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

How to use Larch as backend for Athena and Artemis on Windows
by ASAKURA, Hiroyuki 17 Aug '17

17 Aug '17

Dear all, I would like to use the latest Larch as backend for Athena and Artemis on Windows to handle hundreds of XAS data (, hopefully). But, I'm stuck. I would appreciate any comments and suggestions. Matt announced it is now possible on this list, but I still cannot do it on Windows. [Ifeffit] Larch 0.9.33 http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009091.html > The "server mode" for Athena and Artemis now works on all platforms and I > strongly encourage everyone to use this over the ifeffit back end. Here is what I did. Environment: Windows 10 Pro (Japanese) Demeter 0.9.25 (via official website) Python 3.6 (official distribution) 1. Installation of the latest Larch > git clone https://github.com/xraypy/xraylarch.git (sha1: 5a372cfe1368a8ac10c2ebfc5bef4e9a9a325f6d) > cd xraylarch > python setup.py install # Some dependency related to XRD is not fulfilled. 2. Start Larch server > cd %LOCALAPPDATA%\Programs\Python\Python36\Scripts > python larch_server start larch_server port=4966: started I found a parameter of peakfit backend in demeter.ini and changed to larch, but did not work (as expected). In the dathena.log, Athena still uses ifeffit as backend. > perl version: v5.18.2 > backend: ifeffit Should I compile Demeter package by myself to use the Larch backend? Or, is there any "switch" to use Larch? Thanks in advance, ASAKURA, Hiroyuki -- ASAKURA, Hiroyuki (Ph.D) T. Tanaka Lab., ESICB, Kyoto University, Japan asakura(a)moleng.kyoto-u.ac.jp http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/

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How to use Larch as backend for Athena and Artemis on Mac (Re: Ifeffit Digest, Vol 174, Issue 8)
by Luke Higgins 17 Aug '17

17 Aug '17

Dear All, Following the excellent guide that Hiroyuki & Bruce gave for running larch on Demeter on Windows (Ifeffit Digest, Vol 174, Issue 8). The following steps worked for me to run larch/Demeter on MacOS (Sierra 10.12.6). 1) Install Demeter using the advice from: https://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.h… 2) Installed Anaconda and larch using the following guide: http://cars.uchicago.edu/xraylarch/installation/index.html (Python & larch from source is fine: but then use Hiroyuki’s step 3&4 advice [attached below]) 3) In a new terminal window check larch by: larch --version You should see "larch command-line version 0.2". 4) Running larch and Demeter, run in a new terminal window: larch --port=4966 –rc 5) Open Demeter.pm in a text editor (which for me was buried in: /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter.pm) and change line 44 to: $ENV{DEMETER_BACKEND} ||= 'larch'; 6) This has changed both Athena and Artemis to using larch – haven’t fully tested yet, but looks good. Best Wishes, Luke (from Hhiroyuki, installing python and larch from source files:) 3. Install unofficial Numpy and Scipy, Python libraries 3-1. Download numpy‑1.13.1+mkl‑cp36‑cp36m‑win_amd64.whl and scipy‑0.19.1‑cp36‑cp36m‑win_amd64.whl via http://www.lfd.uci.edu/~gohlke/pythonlibs/ 3-2. pip install numpy-1.13.1+mkl-cp36-cp36m-win_amd64.whl 3-3. pip install scipy‑0.19.1‑cp36‑cp36m‑win_amd64.whl 4. Install Larch and its dependencies 4-1. Start a command prompt 4-2. git clone https://github.com/xraypy/xraylarch.git 4-3. cd xraylarch 4-4. pip install lmfit 4-5. pip install h5py 4-6. pip install pillow 4-7. pip install requests 4-8. pip install sqlalchemy 4-9. pip install matplotlib 4-10. pip install pypiwin32 4-11. pip install wxpython 4-12. pip install wxmplot 4-13. pip install wxutils 4-14. python setup.py install 4-15. larch --version 4-16. You will see "larch command-line version 0.2". Note: I installed Larch dependencies except for pyFAI, CifFile, fabio, tomopy, scikit-image.

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Artemis can't open project file and crashes
by Michelle Hammerton 11 Aug '17

11 Aug '17

Hello, I wonder if anyone can help me. Artemis (version 0.9.25) is unable to open the most recent project files that I have created and just crashes. These files also can't be opened on a different computer. I get the following message in the dartemis log file: You must define a method name at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\vendor\lib\Class\MOP\Mixin\HasMethods.pm line 96 Class::MOP::Mixin::HasMethods::has_method('Class::MOP::Class::Immutable::Moose::Meta::Class::__ANON__::SERIAL::1=HASH(0xb49ab58)', '') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 424 Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x10140bd0)', ' :') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 447 Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x10140bd0)', 'space = I 41/a m d :2') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 382 Demeter::Atoms::read_inp('Demeter::Atoms=HASH(0x10140bd0)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 198 Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0x10140bd0)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\racrw\atoms.inp') called at accessor Demeter::Atoms::file (defined at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\Atoms.pm line 202) line 10 Demeter::Atoms::file('Demeter::Atoms=HASH(0x10140bd0)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Atoms\Xtal.pm line 667 Demeter::UI::Atoms::Xtal::open_file('Demeter::UI::Atoms::Xtal=HASH(0x1afa1b38)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm line 1388 Demeter::UI::Artemis::make_feff_frame('Wx::Frame=HASH(0x1522a180)', 'C:\Users\mhammer1\AppData\Roaming\demeter\stash\_dem_aaczdzkl\feff\qynwh\atoms.inp', 'CuCr2O4_I41-amd2_2006190') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis\Project.pm line 351 Demeter::UI::Artemis::Project::read_project('HASH(0xf7cdf60)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm line 996 Demeter::UI::Artemis::OnMenuClick('Wx::Frame=HASH(0x1522a180)', 'Wx::CommandEvent=SCALAR(0x15dc4558)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\lib\Demeter\UI\Artemis.pm line 440 Demeter::UI::Artemis::__ANON__('Wx::Frame=HASH(0x1522a180)', 'Wx::CommandEvent=SCALAR(0x15dc4558)') called at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 50 eval {...} at C:\Users\mhammer1\AppData\Roaming\DemeterPerl\perl\site\bin\dartemis.bat line 50 So I guess I need to define a method name? What could it be and how do I define it? Thank you for your help (in advance!) Best wishes, Michelle *Michelle Hammerton Msc.* University of Amsterdam <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Demeter on Windows with Inkscape (and possibly other programs)
by Bruce Ravel 10 Aug '17

10 Aug '17

Windows users: I got an interesting bug report today from a fellow who develops a popular open source program for vector graphics editing (Inkscape). Apparently, there is a problem in Demeter's installer that has an impact on the ability of that program (and possibly others) in accessing system font files. The issue with Inkscape is described here: https://github.com/bruceravel/demeter/issues/51 I mention this here on the mailing list in an effort to help the folks who maintain Inkscape. If you use Demeter and Inkscape on your Windows machine, there is a problem and it is my fault :( The simplest solution is to uninstall Demeter, then continue using Inkscape. If that's not true or if someone needs a better solution right now, post here and I will help you work out a solution. I think the real fix to the problem is simple and I will work on a new installer this month. Cheers, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Athena Crashing on Mac
by Daniel Austin Sheffield Uni 04 Aug '17

04 Aug '17

Hi, I emailed relatively recently about Artemis crashing on my MacBook Pro. This is the email i sent: 'I was using Artemis on Mac and it crashed. Now when i try to reopen Artemis it attempts restore what i was doing from an autosave file but it becomes unresponsive and is just stuck on the screen posted below. Does anyone know how i can fix it? Do i have to uninstall and then reinstall the software? i have left it running for over an hour but it still hasn’t worked. Thanks for any help’ Now the exact same thing is occurring with Athena. One of the replies from the previous email instructed me to remove parts of the programme code. I did so an Artemis worked perfectly after, i just needed to save often. The full email that instructed me on this can be found below: Hi Daniel, I had a similar issue, but my solution hasn’t been put up yet on the list: With respect to the error that Katherine Davies reported (02/16/2016; RE: [Ifeffit] problem with Artemis crashing on mac), I came across the same problem when running Artemis on Mac. I believe this issue is caused by a piece of code found in “artemis.pm” (Demeter/UI/artemis.pm) line 512-521: 512 sub process_argv { 513 my ($app, @args) = @_; 514 if (Demeter->co->default("artemis", "autosave") and autosave_exists()) { 515 import_autosave(); 516 } elsif ($args[0]) { # and -e $args[0]) { 517 my $file = File::Spec->rel2abs( $args[0] ); 518 read_project(\%frames, $file) if Demeter->is_zipproj($file, 0, 'fpj'); 519 }; 520 }; I think the error is due to not shutting down the program correctly causing this code to fail. A fix is to comment out lines 514-516 & 519, save the file and reboot Artemis (to edit artemis.pm you will need to make the file writable)– thus getting you past startup and allowing you to turn off the autosave settings from within Artemis as suggested. Put the code back as it was after you have finished. Hope this helps. Best, Luke Higgins I tried searching for similar code in the Athena programme but couldn’t find it. Does anyone have a similar solution, or any solution, to this problem? Thank you so much

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Artemis Crashing
by Daniel Austin Sheffield Uni 02 Aug '17

02 Aug '17

Hi, I was using Artemis on Mac and it crashed. Now when i try to reopen Artemis it attempts restore what i was doing from an autosave file but it becomes unresponsive and is just stuck on the screen posted below. Does anyone know how i can fix it? Do i have to uninstall and then reinstall the software? i have left it running for over an hour but it still hasn’t worked. Thanks for any help, Daniel

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working at the lanthanide K-edges: question about amplitude reduction factors
by Bone, Sharon Elizabeth 28 Jul '17

28 Jul '17

Hello- I recently collected some Nd K-edge EXAFS at APS (~43 KeV). I've started fitting the data and am looking for S02 values in the literature to compare to my own (especially since my fitted S02 values- to two Nd reference materials for which I know coordination numbers- are outside of the typical range of 0.7 - 1), but I haven't found any reported. Has anyone worked at the lanthanide K-edges? Could you point me to a reference for S02? Thanks! Sharon

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Postdoc
by mathieu le meur 24 Jul '17

24 Jul '17

Hello I am very interested with the postdoc doc position with Corwin H. Booth Unfortunately, the link is not working and I cannot apply. Can you help me? Thanks, Mathieu. Get Outlook for Android<https://aka.ms/ghei36>

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LBNL Postdoctoral Fellow Position
by Corwin H. Booth 21 Jul '17

21 Jul '17

Greetings all! I have just posted for a new Postdoctoral Fellow position to work with me at LBNL on projects with the Actinide Chemistry Group here and with Prof. Eric Schelter at U. Penn. Most of the work is to perform and analyze XAFS data. Please take a look at the official posting and apply if you are interested and meet the minimum qualifications. Here is the posting: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=83928 <https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=83928> Very best, Corwin -- Corwin H. Booth Chemical Sciences Division Lawrence Berkeley National Laboratory MS 70A-1150 1 Cyclotron Rd. Berkeley, CA 94720-8175 voice: 510-486-6079 FAX: 510-486-5596 Email: chbooth(a)lbl.gov Web: http://lise.lbl.gov/chbooth/

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Trouble in running Artemis in Mac
by Chang-wook Lee 13 Jul '17

13 Jul '17

I’m using Artemis in Mac. I got a trouble on running the software. Once the Artemis shut down by accident, (during import .inp file), the problem occurred. When I reopen the Artemis, It tries to restore previous file but it never worked. I uninstalled and reinstalled it several times but I can only see same unlimited loading screen… Athena works well. Thanks, Changwook

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