Re: [Ifeffit] Athena (Demeter 0.9.26) does not import all datapoints from ascci file
Hi Tim, On Wed, Mar 28, 2018 at 8:33 AM, Prüßmann, Tim (IKFT) < tim.pruessm...@kit.edu> wrote: > Hi Matt, > > > > that’s it. I manually changed the energy column from keV to eV and it > works. > Huh, OK -- I don't know why that should sometimes cause a problem, but it should be a good clue. We should probably make sure that when Larch or XAS Viewer writes an Athena Project file that it forces energy to be in eV. And somewhat related, we were just having a discussion for Larch about adding more and better routines for reading Spec files. Anyway, I'm glad you sort of found a workaround. --Matt ___ 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] Athena (Demeter 0.9.26) does not import all datapoints from ascci file
Hi Matt, that’s it. I manually changed the energy column from keV to eV and it works. Tim From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville Sent: Tuesday, March 27, 2018 7:50 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Athena (Demeter 0.9.26) does not import all datapoints from ascci file Hi Tim, Hm, that's all weird. I still cannot reproduce this. Reading Kathy's original file, I see 275 data points in Athena. Reading the Larch-generated project file in Athena, I also see 275 points... That's running both Athena+Ifeffit on Windows or running Athena+Larch on MacOS. One thing that might be worth looking into is whether the data being in keV rather than eV might make a difference. That's sort of grasping at straws, but I'm not sure what else to try. On Tue, Mar 27, 2018 at 10:22 AM, Prüßmann, Tim (IKFT) <tim.pruessm...@kit.edu<mailto:tim.pruessm...@kit.edu>> wrote: Hi Matt, the rebin screen was just to show the number of data points. We used column 1 as energy and column 9 as numerator; data type ‘xanes’; no preprocessing. Overall we used identical parameters in 0.9.25 and 0.9.26 The “plan” is to do the standard calibration and normalization steps, but we lose data points by just importing the data. In the example Kathy sent, we go from 275 “real” points to 109 imported points. This effect appears with all Spec files we have tested (measured at different times and to different beamlines -> different number of columns). Importing data from FEFF and FDMNES works, we get the same number of points as in the ascii file. I also tried the XAS Viewer in Larch (0.9.37), which read all points of the Spec file. I exported the data as Athena project and .csv Importing the project file into Athena works and the “about current group” function shows 275 points. However, nothing can be plotted, the plot window stays on the overview from the import screen. The csv file contains all 275 points, but importing to Athena again reduces it to 109 points. Tim From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov<mailto:ifeffit-boun...@millenia.cars.aps.anl.gov>] On Behalf Of Matt Newville Sent: Tuesday, March 27, 2018 2:12 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Athena (Demeter 0.9.26) does not import all datapoints from ascci file Tim, Kathy, I did not respond to Kathy's earlier email, and I apologize for letting it falling off my radar screen. FWIW, I do not see the same problem. I can read the file (with the Spec plugin enabled) and plot the data. There are 275 data points. Reading multi-column files from can be tricky (should we know which columns you chose or what processing steps you took). And spec files can cause no end of trouble. But from the screenshots aattached, it looks like maybe Time meant to rebin the data. Is that related to what Kathy was trying to do? Perhaps you could explain what steps you took in reading the data file and more clearly explain the problem? Like, did you intend to re-bin the data? For sure, the plot labeled as coming from PyMCA looks strange to me --- the derivative of the data has clearly been smoothed from the raw data in the file. I don't know what to make of that. Hope that helps, --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov<mailto: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 ___ 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] Athena (Demeter 0.9.26) does not import all datapoints from ascci file
Hi Tim, Hm, that's all weird. I still cannot reproduce this. Reading Kathy's original file, I see 275 data points in Athena. Reading the Larch-generated project file in Athena, I also see 275 points... That's running both Athena+Ifeffit on Windows or running Athena+Larch on MacOS. One thing that might be worth looking into is whether the data being in keV rather than eV might make a difference. That's sort of grasping at straws, but I'm not sure what else to try. On Tue, Mar 27, 2018 at 10:22 AM, Prüßmann, Tim (IKFT) < tim.pruessm...@kit.edu> wrote: > Hi Matt, > > > > the rebin screen was just to show the number of data points. > > > > We used column 1 as energy and column 9 as numerator; data type ‘xanes’; > no preprocessing. > > Overall we used identical parameters in 0.9.25 and 0.9.26 > > > > The “plan” is to do the standard calibration and normalization steps, but > we lose data points by just importing the data. In the example Kathy sent, > we go from 275 “real” points to 109 imported points. > > > > This effect appears with all Spec files we have tested (measured at > different times and to different beamlines -> different number of columns). > > > > Importing data from FEFF and FDMNES works, we get the same number of > points as in the ascii file. > > > > I also tried the XAS Viewer in Larch (0.9.37), which read all points of > the Spec file. I exported the data as Athena project and .csv > > Importing the project file into Athena works and the “about current group” > function shows 275 points. However, nothing can be plotted, the plot window > stays on the overview from the import screen. > > The csv file contains all 275 points, but importing to Athena again > reduces it to 109 points. > > > > > > Tim > > > > > > > > *From:* Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] *On > Behalf Of *Matt Newville > *Sent:* Tuesday, March 27, 2018 2:12 AM > *To:* XAFS Analysis using Ifeffit > *Subject:* Re: [Ifeffit] Athena (Demeter 0.9.26) does not import all > datapoints from ascci file > > > > Tim, Kathy, > > > > I did not respond to Kathy's earlier email, and I apologize for letting it > falling off my radar screen. > > > > FWIW, I do not see the same problem. I can read the file (with the Spec > plugin enabled) and plot the data. There are 275 data points. Reading > multi-column files from can be tricky (should we know which columns you > chose or what processing steps you took). And spec files can cause no end > of trouble. But from the screenshots aattached, it looks like maybe Time > meant to rebin the data. Is that related to what Kathy was trying to do? > > > > Perhaps you could explain what steps you took in reading the data file and > more clearly explain the problem? Like, did you intend to re-bin the data? > > > > For sure, the plot labeled as coming from PyMCA looks strange to me --- > the derivative of the data has clearly been smoothed from the raw data in > the file. I don't know what to make of that. > > > > Hope that helps, > > > > --Matt > > > > ___ > 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 ___ 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] Athena (Demeter 0.9.26) does not import all datapoints from ascci file
Tim, Kathy, I did not respond to Kathy's earlier email, and I apologize for letting it falling off my radar screen. FWIW, I do not see the same problem. I can read the file (with the Spec plugin enabled) and plot the data. There are 275 data points. Reading multi-column files from can be tricky (should we know which columns you chose or what processing steps you took). And spec files can cause no end of trouble. But from the screenshots aattached, it looks like maybe Time meant to rebin the data. Is that related to what Kathy was trying to do? Perhaps you could explain what steps you took in reading the data file and more clearly explain the problem? Like, did you intend to re-bin the data? For sure, the plot labeled as coming from PyMCA looks strange to me --- the derivative of the data has clearly been smoothed from the raw data in the file. I don't know what to make of that. Hope that helps, --Matt ___ 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
