October 2016 - Ifeffit - millenia.cars.aps.anl.gov

athena LCF issue
by fred.mosselmans＠diamond.ac.uk 08 Nov '16

08 Nov '16

Dear Bruce, I realise you may be travelling soon , This is not a very serious bug as I have work rounds. I was demonstrating linear combination fitting in Athena using the gold thiobacteria example this week. I am using 9.25 on a windows 7 computer. I read in all the data from the cynaobacteria project file I mark 5 or 6 standards In the LCF tab I use marked groups, untick the sum weights to 1 option leaving just the all weights between 0 and 1 option selected. I pick a sample spectrum eg 4.73 I select fit all combinations It rolls through them and reports the apparently correct results but an error message is reported: Redundant argument in sprint at C:/... /AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena/LCF.prm line 780, <F> line 122 Clicking any of the answers in the combinatorics tab brings up this error again. If I do a fit of lot of spectra using the same set of standards, I get a similar error message except this time it is line 906 and some of the combined spectra don't plot properly until you refit them as a single spectra in the standards tab I attach a log file but not a project as I assume you can find that on github! Regards Fred J.F.W. Mosselmans Prinicipal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Larch mback error report
by Sean Fackler 02 Nov '16

02 Nov '16

Dear Larch developers (Matt), I believe I found an error in the mback function where I get a NameError saying the name ‘f1_chantler’ is not defined. I found that simply adding f1_chantler to the larch_plugins.xray import section in mback.py fixes the problem. I have included the modified mback.py code, my input data (SigScan226827.txt), project code (mback_test.py), and the error I received (mback_error.txt). I am running python 2.7 with anaconda as my manager, macOS Sierra v10.12, on a mid-2015 15” MacBook pro. I hope this report is correct and helpful. Regards, Sean Sean Fackler, PhD Joint Center for Artificial Photosynthesis Lawrence Berkeley National Lab 1 Cyclotron Rd Mail Stop 30R0205 Berkeley CA, 94720 Mobile: 609-613-8734

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Athena and "norm" file groups
by Mike Massey 19 Oct '16

19 Oct '16

Hi everyone, Apologies if this has been covered before, I'm just getting around to upgrading to Demeter. I have a bunch of old project files with a mishmash of data from different sources, and I'm having trouble getting them to work fully with the new software. Any group with a data type of "xmu" (energy space) seems to work as expected, but any group with a data type of "norm" (normalized data) doesn't seem to work properly when it comes to spline or post-edge background subtraction (which is handy if I want to do LCF, for example). Is this a bug or a feature? Has anybody yet developed a workaround? Any thoughts or advice would be greatly appreciated. The ultimate workaround is to use different data, but I'd like to use existing projects if possible (saves a lot of time and brain damage). Cheers, and thanks! Mike

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General question
by Dimitar Popmintchev 14 Oct '16

14 Oct '16

Hi All, I would like to ask, after a fit (in Artemis) which column in the output file gives the uncertainty for peaks position dR (R+/-dR i.e. 3+/-0.02 Angstroms) ? Is there additional information that could be extracted from wavelet transform ? Thank you. Dimitar

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Artemis crash on import
by George Sterbinsky 13 Oct '16

13 Oct '16

Hello, I am using Demeter on Mac OS X 10.11.6. I recently updated Demeter to version 0.9.25 using the command "sudo port upgrade demeter". In Artemis, choosing the menu item "open project or data" causes Artemis to crash. I've pasted the information printed to the terminal below. This includes everything printed to the terminal from the point at which Artemis was started. Please let me know if any additional information would help in resolving this issue. Thank you, George $ Artemis 2016-10-13 14:51:18.097 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data gnuplot: unable to open display '/private/tmp/com.apple.launchd.U9mQNzlNS1/org.macosforge.xquartz:0' gnuplot: X11 aborted. 2016-10-13 14:51:22.884 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:22.885 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.096 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.097 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:23.443 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:25.277 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:25.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:26.809 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:27.278 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.221 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:28.555 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:51:34.322 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:30.445 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:30.446 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:32.009 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:34.926 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:38.016 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:38.017 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data Oct 13 14:52:38 perl5.24[20180] <Warning>: Window Server is not available. Oct 13 14:52:38 perl5.24[20180] <Warning>: Window Server is not available. Segmentation fault: 11

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Re: [Ifeffit] Installing Demeter on Mavericks
by Katy Evans 13 Oct '16

13 Oct '16

Dear All, Apologies - its another mac question! I went through the instruction on installing Demeter on Mac OSX, installed Macports successfully. I then tried to install Demeter, and got an error message. So I installed xorg server separately, no error message, and then tried Demeter again, with the following command and response. I noticed when installing xorg that the pgplot was pgplot +gcc49, not +gcc48, which the Demeter installation seems to be looking for. Athena opens and does stuff but no plot window. Has anyone experienced and resolved this? Thanks, cheers, Katy $sudo port install demeter-devel ---> Computing dependencies for ifeffit ---> Fetching distfiles for ifeffit Error: Install pgplot +gcc48 Error: org.macports.fetch for port ifeffit returned: pgplot +gcc48 not installed Please see the log file for port ifeffit for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_ifeffit/ifeffit/main.log Error: Unable to upgrade port: 1 Error: Unable to execute port: upgrade ifeffit failed

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porting wxpython-3.0.2.0 to python35
by Karl-Michael Schindler 09 Oct '16

09 Oct '16

> Date: Tue, 4 Oct 2016 07:57:37 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] ifeffit on Mac OS X: fink package > Message-ID: <CA+7ESboGXfXnNWqaKYxSFHsUuwq7rG3E91x0_1x2C1E8bEesMw(a)mail.gmail.com> > > I've seen notices of issues > with wxPython too, and it looked like a more serious problem than the > „non-approved developers" thing. In fink, once i had the package wxwidget fixed, wxpython-3.0.2.0 worked without any change with Python27. I also tried to build wxpython-3.0.2.0 with Python35, but i got stuck with 27 → 35 issues, where os.environ.has_key("WXWIN") would need to be replaced in wxPython/config.py. I was able to fix 4 small issues in wxPython/config.py, but would need some advice/support with the one above. Any chance? Michael.

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wxwidgets on Mac OS X 10.12
by Karl-Michael Schindler 09 Oct '16

09 Oct '16

Hi Building version 3.0.2 wxwidgets on Mac OS X 10.12 required the following patches. 1 & 2 should apply to any way of building: 1) Remove the references to QuickTime/QuickTime.h perl -pi -e 's|#include <QuickTime/QuickTime\.h>||' src/osx/core/bitmap.cpp perl -pi -e ‚s|#include <QuickTime/QuickTime\.h>||‘ src/osx/carbon/dataobj.cpp 2) add - -disable-mediactrl to the configure parameters. 3) All treatments of the libraries libwx_…media.…dylib had to be removed. This could be specific to packaging with fink. The full package description is here: http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.9-libcxx/stable/main/f… The diff for 10.12 is here: http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.9-libcxx/stable/main/f… After this mods wxpython was happy as well. Michael

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Re: [Ifeffit] ifeffit on Mac OS X: fink package
by Karl-Michael Schindler 07 Oct '16

07 Oct '16

Hi Matt > Am 04.10.2016 um 19:00 schrieb ifeffit-request(a)millenia.cars.aps.anl.gov: > > Message: 3 > Date: Tue, 4 Oct 2016 07:57:37 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] ifeffit on Mac OS X: fink package > Message-ID: > <CA+7ESboGXfXnNWqaKYxSFHsUuwq7rG3E91x0_1x2C1E8bEesMw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Michael, > > Out of curiosity, is there a reason to prefer Fink over MacPorts (which has > Ifeffit and Demeter already available)? I wouldn't say that MacPorts or > wxPerl on MacPorts are perfect, but it does work for many of us. > > As an aside, if you built ifeffit, building Larch should be much easier, > assuming that the scientific python stack is available for Fink. It's > basically "python setup.py install". Or, one can install Anaconda Python. > > Also, Bruce and I have been working on getting to the point where Demeter > uses Larch by default. Some of this is at > https://github.com/bruceravel/demeter/pull/40, and Athena with Larch is > working for me on Mac OSX. I think we have the basic functionality > needed, and are at the testing and tweaking stage. > > Making a MacPorts (and/or Fink?) installer for Larch looks like it would be > pretty easy, and that could further simplify distribution for OSX. That > is, Anaconda Python is very good, but means that one has to install Demeter > with MacPorts and also Larch from an Anaconda channel. Using a single > packaging system so that "<something> install demeter" installed Larch + > Demeter would certainly be easier. I think that we'd probably be better > off choosing one of the "port Unix tools to OSX" systems. I don't have a > strong opinion, and it's been awhile since I used Fink. > > Opinions on Fink vs MacPorts (or the others) would be helpful. > > Thanks, Regarding Fink vs MacPorts: Depending on the package, MacPorts is sometimes more recent package descriptions than Fink and has probably closer connection to apple. I have not much experience with homebrew and larch is my first try with anaconda. In my opinion, the biggest difference is that Fink uses its own tree to install things (default /sw), whereas MacPorts uses /usr/local or /opt, which means that fink has a cleaner separation of what is installed through it or by other means. With a large number of packages, this gives Fink an advantage, when it comes to weeding out interfering stuff installed by other means, like from a disk image. In reverse, deleting all of /sw gives you a pretty clean table to restart Fink. Since MacPorts and Fink do not mix well, you have to make a decision at some point and the reason above (many packages) made me choose Fink. I started to use it as some sort of sophisticated note book, when i ported some software and with time i became package maintainer with commit right. My main activities are Pascal, tools for Fortran (in particular of type old school) and some science packages. Until now, i was always able to fix most problems, i encountered. That’s why I stick to Fink. For me, changing to another one, does not yield a big advantage. Therefore, the cost and effort of a change weigh more. My background/intentions: My PhD student uses demeter on Windows, but i would like to be able to have a look at the results on my Mac. In the recent past, i had goes at larch and demeter, but got stuck at various points with either outdated perl or python packages as well as a wx package not yet building on the latest OS X (10.12). With larch I made some progress using anaconda, but the resulting GUI apps crashed with 10.12. Maybe a code signing issue. My idea is to mimic the installation by anaconda and/or MacPorts as good as possible with Fink in order to get a working package. In detail, I think that i need to carefully check the versions of the dependencies and update fink packages accordingly. I am not much of a hero when it comes to Python or Perl, but sure enough, if I can contribute to larch/demeter i will report it. I do not have any objections against MacPorts of Homebrew, but consider the scripts within the fink package descriptions obvious enough that it should not be a big problem to port them to MacPorts or Homebrew for someone, who is familiar with those systems and i am willing to help. No interest in a holy war of any kind ;-) The python packages look easier to me. I got the impression that python 2.7 based larch is the most stable one. Therefore, i think to start with that one and once that is at least working continue on the python 3.5 based one. Correct me if i am wrong on this. I am afraid that Demeter is a heavier task, since the current version of perl on OSX is 5.18.2. Not sure yet, how to proceed there. Setting up the package description for a newer version of perl sounds like overkill for the amount of time and effort i can contribute, but time will show. I would be happy to have a working „fink install demeter“. I have some background in creating Fink based GUI applications and even disk images with standalone applications using Makefiles. But one step after the other. Sounds like this is a vivid and comforting community, where i would enjoy to contribute. Michael. P.S. This became a long post.

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ifeffit on Mac OS X: fink package
by Karl-Michael Schindler 07 Oct '16

07 Oct '16

Hi all. I just want to announce that ifeffit is now available as package with fink. All you need for using ifeffit is the command: fink install ifeffit I know that xraylarch is to be used as successor and i am working on it as well as on demeter, but i did not manage to build it so far. Michael.

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