Matt, As you know I am a strong supporter of such a model compound database. I am fairly certain that most people that have collected an XAFS spectra have at some point wanted to compare their data with a model compound or two that they didn't have on hand when they collected their data at the beamline. Not only would such a database help those that need a spectra that they didn't collect, but it would also help those that are attempting to collect model spectra and would like a comparison of data quality with others that have collected spectra on the same compound. > I think there are a few important features for such a database: > - through-the-web uploading and annotating of data, probably > after 'logging on' (as with the FAQ). > - simple visualization, even if just plotting mu(E). > - link to crystallographic info. Say, an atoms.inp. > - easy searching. > - either "user comments" added by others (aka Amazon-style > reviews) or some way to indicate that the data is "good". These are all excellent features to add to the database. I especially like the "user comments"/rating feature, this would be very helpful as the database grows and some spectra are collected on similar compounds. This would help users find the spectra with the highest data quality as determined by the community. Other fields that I believe would be of some value in your current model database would be: - add separate fields for compound name and elemental composition (should make searching easier for elements) - add fields for source of model compound (i.e. purchased from vendor {vendor name, purity, etc} or if synthesized {give journal reference to synthesis procedure}) - add check box if phase purity has been checked by other analytical methods and add a text field where the user could describe what other techniques were used. - add field for which edge was collected (k-edge, L1-edge, etc). - under link to crystallographic info you could add a field for Journal Reference to crystal structure. Hope this helps, Dave
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville Sent: Friday, August 19, 2005 12:04 AM To: XAFS Analysis using Ifeffit Subject: RE: [Ifeffit] Cu oxides spectra
Hi Dave,
Excellent start to a Model compounds XAFS library.
Well, actually it's close to a decade old. But it *is* still only a start. ;)
How can I add data to this collection? I have collected ~50 reference spectra and would like to donate them to the world. I believe everyone in the XAFS community could benefit by sharing of reference spectra with one another and I would like to do my part.
Do you have a page that I could enter the spectra info and upload the data? Or would it be better to create a spreadsheet with the spectra info and zip up all raw spectra data? I am willing to format it in any form that works for you.
Right now, you can just mail me the spectra and any information you have on them. I'd prefer them as column data of energy, xmu, and any other channels you might have (i0, a reference foil, etc), and in individual files rather than a spreadsheet.
I think it's definitely worth looking into re-implementing this Model Data database. Looking at the code and data I have, I think this is definitely possible, and it does seem like it is time to revisit this idea.
I think there are a few important features for such a database: - through-the-web uploading and annotaing of data, probably after 'logging on' (as with the FAQ). - simple visualization, even if just plotting mu(E). - link to crystallographic info. Say, an atoms.inp. - easy searching. - either "user comments" added by others (aka Amazon-style reviews) or some way to indicate that the data is "good".
Does anyone else have thoughts or suggestions for such a database of model compound data? Is a database like this worth doing?
Thanks,
--Matt
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Carlo, Thanks for the offer of help! Dave, thanks for the suggestions, I think those are all good. In fact, I think none of this is that hard to do, but it will take some time. For what it's worth, I think the data should be stored in a 'proper' relational database, if for no other reason than to make it easier and faster to search. It will also make many of the 'fancier' features (user comments) easier to implement. At this point, I think the most immediate need is (as Dave mentioned yesterday) to identify a reasonable format for the data at both upload time and at download time. For upload, we'd certainly want a web form where fields could be filled in or parsed from a file following a 'Standard Data File Format'. There have been a couple attempts at a 'Standard' data format either for data collection or at least data exchange. I would guess that if we do this right with a newly revised database that we could set what that standard was (at least for data exchange). Certainly we'll make ifeffit/athena/artemis read these files easily. But we should probably think about what is needed for a more universal and long-term format. I know Bruce has thought about this some and worked on a proposed format. Hopefully he'll post that. --Matt
Hi Bruce (and everyone), I'm usually reluctant to suggest new "convenience" features for the software, because what might be convenient for me on one task might just clutter up the software for someone else. But here's an idea I think might be generally useful: Athena should have some way of memorizing common plot options. In other words, I'd like some way of making a single-click or key shortcut for, e.g.," Emin = -10, Emax = +400, mu(E)=on, background=on, plot single-spectrum E." I find when I'm reducing a lot of data I'm spending a lot of time changing all the options back and forth between looking at pre- and post-edge lines, derivative spectra, backgrounds, etc., particularly since I prefer a different energy range for each. I'm agnostic on the form the saved shortcut should take, though, which is one reason I'm posting to the list rather than just emailing you. My best idea is to have the shortcuts listed under another tab under "Plotting options," but that's starting to look a little crowded, and I already feel responsible for the "Ind" tab (which is very useful to me--thanks!). :) I'm also agnostic as to whether these shortcuts should be global to all projects (as if they were a "setting") or not. --Scott Calvin Sarah Lawrence College
On Friday 19 August 2005 14:18, Matt Newville wrote:
There have been a couple attempts at a 'Standard' data format either for data collection or at least data exchange. I would guess that if we do this right with a newly revised database that we could set what that standard was (at least for data exchange). Certainly we'll make ifeffit/athena/artemis read these files easily. But we should probably think about what is needed for a more universal and long-term format. I know Bruce has thought about this some and worked on a proposed format. Hopefully he'll post that.
Hi all, I have summarized some of the discussion on this topic at this web page: http://leonardo.phys.washington.edu/~ravel/software/fileformat.html I have also provided a link to the rough draft of a file format standard that Ken McIvor and I hacked up a couple months ago. There is also a link to this page in the "Ifeffit and friends" box on the left hand side of each of my software web pages. Regards B -- Bruce Ravel ----------------------------------- bravel@anl.gov -or- ravel@phys.washington.edu *** My cell phone number has changed. Please ask if you need the new number Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
participants (4)
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Barton, David (DG) -
Bruce Ravel -
Matt Newville -
Scott Calvin