January 2003 - Ifeffit - millenia.cars.aps.anl.gov

ifeffit and Mac OSX
by Matt Newville 04 Jul '04

04 Jul '04

Hi Raja, On Mon, 7 Oct 2002, rajasekaran swaminathan wrote: > Hi Matt, > > I tried again over the past few days to install the binary > installer on my mac (OS X.2). I couldn't find an attached aquaterm > / pgplot demo. The Aquaterm program opens, but I cannot see any > windows come out from that application. I mean, it is just like a > blank application. When I type ifeffit on Terminal app, it doesnt > recognise the presence of ifeffit in the ifeffitosx directory. i.e. > it says that the command is not found. The executable works > perfectly well on a Windows machine, and I was wondering whether > there are any such equivalents for a Macintosh machine. I also dont > think that the installer comes with athena/artemis/tkatoms etc.. Do > you have any other recommendations to resolve this issue? Also,if > it is possible, can I get a CD of these programs for a Macintosh > equivalent to an executable version for the Windows? > > I appreciate your help in this regard. I have used the binary installer once on a OS 10.1 system. It worked for me (after following the simple included instructions, of course) and plotting with Aquaterm did work. I haven't tried 10.2. I know the Mac binary installer does not include athena, artemis, or tkatoms. I believe it only provides the command-line ifeffit. I'm not sure I can answer many other questions about it. I don't know enough about it or 10.2 v. 10.1 issues to know how well it would work with 10.2. If the aquaterm/pgplot demos don't work, I'd guess it's a more serious problem and that the binary installer may not work. Is the Fink / X-Windows / PGPLOT installation procedure too big of a hassle? I know that can work, and that athena will work too. I also believe that the instructions are simpler for 10.2 than 10.1 (especially with respect to getting perl/Tk to work), but haven't tried this myself. I'm copying this message to the ifeffit mailing list, hoping that someone else may have better answers to these questions. How necessary is a complete binary installer for Mac OSX? Thanks, --Matt

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RE: [Ifeffit] athena 0.9.012 + an updater utility
by Kelly, Shelly D. 30 Jan '03

30 Jan '03

Hi Bruce, I believe that the set edge step button is broken in Athena when the Clnorm background is used. To reproduce this error: 1 read in a xmu data set 2 set the background to clnorm and plot the normalized bkg. 3 push the set step height button and change the value. 4 replot the background and watch the set height value go back to the original value. If you need a project file let me know. Shelly > -----Original Message----- > From: Bruce Ravel [mailto:ravel@phys.washington.edu] > Sent: Thursday, January 30, 2003 10:21 AM > To: ifeffit mailing list > Subject: [Ifeffit] athena 0.9.012 + an updater utility > > > > Hi folks, > > I just release a new version of Athena, a new Windows executable for > Athena, and a new source code tarball. You can find them in the > normal places. There are only two new things, but they are both > pretty important. > > 1. Fixed a serious bug in how Athena handles filenames with long, > similar names. There was a problem in how Athena was translating > long filenames into ifeffit group names that could lead to very > broken behavior. > > 2. For unix and Mac users, I wrote a perl script called > "horae_update" which gets installed upon installation into > /usr/local/bin (or wherever athena and artemis go). The purpose > of this script is to automate updating athena and artemis to the > very latest versions. It fetches the latest source code tarball > from the web, unpacks it, builds it, and (if you run it as root) > installs it. Very handy. > > The updater is only loosely tested, so I am eager for feedback > from people, and particularly from the OSX crowd. It seems to > work ok for me and makes updating the codes a snap. > > I plan to write a similar program for Windows users soon. My plan > is to have a button in the Ifeffit menu on the Start Menu that > says something like "Update Athena and Artemis". Clicking it will > fetch and install the latest Windows executables. I'll make an > announcment here when it is ready. > > Regards, > B > > > > -- > Bruce Ravel ----------------------------------- > ravel(a)phys.washington.edu > Code 6134, Building 3, Room 222 > Naval Research Laboratory phone: > (1) 202 767 5947 > Washington DC 20375, USA fax: > (1) 202 767 1697 > > NRL Synchrotron Radiation Consortium (NRL-SRC) > Beamlines X11a, X11b, X23b, X24c, U4b > National Synchrotron Light Source > Brookhaven National Laboratory, Upton, NY 11973 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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athena 0.9.012 + an updater utility
by Bruce Ravel 30 Jan '03

30 Jan '03

Hi folks, I just release a new version of Athena, a new Windows executable for Athena, and a new source code tarball. You can find them in the normal places. There are only two new things, but they are both pretty important. 1. Fixed a serious bug in how Athena handles filenames with long, similar names. There was a problem in how Athena was translating long filenames into ifeffit group names that could lead to very broken behavior. 2. For unix and Mac users, I wrote a perl script called "horae_update" which gets installed upon installation into /usr/local/bin (or wherever athena and artemis go). The purpose of this script is to automate updating athena and artemis to the very latest versions. It fetches the latest source code tarball from the web, unpacks it, builds it, and (if you run it as root) installs it. Very handy. The updater is only loosely tested, so I am eager for feedback from people, and particularly from the OSX crowd. It seems to work ok for me and makes updating the codes a snap. I plan to write a similar program for Windows users soon. My plan is to have a button in the Ifeffit menu on the Start Menu that says something like "Update Athena and Artemis". Clicking it will fetch and install the latest Windows executables. I'll make an announcment here when it is ready. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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minimize function
by Kelly, Shelly D. 28 Jan '03

28 Jan '03

Hi, I would like to use the minimize function to fit a line to some data points. I could not find documentation on the r-square factor that is referred to as the confidence level for the fit. Thanks Shelly

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Ifeffit 1.0076
by Matt Newville 27 Jan '03

27 Jan '03

Happy New Year Everyone, I've just posted a new release of Ifeffit: 1.0076. This has many small fixes and added features, including: - fixed plotting bug in which all legends were not always shown - added 'unguess' command - added 'window' command (generate an FT window without actually doing the FT) - fixed a bug in reading 1-row data files - allow (consistently) '&', ':', and '?' in variable and group names - added the math functions nofx(), join(), and slice() for array manipulations - further tweaks to configuration procedure. There are a few more details are in the ChangeLog. I hope to get changes to the Reference Manual posted within a week. The Windows installer now includes the current versions of Athena, Artemis, Atoms, SixPack, and GIFEFFIT. I have not tried this version on Mac OS X. The installation using Fink and PGPLOT (not to mention Perl/Tk for Athena and Artemis) on Mac OS 10.2 seems especially fragile. For future work, the changes at the top of my list include: - adding an automated way to have feffit() apply more than 1 k-weight at a time, to help overcome the k-dependent biases due to the high correlations of XAFS parameters. - trying to improve the pre-edge subtraction and normalization algorithms. - getting the docs up-to-date. - working on changing the interface of Feff6 so that it can be included in Ifeffit. The still seem to be unresolved issues with QEXAFS data, and probably other things that should be done. Suggestions for improvements or added features are welcome. In fact, I'd like to ask everyone to think about what features you'd like to see added or changed. Thanks, --Matt Newville

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athena 0.8.010
by Bruce Ravel 15 Jan '03

15 Jan '03

Hi folks, The release I made of my software last week was riddled with problems. While I think the Windows executable was ok, the source code tarball for use on linux and Mac OSX was horribly broken. Thanks to helpful interactions with Paul Fons, Jeff Terry, and Shelly Kelly I think I have ironed out all the problems. This release, therefore, is mostly a bug-fix release. The only new bit of functionality this time involves some changes to how derivative spectra are plotted. There are no changes to artemis in this release. The source code and the new Windows executable for athena 0.8.010 are in their normal locations. If you use the source code, you should be running at least version 1.0072 (which dates all the way back to June 2002) of ifeffit. If you ifeffit is older than that, you should upgrade to the latest from Matt's website before installing athena and artemis. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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trouble, trouble, trouble
by Bruce Ravel 10 Jan '03

10 Jan '03

Hi folks, The release I made yesterday seems to be the buggiest one I have released in quite some time. I have been getting lots of reports of problems with the latest source code tarball. Sigh. I am working on a new release -- hopefully things will be looking better on Monday. If anyone needs a copy of the previous release, you can grab it at http://leonardo.phys.washington.edu/~ravel/software/exafs/packages/horae-00… The entire archive of old versions is at http://leonardo.phys.washington.edu/~ravel/software/exafs/packages/ Sorry for the confusion and thanks especially to Jeff Terry, Paul Fons, and Shelly Kelly who have been very generous with their time and their useful bug reports. Regards, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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Athena 0.8.009
by Bruce Ravel 09 Jan '03

09 Jan '03

Hi Folks, Since it has been almost a month since my last release of software and since I expect to be busy for the next couple of week, I decided to release all the stuff I worked on over the holidays. There are no changes to Artemis this time, but lots of changes to Athena. A new tarball and a new Windows executable for Athena are on my website. Lots of bug fixes this time, so I recommend that everyone upgrade. Check out the change log on my web page for all the new stuff. The highlights are 1. Fixed the problem involving long file names. Now the group name used by Ifeffit is constrained to 8 characters and is different from the string displayed in the groups list. This solves a number of recent complaints about mysterious misbehavior. It has the additional benefit of allowing you to change the string displayed in the group list to something that has spaces or non-alphanumeric characters. 2. Implemented a "recent files" feature under the File menu. This remembers the 8 most recent files that you read into Athena and allows you to reread them quickly. It uses an external file, so it "remembers" between sessions with Athena. 3. Added a dialog accessible from the Plot menu which allows you to quickly and easily set the y-offset values for marked groups in a way that is suitable for stacked plots. There are several other bug fixes and small improvements. And the documentation lags ever farther behind -- sigh! Extra thanks this time around to Dale Brewe. He pointed out an alarming number of problems one December afternoon while I was working at his beamline. I think I fixed all of them. Regards, B P.S. I have not yet addressed the problem in Artemis which Michel Schlegel pointed out earlier this week. What's mpre, command line users will notice that Artemis spits up a cryptic warning about an "Un-named file" as it starts up. I believe that warning can be safely ignored. -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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athena, OS X, and Apple's new X11
by Jeff Terry 09 Jan '03

09 Jan '03

Hi All, I just wanted to let everyone know that Artemis, Athena, and tkAtoms work with Apple's new implementation of X11. Jeff

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a problem with windows on Windows ...
by Bruce Ravel 07 Jan '03

07 Jan '03

Hi all, Michel Schlegel pointed out that there is a problem in the most recent version of Artemis wherein the Fourier transform window does not get properly displayed. Oddly, I could only reproduce this problem on Windows and not on my linux machine. So, for you Windows users -- you will either have to live without plots of window functions until I can get around to finding and fixing the bug or you may want to consider not upgrading Artemis until the next version. This window problem does *not* seem to be an issue for Athena either on Windows or on linux. When I release a version of Artemis that fixes this problem, I will, as usual, make an announcement here. Happy New Year! B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 222 Naval Research Laboratory phone: (1) 202 767 5947 Washington DC 20375, USA fax: (1) 202 767 1697 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b, X24c, U4b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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