Re: [Ifeffit] Importing Multiple Data Sets into Athena
Hi all, I think that the issue that Bruce is referring to is due to a difference of operating system and programs. The data i receive, as Kathy points out, is absolutely fine and i have had no issue whatsoever with the beamline or the files it produces. So, i think it might be an idea from now for all issues posted to the list to be preceded with OS/programs (and potentially computer) details so that such problems aren't misassigned and blame (or problem) pointed in the wrong direction? So in the interests of clarity and practicing my own suggestion: Windows XP SP3, Using native Wordpad (not native Notepad - as this removes formatting). NB: it would seem that other software does something similar to what Bruce is reporting (Win7 perhaps?). The issue had already been overcome by the methodology as Kathy suggested. So thanks for that. However, i was merely pointing out the fact that group importing did not work as a point for 'looking at' before future releases in the interests of software development and improvement. That being said i appreciate the effort put in by the people on the lists, so thanks for the hard work and perseverance. Dan -- From: Bruce Ravel bra...@bnl.gov Sent: Thursday, September 06, 2012 3:04 PM To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Importing Multiple Data Sets into Athena On Thursday, September 06, 2012 10:29:43 AM Daniel Whittaker wrote: Hi Scott, I have attached 3 of the data files and the Zr foil ref scan (already calibrated). I first import the reference Zr foil scan and then the 3 files. The Numerator for the data is column 30 and i also import the ref channel where the numerator is column 7. If i choose to set ref to standard values (as you would expect that to work) it fails and makes processing difficult. The only way round it i see is to import each data set individually and set the element, edge and value of E0 manually (for the reference - the data is read correctly) before then using the align marked groups function to align all the data to the standard Zr foil i imported at the start. Having played with the setting on the preprocess tab if you check the align to standard radio button it aligns the data (not the reference channel) despite the fact the same element radio is not checked - should the preprocessing not apply to the reference channel (if present) before the data channel? As i say it is not a huge problem and i only report it in the interest of bug removal. I am very glad that you did so. The only way that the programs can improve is if people let me know when they run into problems. I cannot fix problems that I do not know about. That said, if the attached data files are representative of the files you bring home from the beamline, the fact that Athena's automated alignment feature doesn't work for you is the very least of your problems. Each of those three data files has 33 columns of data but have been wrapped so that no line is longer than 80 characters. As a result, Athena cannot read these files without lots of help. Is this really how the beamline you use sends your data home with you? If so, they are doing you and their other users quite a disservice. Do you use some tool to preprocess these things before importing into Athena? Or has someone written an Athena filetype plugin to be able to read these monstrosities? Or have the data files become damaged (perhaps by reading into and writing from a text editor or a word processor) before you sent them to me? It is certainly good practice to provide example data that demonstrates the bug you are reporting. I am grateful that you finally did so. I wish, though, that the data were not such a challenge to read. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage:http://xafs.org/BruceRavel Software:https://github.com/bruceravel ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Importing Multiple Data Sets into Athena
Hi Dan, On Fri, Sep 7, 2012 at 7:53 AM, Daniel Whittaker daniel.whitta...@postgrad.manchester.ac.uk wrote: Hi all, I think that the issue that Bruce is referring to is due to a difference of operating system and programs. The data i receive, as Kathy points out, is absolutely fine and i have had no issue whatsoever with the beamline or the files it produces. So, i think it might be an idea from now for all issues posted to the list to be preceded with OS/programs (and potentially computer) details so that such problems aren't misassigned and blame (or problem) pointed in the wrong direction? Except that the problem you had is actually not related to which operating system is used. Athena and the other programs are (very intentially) as independent of OS as possible. We do see some OS-dependent problems, and being clear about what OS and versions of the software you're using are always helpful, but I wouldn't want to put too much emphasis on how to format an issue to the mailing list. So in the interests of clarity and practicing my own suggestion: Windows XP SP3, Using native Wordpad (not native Notepad - as this removes formatting). NB: it would seem that other software does something similar to what Bruce is reporting (Win7 perhaps?). The files that you had problems with are **different** from the ones that are read correctly. It doesn't matter what OS is used, if the files are changed they may not work. In particular, randomly inserting newlines into files that are read as line-delimited is probably going to cause failures on all OSes. I'm no fan of Windows Notepad, but it does *not* change or remove the formatting of files for me. On the other hand, opening these files with Wordpad and then saving it *will* change the formatting. For me at least, Wordpad changes the formatting of the original files by adding carriage return (\r) to every linefeed (\n), but Athena (on any OS) can still read thes files just fine. The issue had already been overcome by the methodology as Kathy suggested. So thanks for that. However, i was merely pointing out the fact that group importing did not work as a point for 'looking at' before future releases in the interests of software development and improvement. That being said i appreciate the effort put in by the people on the lists, so thanks for the hard work and perseverance. But the group importing didn't work because importing those individual files didn't work. And that was because those files had randomly inserted newline characters. It's hard for me to see this a problem with Group Importing or Importing Data at all. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Importing Multiple Data Sets into Athena
I feel I should weigh in here. There were two separate issues in the files Dan sent the other day -- one was the issue he intended to report, the other was a problem of his own creation. The intended issue was a problem importing data for which the reference spectrum was of a different element than the main data. In that case, the element and edge of the reference were being incorrectly identified. This was a legitimate bug and a legitimate bug report. I fixed the problem and pushed the fix to github. It will be included in the next release of the Windows installer. I will say now, as I have said many times before, that the software benefits enormously by users who are kind and diligent enough take the time to report their issues to me in a way that I can take action on. My software is much better today thanks to bug reports like the one Dan submitted. Obviously, I am quite grateful to him and to everyone else who has ever reported a software issue. The unintended issue was that the data files he sent had been altered (apparently by reading into and saving from WordPad) in a way that rendered them unreadable by Athena. Happily another member of our community supplied the original, unaltered data files. Because I wanted to get to work on the primary problem, that of the incorrectly imported reference, I had to fritter away a good 20 or 30 minutes writing a one-off program to undo the damage that had been done to the files that were sent. A bit of understand of what constitutes a data file would have spared me that effort. On that topic I have another comment. Although Athena attempts to hide the details of interpreting the contents of data files form the user and (if I pay pat myself on the back) does a pretty good job of it, it is still worth while for the scientist to have a passing understanding of the contents of a data file. All data files contain a sequence of numbers measured at a sequence of energy points. By far the most common way of indicating the separation between a group of numbers (such as the signal on I0) measured at successive data points is by placing those numbers all on one line of the file and separating lines by a line break. Athena has to make some assumptions about how the numbers are presented in the file or it will not be able to correctly interpret those numbers and the relationships between them. If you insert line breaks willy-nilly into the file, it should not be surprising that Athena will get confused. My point here is that, although Athena is largely successful at hiding uninteresting detail! s from the user, there is merit in having a basic understanding of how data is transmitted from the beamline all the way to your computer. Thus, I took the time to write this paragraph. B From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Daniel Whittaker [daniel.whitta...@postgrad.manchester.ac.uk] Sent: Friday, September 07, 2012 8:53 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Importing Multiple Data Sets into Athena Hi all, I think that the issue that Bruce is referring to is due to a difference of operating system and programs. The data i receive, as Kathy points out, is absolutely fine and i have had no issue whatsoever with the beamline or the files it produces. So, i think it might be an idea from now for all issues posted to the list to be preceded with OS/programs (and potentially computer) details so that such problems aren't misassigned and blame (or problem) pointed in the wrong direction? So in the interests of clarity and practicing my own suggestion: Windows XP SP3, Using native Wordpad (not native Notepad - as this removes formatting). NB: it would seem that other software does something similar to what Bruce is reporting (Win7 perhaps?). The issue had already been overcome by the methodology as Kathy suggested. So thanks for that. However, i was merely pointing out the fact that group importing did not work as a point for 'looking at' before future releases in the interests of software development and improvement. That being said i appreciate the effort put in by the people on the lists, so thanks for the hard work and perseverance. Dan -- From: Bruce Ravel bra...@bnl.gov Sent: Thursday, September 06, 2012 3:04 PM To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Importing Multiple Data Sets into Athena On Thursday, September 06, 2012 10:29:43 AM Daniel Whittaker wrote: Hi Scott, I have attached 3 of the data files and the Zr foil ref scan (already calibrated). I first import the reference Zr foil scan and then the 3 files. The Numerator for the data is column 30 and i also import the ref channel where the numerator is column 7. If i choose to set ref to standard values (as you would expect that
Re: [Ifeffit] Problem with Demeter Artemis 0.9.10
Hi Matt, Thanks for the report. I'll look into it and let you know what I find. Clearly the only work-around right now is to recreate your fitting model from scratch in the new Athena. Admittedly not a very satisfying answer,... B From: ifeffit-boun...@millenia.cars.aps.anl.gov [ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Matt Frith [matt.fr...@gmail.com] Sent: Friday, September 07, 2012 12:01 AM To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Problem with Demeter Artemis 0.9.10 Hi All, I have come across an bug with Demeter 0.9.10. When I go to open an old format Artemis project file I will see, Converting old-style project file to Demeter serialization written in the progress bar, and then the program will quit without opening the file. The problem occurs on both 32 and 64bit Windows 7. I uninstalled the program and reinstalled Demeter 0.9.9 and there are no issues with 0.9.9. The dartemis.log contains: Can't locate object method inp_is_feff8 via package Demeter::Feff::External at C:/strawberry/perl/site/lib/Demeter/Fit/Horae.pm line 110. I hope this is helpful. It seems to be similar to the problem posted by Riamundo, and I hope that I have not missed a previously posted solution. Attached is one of the project files that I have used. Sincerely, Matt Frith ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
