Hi Jesse, Sorry for the trouble. I see the same behavior with your data. What is happening is that the first data point for the "mu_fluo_det0" array (and the "fluo_det0" array, and a few other arrays too) is NaN. That looks to be the case for most, if not every scan in this file. That is messing up the pr-edge and normalization calculation. Basically, `pre_edge()` is removing the point with the NaN from the normalization array, leaving it one point short, and the plotting routines then give up trying to plot x and y arrays of different sizes.
We generally try to be tolerant of and handle NaNs, but we are failing in this case. I think we can fix this. I’ve started looking at it and am trying to decide on the best strategy here. --Matt ________________________________ From: Ifeffit <ifeffit-boun...@millenia.cars.aps.anl.gov> on behalf of jesse walters <thegeoje...@gmail.com> Sent: Wednesday, April 10, 2024 7:22 AM To: ifeffit@millenia.cars.aps.anl.gov <ifeffit@millenia.cars.aps.anl.gov> Cc: Francesco Ressico <francesco.ressi...@unibo.it> Subject: [Ifeffit] Difficulty with normalization of XAS spectra This Message Is From an External Sender This message came from outside your organization. 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!Y9GJy37brG0k4qCt4bqHjK6e2Z7LEYwZ1ZzcvayMccEQ2gcoi04DttFbatHGMMIv2Td6Pn1rBtw9LkWVVgSeaBKPREpXoqTHhIQ0XGs$ <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 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
