Hi Dan, I had the same problem recently. It can be avoided by importing each scan seperately. Regards Tim Karlsruher Institut für Technologie (KIT) Institut für Nukleare Entsorgung (INE) Tim Prüßmann Hermann-von-Helmholtz-Platz 1 D-76344 Eggenstein-Leopoldshafen Tim.Pruessmann@kit.edu www.ine.kit.edu KIT - Universität des Landes Baden-Württemberg und nationales Großforschungszentrum in der Helmholtz-Gemeinschaft -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Daniel Whittaker Sent: Thursday, September 06, 2012 10:30 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Importing Multiple Data Sets into Athena 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. Thanks, Dan -------------------------------------------------- From: "Scott Calvin" Sent: Wednesday, September 05, 2012 6:13 PM To: "XAFS Analysis using Ifeffit" Subject: Re: [Ifeffit] Importing Multiple Data Sets into Athena

Hi Dan,

Could you attach the data files you are trying to import? We can see if the problem is reproducible on our systems.

--Scott Calvin Sarah Lawrence College

On Sep 5, 2012, at 10:50 AM, Daniel Whittaker wrote:

Hello all,

I am having a small issue when importing multiple data sets into Athena all of which have a reference channel.

The issue i am experiencing is that when importing multiple data sets together they do not all import correctly. The first data set (of all selected) imports fine (The data is Np and the reference Zr foil) - it imports the reference file which can be aligned to the calibration Zr foil file. However, the remainder of the files do not work at all, the reference channel does not import correctly at all. I have tried (best as i can tell) all of the pre-process options to no avail. When i import them individually it works although I have to tell it what element the ref channel is and the edge and E0 (couldn't the edge and E0 be linked such that selection of one filled the other?) but this isn't too much of an issue. It is by no means a massive problem but i thought i would ask if there is a way around it or if it is a real bug? All other multiple data processing - such as "align marked groups" - works fine. Regards, Dan Whittaker

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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" Sent: Thursday, September 06, 2012 3:04 PM To: "XAFS Analysis using Ifeffit" 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 ------------------------------------ bravel@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

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 details 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-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Daniel Whittaker [daniel.whittaker@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" Sent: Thursday, September 06, 2012 3:04 PM To: "XAFS Analysis using Ifeffit" 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 ------------------------------------ bravel@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

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Hi Dan, Your project certain exposes a problem. I see the same behavior on the computer I am sitting at right now. The problem seems to be in a part of the code I thought I didn't touch between 0.9.11 and 12, so I am surprised that it cropped up today. Sigh..... I'll look into it once I am back in my office and let you know what I find. B ________________________________________ From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Daniel Whittaker [daniel.whittaker@postgrad.manchester.ac.uk] Sent: Thursday, September 27, 2012 10:23 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Issue On Re-Open of File in Artemis Hello User Community, I am having an issue with a project i was working on yesterday - one i hope can be resolved rather easily. I was working on the project yesterday then i saved the file and closed Artemis and all was well. However, today when i try and open the file and continue working on it it instantly crashes the software on pressing FIT. First thing this morning i updated to version 0.9.12. I am modelling using the first shell fit that is built in - possible source of error? I dont know the root cause of the issue as everything i have done here i have done before with other datasets with no issue. I have tried starting from scratch and reinstalling the software too but the issue persists - it all works well (when startingg from scratch) until it is saved and then tried to reopen. [Using Windows XP SP3 Install version 0.9.12] Any help would be much appreciated. Regards, Dan

Dear friends, We are doing an experiment of temperature based phase transition. I need to get the values of all four GDS parameters with errors. I know the theoretical model (i. e., atoms page). But to get all the four parameter values with errors (amp, enot, delr, ss ). For this I cannot "set" all the parameters as well ass I cannot guess all the parameters. Any suggestions for this problem ?.