffit" *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. image.png The data can be read into the XAS viewer, but I don't have the regular plotting options in these dropdown menus. image.png 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.v...@rug.nl <mailto:s.van.der.v...@rug.nl>| ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] XAS viewer unit detection during data reading
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" To: "XAFS Analysis using Ifeffit" 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: [ mailto:s.van.der.v...@rug.nl | s.van.der.v...@rug.nl ] | ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
[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. [image: image.png] The data can be read into the XAS viewer, but I don't have the regular plotting options in these dropdown menus. [image: image.png] 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.v...@rug.nl | ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
