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

macports instructions
by Bruce Ravel 29 Nov '16

29 Nov '16

Hi all, In light of recent questions about the MacPorts package, I have updated the Mac installation instructions at the Demeter website. This page: http://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.ht… combines the basic instructions and includes a troubleshooting section that covers the "libcxx" issue. The main Demeter web page now links to that page. If some of you Mac users could give the new document a read and provide any suggestions for clarification or improvement, I would be grateful. Cheers, Bruce -- 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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Problems with gnuplot graphics on Mac OS 10.12.1
by Paul Fons 29 Nov '16

29 Nov '16

Hi All, I have installed demeter using Macports on 10.12.1 and while hephaestus seems to run normally, athena has some trouble with graphics. The usual athena perl based panel shows up just fine, but upon loading some data, there is always an error when gnuplot is invoked to plot graphics (as reproduced below). It would seem that the command “set” is missing the first letter. Does anyone have a suggestion as to what to check to fix this? Axion:perl5.24 $ use_macports.sh athena gnuplot> et label '{/Symbol \305}' at 400.79999,853.0387 center front textcolor ls 12 ^ line 0: invalid command

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error on installing demeter on MacOSX 10.9.5
by christophe den auwer 26 Nov '16

26 Nov '16

Dear all, I am trying to install Demeter on OS 10.9.5 and I am stuck! I installed Xcode 6.2 fine with the licence agreement and everything. Then I installed MacPort 2.3.5 fine as well. I also checked updated version and everything worked fine. Then I tried to install Demeter and got stuck with the following lines : Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.9.0_0+universalError: Failed to install libcxx Please see the log file for port libcxx for details: Error: Processing of port demeter failed I attached to my message, if of any use, the full procedure and feedback from terminal window. If someone could help that would be really great!!! Thanks a lot Christophe ------------------------------------------------- Christophe Den Auwer Professeur Institut de Chimie de Nice Université de Nice Sophia Antipolis 06108 Nice, France 0492076362 christophe.denauwer(a)unice.fr --------------------------------------------------

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Larch 0.9.31
by Matt Newville 22 Nov '16

22 Nov '16

Hi Folks, Version 0.9.31 of Larch has been released. It can be installed using Anaconda Python 2.7 (the recommended approach on Windows and Mac OSX, and a fine choice on Linux too) with conda upgrade xraylarch The source kit can be downloaded from PyPI ( https://pypi.python.org/pypi/xraylarch/0.9.31) or installed on systems that already have Python installed with pip install --upgrade xraylarch Larch is in active development (at https://github.com/xraypy/xraylarch) and this release includes several important new features and capabilities. Some of these are still "in progress" and could greatly benefit from community inputs and comments at every level. In no particular order, some of the highlights include: > Larch server (bin/larch_server) is now much improved and more ready for Athena/Artemis to use. There are still some issues getting Larch Server + Athena working on Mac OSX, but Windows and Linux seem to be working. Using Athena/Artemis with Larch should still be considered experimental, but we're hoping that Larch will soon be the normal backend for Athena and Artemis. > Autobk background removal now calculates arrays for the uncertainty in chi (delta_chi) and mu_0 (delta_bkg) at each k or energy point. These are derived from the uncertainties in the fitted spline coefficients. It has long been argued that uncertainties from the background removal should dominate the uncertainties in chi(k), and so should be used included as the uncertainty in the fits to EXAFS data. Indeed, preliminary tests show that using these uncertainties in the fits does bring reduced chi-square much closer to 1. > Much better support for Python3. Larch is still only supported for Python2.7, mainly due to the dependency on wxPython which is not yet officially supported for Python3. Still, most parts of Larch are Python3 compatible, including the GUIs. If Python3 is a priority for you, let us know (here or on Github), and we'll try to make that happen sooner rather than later. > Support for dealing some X-ray Diffraction data has been added especially for the X-ray Fluorescence maps supported in the Larch XRF MapViewer. New GUI apps for viewing and working with 2D and 1D diffraction images are included in this release. These are the work of Margaret Koker, and are the beginning of support for XRD visualization and analysis in Larch. > XYFit, a GUI for XANES peak fitting has been begun, and can be used for simple sum-of-line-shapes. The abilities of XYFit are currently similar to Athena's peak fitting panel. There are missing important features, but development of this is very active with many features expected to be added over the next few months. The new GUI components should definitely be considered as experimental and ready for friendly comments, suggestions, and bug reports. These are not quite ready for production use yet, but we're hoping that you can help with feedback and suggestions. So, please consider giving these tools a try, and let us know what you think. --Matt Newville

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trouble installing deter on a mac
by justin park 20 Nov '16

20 Nov '16

Hello, I have followed the steps to install macports on my mac and it seems to be working. However when I went to port in demeter it start and fails rather quickly giving this error message. Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0+universal What do I need to do in macports to get it to properly fetch libcxx? Thanks, Justin

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Time reversibility of multiple scattering paths
by Inwood D. 18 Nov '16

18 Nov '16

Hi All, I've just been reading the paper with the following reference: Nashner, M. S.; Frenkel, A. I.; Adler, D. L.; Shapley, J. R.; Nuzzo, R. G. Structural Characterization of Carbon-Supported Platinum - Ruthenium Nanoparticles from the Molecular Cluster. J. Am. Chem. Soc. 1997, 7863, 7760-7771. In particular I was interested about the data analysis section on page 7763 (footnote 32) where the authors talk about time reversibility of multiple scattering paths. It is mentioned that the collinear DS path, in the fcc structure, (M - M(1) - M(4) - M) is time reversed, so has twice the degeneracy, but that the collinear TS path (M - M(1) - M(4) - M(1) - M) is not time reversed. Why is the DS path time reversible, but not the TS path despite the apparent 'symmetry' of the TS path? What makes a scattering path time reversible? Does time reversibility only apply to collinear paths or can it also apply to triangular paths as well? Thanks for your help, David David W Inwood PhD Researcher Chemistry University of Southampton Southampton, UK SO17 1BJ

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Athena crashing with "Larch_Server not found"
by Frederik Eistrup 14 Nov '16

14 Nov '16

Dear List, Recently installed Demeter on Ubuntu for a master's lab work at Bessy II (HZBerlin), with help from David Hughe's instructions (https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h…) When I run Athena ("dathena" in comand line) the interface window appears but command line has output: $ dathena Trying Larch server: /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4966 start Can't exec "larch_server": No such file or directory at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Larch.pm line 66. Later, when i try to import a data-file, column selection windows shows up as it should, but after i've chosen numerator and press OK, the whole Athena crashes. Message on terminal (sorry I know its massive...): Attribute (bkg_pre1) does not pass the type constraint because: Validation failed for 'LaxNum' with value 9997,000 at accessor Demeter::Data::bkg_pre1 (defined at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 258) line 7 Demeter::Data::bkg_pre1('Demeter::Data=HASH(0xd91e330)', '9997,000') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Defaults.pm line 48 Demeter::Data::Defaults::resolve_defaults('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 290 Demeter::Data::Mu::initialize_e0('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 270 Demeter::Data::Mu::put_data('Demeter::Data=HASH(0xd91e330)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 734 Demeter::Data::_update('Demeter::Data=HASH(0xd91e330)', 'all') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 648 Demeter::UI::Athena::IO::_group('Demeter::UI::Athena=HASH(0xbcd018)', 'Demeter::UI::Athena::ColumnSelection=HASH(0xd949d08)', 'Demeter::Data=HASH(0xd91e330)', 'HASH(0xd91a8e8)', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', 0, 0) called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 531 Demeter::UI::Athena::IO::_data('Demeter::UI::Athena=HASH(0xbcd018)', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', '/home/frederik/Desktop/Spectroscopy with Synchrothron Radiation/Praktikum_results/nanoXANES/Prakt_W_XANES_E_d70_1.log', 1, 0) called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 193 Demeter::UI::Athena::IO::Import('Demeter::UI::Athena=HASH(0xbcd018)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 862 Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0x9a617f0)', 'Wx::CommandEvent=SCALAR(0xc3a9480)', 'Demeter::UI::Athena=HASH(0xbcd018)') called at /home/frederik/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 784 Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0x9a617f0)', 'Wx::CommandEvent=SCALAR(0xc3a9480)') called at /home/frederik/perl5/bin/dathena line 31 eval {...} at /home/frederik/perl5/bin/dathena line 31 So, where is the problem? Can anyone helo with this? Made sure larch was installed through sudo apt-get install, but all stays the same. Thanks for any help! Frederik David Hughes' guide to Demeter Installation on Ubuntu ...<https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h…> bruceravel.github.io David Hughes' guide to Demeter Installation on Ubuntu¶ These instructions cover a non-root manual build of Bruce Ravel's Demeter package under Ubuntu 12.04. Found out that Athena

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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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port for demeter failure
by justin park 04 Nov '16

04 Nov '16

Hello, I have followed the steps to install macports on my mac and it seems to be working. However when I went to port in demeter it start and fails rather quickly giving this error message. Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.7.1_0+universal What do I need to do in macports to get it to properly fetch libcxx? Thanks, Justin

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Postdoc Position
by Mengling Stuckman 03 Nov '16

03 Nov '16

Hello, all, Thanks to Bruce for the support of posting spectroscopy-related positions! My advisor, Christina Lopano, (christina.lopano(a)netl.doe.gov) at DOE-National Energy Technology Lab (NETL), is looking for a post-doc, as a synchrotron geochemist. You can see more information about the position here: https://www.zintellect.com/Posting/Details/2710 You can also reference the following website for more DOE-NETL related positions: http://orau.gov/netl/applicants/current-opportunities.html Please let anyone who might be interested know. Thank you, Mengling -- Mengling Stuckman ORISE Research Fellow National Energy Technology Laboratory U.S. Department of Energy Pittsburgh, PA mengling.stuckman(a)netl.doe.gov Office: 412-386-7387

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Larch mback error report
by Sean Fackler 01 Nov '16

01 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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Smoothing aligned data in Athena
by Godfrey, Ian 29 Sep '16

29 Sep '16

Dear All, I have a bug to report when using the Athena data smoothing feature with aligned data. Exemplar project and log files are attached, along with a screenshot. I am running Windows 10 x64 with Athena 0.9.25 x64. Summary: When using the data smoothing feature in Athena with data that has previously been aligned using the alignment feature, the smoothing is performed on the non-aligned data, and the resulting, processed dataset is shifted in E. Recipe: Open Athena Import a dataset that has a reference channel Import a second dataset with reference Import a standard dataset, with a slightly off alignment wrt to the first two datasets (I imported all three from Athena projects, rather than raw datafiles) Use the alignment tool to align the reference channel of one of the datasets to the standard (I used the automatic alignment) Go to the smoothing tool. You can immediately see that the smoothed curve is in the wrong place for the aligned dataset. The dataset that wasn't aligned will appear correctly Many thanks, Ian ---- Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Re: [Ifeffit] problem in data processing in athena (Arkaprava Das)
by Abhijeet Gaur 24 Sep '16

24 Sep '16

Dear Arkaprava, Can you tell us from which beamline at RRCAT you have recorded this data. As far as I know the EXAFS beamlines BL-8 and BL-9 at RRCAT does not have this strange format. As Matt says it is definitely from a solid state detector data. You should consult the beamline scientist for other details about the data acquisition. With best wishes Abhijeet On Sat, Sep 24, 2016 at 12:31 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. problem in data processing in athena (Arkaprava Das) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Sep 2016 11:54:34 +0530 > From: Arkaprava Das <arkapravadas222(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] problem in data processing in athena > Message-ID: > <CAGJE4TqbXjnV3BN8M8BEL7kx61-yo9Vx0YuoyvjhF=hv-EAuTw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Respected Sir, > I am a research scholar in Inter university accelerator centre, new Delhi, > India. I am facing one peculiar problem in athena data processing. I have > attached the .xls file in the mail for Zr k edge which has been generated > in the beam line at RRCAT. when I import this file in athena it always > shows a question mark in the place of Chai (?) at the y axis. I am not able > to sort out this issue that why that question mark is coming. I have > attached the snapshot of plot window also. > > I shalll be highly obliged if yo kindly help me in resolving the issue. > > Yours sincerely > > Arkaprava >

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problem in data processing in athena
by Arkaprava Das 24 Sep '16

24 Sep '16

Respected Sir, I am a research scholar in Inter university accelerator centre, new Delhi, India. I am facing one peculiar problem in athena data processing. I have attached the .xls file in the mail for Zr k edge which has been generated in the beam line at RRCAT. when I import this file in athena it always shows a question mark in the place of Chai (ϰ) at the y axis. I am not able to sort out this issue that why that question mark is coming. I have attached the snapshot of plot window also. I shalll be highly obliged if yo kindly help me in resolving the issue. Yours sincerely Arkaprava

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Re: [Ifeffit] problem in data processing in athena (Arkaprava Das)
by fred.mosselmans＠diamond.ac.uk 24 Sep '16

24 Sep '16

Dear Arkaprava, The beamline writes a bizarre no. of zeros in to the file. Also there are no headers on the columns which is pretty poor IMO. If you remove most of the zeroes (I just used replace in Wordpad) Athena understands the file fine, though I couldn't tell what the columns were so as there are no headers, so just guessed 5 might be the data. I don't think it is given the y scale but hopefully this shows how to do it. I think saving the file to an extension usually used for excel is a pretty odd thing to do also. So this is when Bruce might say ask the beamline staff not to output such strange data format and life would be easier for you. Thanks Fred J.F.W. Mosselmans Prinicipal Beamline Scientist I18 Diamond Light Source Ltd Diamodn 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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Ni(I), Ni(II), and Ni(III) Reference XAS required
by mazhar iqbal 20 Sep '16

20 Sep '16

Hello Can some please provide me the standard XAS of Ni(I), Ni(II), and Ni(III). Thanks in advance

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artemis doesn't read user's epsilon(k)
by Victor Streltsov 18 Sep '16

18 Sep '16

Hi Bruce, Epsilon(k) input "A user specified values for measurement uncertainty" in Artemis does not change the default value determined by Ifeffit. It assumes that input is a value of 0. I've tried the latest Artemis versions for Windows and Linus and they both behave the same. Best regards, Victor Streltsov

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