Dear Robert, Apologies, the large h5 files were how the data were sent to me. I figured out how to export a single csv file, which is attached. Unfortunately, these data were collected without my input and I am trying to help the student make the data usable if possible. For my own projects I collected Fe K edge XAS spectra from 7000 to 7350 eV. I have not seen all the data from the session, but I believe the data were only collected over the range 7100 to 7150 eV for all analyses. I guess these are not useable?
Cheers, Jesse On Sat, Apr 13, 2024 at 7:17 PM Robert Gordon <moyie.instit...@gmail.com> wrote: > Two things: 1. This is a volunteer community. Asking us to download a > massive file and parse through it to find a data file is not a reasonable > request. Pick an example and attach it as a txt file (energy, mu(E) or E, > I0, IF ). In fact, since > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > > ZjQcmQRYFpfptBannerEnd > Two things: > > 1. This is a volunteer community. Asking us to download a massive file and > parse through it to find a data file is not a reasonable request. Pick an > example and attach it as a txt file (energy, mu(E) or E, I0, IF ). In fact, > since the graph looks like the data were grossly over-sampled for XANES, > you might want to sieve it to a more reasonable step size such as 0.1 to > 0.3 eV through the edge. That will also help with file size. > > 2. If the graph you attached is representative of the data, the data were > not collected over a large enough energy range for normalisation. Next > time, try +/- 100 - 200 eV below and above the edge (maybe 250 above). > > -R. > > On 2024-04-10 5:22 a.m., jesse walters wrote: > > Hi all, I have some spectra collected by a collaborator, Francesco > Ressico, a PhD student at Uni Bologna, (see attached .h5 file below) and > we are having trouble normalizing the Fe K edge spectra. The data are for > serpentine group minerals > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > > ZjQcmQRYFpfptBannerEnd > Hi all, > > I have some spectra collected by a collaborator, Francesco Ressico, a PhD > student at Uni Bologna, (see attached .h5 file below) and we are having > trouble normalizing the Fe K edge spectra. The data are for serpentine > group minerals and were collected in fluorescence mode. In the attached > file, the correct X array value is 'energy_enc', the data type is 'xas', > and the y array should be 'mu_fluo_det0'. The spectra are already > normalized for the incoming beam energy (although this can also be done > using 'flou_det0/i0'). There are multiple spectra in the file, any one of > them can be chosen to test the procedure. > > After loading the spectra, I am able to plot the raw spectra correctly > (see attached). But when I try to normalize the pre and post edge regions > and plot the normalized spectra, the software only gives a blank plot. I > have tried changing the normalization type, polynomial type, range, etc for > both the pre and post edge, but nothing seems to work. I also tested > different spectra, but with similar results. > > Does anyone have suggestions for how these data can be normalized? > > The h5 file is too large, so here is a dropbox link > https://urldefense.us/v3/__https://www.dropbox.com/scl/fi/d8k5s67vli0mq97ac520y/COR21_79_Xastransect_79_F1_THC.h5?rlkey=33ragg4p6x9rx65t9yvi5kewe&dl=0__;!!G_uCfscf7eWS!fBIOzph-Db3ioZGTdqQZ83ckH_bkFR9tjSSpr359OiRFNixZF62emsiEQqIS4y25emWz1jQZvQjSeNOMPzqwDKMCy1IZOJZ65g$ > > <https://urldefense.us/v3/__https://www.dropbox.com/scl/fi/d8k5s67vli0mq97ac520y/COR21_79_Xastransect_79_F1_THC.h5?rlkey=33ragg4p6x9rx65t9yvi5kewe&dl=0__;!!G_uCfscf7eWS!btLKhnEiyp5gMQfSDnHdxqgt2ie5vcVHW7e142vokJ-wEX6zZSIOcAyHsf5THg9ZlyyIsx7Vfm27ycKWAQg1_cysDdnW65aCQA$> > > Sincerely, > Jesse Walters > > -- > Jesse B. Walters > Ambizione Fellow > Institut für Geologie > Universität Bern > > _______________________________________________ > Ifeffit mailing > listifef...@millenia.cars.aps.anl.govhttp://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit__;!!G_uCfscf7eWS!Y2vfGwfONNMo1aLgkAnnXaF5bQ8shgtgTi51NUeYhIeIHAvFmLRm9we3b2lAA2ZANf1WrgLChlCGWCg0N--jlHp3IM5xIQjzt3Hd7wM$> > Unsubscribe: > https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options/ifeffit__;!!G_uCfscf7eWS!fBIOzph-Db3ioZGTdqQZ83ckH_bkFR9tjSSpr359OiRFNixZF62emsiEQqIS4y25emWz1jQZvQjSeNOMPzqwDKMCy1LoVDb7bw$ > > <https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options/ifeffit__;!!G_uCfscf7eWS!Y2vfGwfONNMo1aLgkAnnXaF5bQ8shgtgTi51NUeYhIeIHAvFmLRm9we3b2lAA2ZANf1WrgLChlCGWCg0N--jlHp3IM5xIQjzNgtGmzg$> > > > _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit__;!!G_uCfscf7eWS!fBIOzph-Db3ioZGTdqQZ83ckH_bkFR9tjSSpr359OiRFNixZF62emsiEQqIS4y25emWz1jQZvQjSeNOMPzqwDKMCy1J48XUeQw$ > > Unsubscribe: > https://urldefense.us/v3/__http://millenia.cars.aps.anl.gov/mailman/options/ifeffit__;!!G_uCfscf7eWS!fBIOzph-Db3ioZGTdqQZ83ckH_bkFR9tjSSpr359OiRFNixZF62emsiEQqIS4y25emWz1jQZvQjSeNOMPzqwDKMCy1LoVDb7bw$ > > -- Jesse B. Walters Ambizione Fellow Institut für Geologie Universität Bern
#saved Sat Apr 13 19:28:23 2024 #saving x array=energy, y array=mu #COR21_79_Xastransect_79_F1_THC.h5 scan30.1 mu_fluo_det0: COR21_79_Xastransect_79_F1_THC.h5 scan30.1 mu_fluo_det0 #------------------------------------------ # energy, COR21_79_Xastransect_79_F1_THC.h5 scan30.1 mu_fluo_det0 7099.99948, nan 7100.09054, 0.00215646 7100.19105, 0.00204590 7100.29093, 0.00200017 7100.39065, 0.00195975 7100.49108, 0.00203066 7100.59071, 0.00203860 7100.69061, 0.00205946 7100.79121, 0.00206315 7100.89116, 0.00201349 7100.99123, 0.00201771 7101.09136, 0.00206835 7101.19094, 0.00208537 7101.29087, 0.00217270 7101.39120, 0.00211457 7101.49106, 0.00211655 7101.59108, 0.00211963 7101.69136, 0.00212374 7101.79124, 0.00209313 7101.89138, 0.00215771 7101.99100, 0.00220208 7102.09116, 0.00209760 7102.19132, 0.00223845 7102.29152, 0.00213821 7102.39148, 0.00217297 7102.49126, 0.00215688 7102.59186, 0.00227468 7102.69118, 0.00224350 7102.79098, 0.00218986 7102.89115, 0.00222098 7102.99099, 0.00226953 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