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Issues reinstalling Larch, error creating desktop shortcut for macOS
by Lauren N. Pincus 04 Jan '22

04 Jan '22

Hi Matt, I'm having an issue with reinstalling Larch. I'm using macOS Catalina 10.15.7. I had Larch previously installed and it was working well, but found I was no longer able to open up XAS Viewer. The application would start and then quit. So, I removed Larch from my system and tried to reinstall it. I first used the mac installer but would get an error that the "Installation failed. The installer encountered an error that caused the installation to fail." I then tried the installation using the script in terminal. This appeared successful, but no desktop shortcut was created. I tried to create a desktop shortcut using larch -m but get the following error: (base) laurenpincus@lnp24mbp2020 ~ % larch -m Traceback (most recent call last): File "/Users/laurenpincus/xraylarch/bin/larch", line 5, in <module> from larch.apps import run_larch File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/__init__.py", line 52, in <module> from . import builtins File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/builtins.py", line 22, in <module> from . import io File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/__init__.py", line 39, in <module> from .specfile_reader import (str2rng_larch, read_specfile, open_specfile, File "/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/larch/io/specfile_reader.py", line 26, in <module> from silx.io.convert import write_to_h5, _is_commonh5_group ImportError: cannot import name '_is_commonh5_group' from 'silx.io.convert' (/Users/laurenpincus/xraylarch/lib/python3.9/site-packages/silx/io/convert.py) (base) laurenpincus@lnp24mbp2020 ~ % Thanks, Lauren Lauren Pincus, PhD NSF Earth Sciences Postdoctoral Fellow Princeton University Department of Geosciences

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Re: [Ifeffit] [Ext] Re: Problem in xrayLarch installation
by Jeffrey Terry 20 Dec '21

20 Dec '21

We’ve had to come up with a slightly different install plan for Windows users of our analysis package EXAFS Neo that is built on top of xrayLarch. We recommend a slightly different route using both conda and pip. You can read through out full recommended analysis route for xrayLarch in the Prerequisites section of our readme file at: https://github.com/laumiulun/EXAFS-Neo-Public We are pretty confident that the installation method given there works for xrayLarch installation on Mac, Windows, and Linux. Jeff Jeff Terry Interim Chair, Department of Social Sciences Professor of Physics Professor of Mechanical, Materials, and Aerospace Engineering Editor, Applied Surface Science Prairie Chapter Chair, AVS Illinois Institute of Technology 3101 S. Dearborn St. Chicago IL 60616 630-252-9708 Sent from my iPhone > On Dec 15, 2021, at 2:42 AM, Mauro Rovezzi <mauro.rovezzi(a)esrf.fr> wrote: > Dear Latif, > > Thanks for reporting this. Unfortunately `pip` is not able to correctly install all dependencies of Larch. The way to go is to install those dependencies via `conda`. > > Under Windows, this is achieved by running the script `GetLarch.bat` (https://raw.githubusercontent.com/xraypy/xraylarch/master/installers/GetLar…) This script will download and install a minconda distribution, plus install Larch in it. > > Seen you already have Anaconda installed, you could simply run the following commands from your Anaconda prompt: > > conda install -yc conda-forge wxpython tomopy scipy matplotlib scikit-image scikit-learn pymatgen pycifrw > pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch > > If this does not work, please, let me know. I have created a related Github issue in order to avoid such troubles in the future: > > https://github.com/xraypy/xraylarch/issues/333 > > Best, > Mauro > > On 2021-12-15 08:20, Latif Ullah Khan wrote: >> Dear Sir Madam, >> I hope you are doing well, I Latif Khan, working as a beamline scientist at XAFS beamline SESAME light source. I was using LARCH on my Anaconda python environment at window PC. Now I re-install and upgrade the Anaconda to python 3.9. I am trying to install the xrayLarch from Anaconda command prompt (python 3.9), using “pip install xraylarch” . However, it is not installing and give me an following error: >> If you kindly help me in this regard, I will be grateful to you. >> Thank you in advance >> Best regards >> Latif >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Re: [Ifeffit] Ifeffit Digest, Vol 226, Issue 9_Problem in wavelet code
by Latif Ullah Khan 20 Dec '21

20 Dec '21

Dear Matt Newville and Mauro, Many thanks for the kind reply and great support in installation of the XrayLarch through window. Unfortunately, I could not install through Anaconda prompt using command " conda install -yc conda-forge wxpython tomopy scipy matplotlib scikit-image scikit-learn pymatgen pycifrw pip install wxmplot wxutils lmfit asteval pyshortcuts pyfai xraylarch" as suggested by Mauro. Fortunately I succeeded to install through window command prompt using the source code. Now I am using through VS Studio code. I just adopted the code for wavelet transformation written by Matt Newville, however, I faced some problem in plotting the 2D CCWT image, I am sharing the code with input data and also the code. Its showing some error in following syntax, probably "imopts" has problem: plt.imshow(f.wcauchy_mag, win=1, label='Wavelet Transform: Magnitude', **imopts) plt.imshow(f.wcauchy_re, win=2, label='Wavelet Transform: Real Part', **imopts) If you kindly help me in this regard, I will be grateful to you. Thank you in advance Best regards Latif -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, December 15, 2021 6:08 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 226, Issue 9 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. Re: Problem in xrayLarch installation (Matt Newville) 2. Re: Any coorelation about 'white line" in K-edge XAS with oxidation states? (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Dec 2021 09:23:47 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: "Ifeffit-request(a)millenia.cars.aps.anl.gov" <Ifeffit-request(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem in xrayLarch installation Message-ID: <CA+7ESbqCSsM+==XmUgzkjzjPHTOJjfLRGw8JRDqN5CGUxzJCuQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Latif, Sorry for the trouble. As Mauro said, some of the packages needed (and pymatgen is one of these) are not super-well supported for installing with pip. FWIW, I agree that the needed combination of conda and pip is sort of unfortunate. But most of the "problem packages" are either Windowing systems (wxPython: that have been challenging to have consistent binary support on Linux is very challenging) or packages of scientific code written by and for scientists, some with excellent engineering support and some (like us!) with "less" support. Conda is a popular option for many of these. We try to support the simpler / more ubiquitous pip where we can. Anyway, that's basically why we have the binary installers and installation scripts. But also: thanks for the report and we are trying to clean up or at least document some of these kinds of issues where we can: https://github.com/xraypy/xraylarch/issues/333 --Matt

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Any coorelation about 'white line" in K-edge XAS with oxidation states?
by Marco Wang 16 Dec '21

16 Dec '21

Dear everyone: Ihave some questions about the interpretation of "white line", from anarticle (https://doi.org/10.1038/s41467-021-27116-8) and the figure was attached. In the article, it is said that “the sample was fully reduced to Ni (0) state at ~480 °C judging from the edge position and ‘white-line’ profiles”. First, we assumed that the metal was coordinated with the same anion. We all know that K-edge transition in 3d and 4d metalis' spin forbidden, so it may be inappropriate to conclude that the intensity of the "white line" is correlated with metals' oxidation states. But in other words, the probability for s→d transition may be proportional to thenumber of empty d orbitals, so it seems like if the the intensity of "white line" is higher, the oxidation state is higher. So, how should we correctly interpret the “white line” and edge energy from XAS spectrum of metals’ K-edge and L-edge? Thank you in advance for your time. Marco Wang

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Problem in xrayLarch installation
by Latif Ullah Khan 15 Dec '21

15 Dec '21

Dear Sir Madam, I hope you are doing well, I Latif Khan, working as a beamline scientist at XAFS beamline SESAME light source. I was using LARCH on my Anaconda python environment at window PC. Now I re-install and upgrade the Anaconda to python 3.9. I am trying to install the xrayLarch from Anaconda command prompt (python 3.9), using "pip install xraylarch" . However, it is not installing and give me an following error: If you kindly help me in this regard, I will be grateful to you. Thank you in advance Best regards Latif [cid:image001.png@01D7F194.F5C60C50]

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Re: [Ifeffit] XEOL
by Eugenio Otal 06 Dec '21

06 Dec '21

Dear Robert, sorry for the late reply, life... Brilliant suggestion! I will let you know the results if the proposal is approved. Best regards, euG If you can move between Nd L3 and Br K, why not stop at Nd L1 if you want to see if a Nd s-type initial state has any influence on the XEOL? You should not need to go up to Nd K. Some references: https://aip.scitation.org/doi/abs/10.1063/1.477320?journalCode=jcp https://iopscience.iop.org/article/10.1149/1.3211180 and a book chapter https://www.worldscientific.com/doi/10.1142/9789812775757_0015 On 2021-11-25 5:50 p.m., Eugenio Otal wrote: > Hi all, > I am planning XEOL measurements and I have a doubt. > My system is Nd coordinated to Eosin, tetrabromofluorescein. I want to > measure XEOL exciting on the Br K-edge (13.4keV) and the Nd > L3-edge(6.2keV) and measure the emission spectra of the dye and the > Nd. I just measured the emission of the Nd exciting at 530nm and it > worked perfectly. > My question is, I have access to Nd K-edge, is it worthy?to measure > XEOL at the K-edge? I am in the time limit to?request an?extra shift. > I would appreciate some bibliography. > Best regards. > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Larch 0.9.57
by Matt Newville 02 Dec '21

02 Dec '21

Hi All, Larch version 0.9.57 has been released and is available on PyPI ( https://pypi.org/project/xraylarch) It should now be installed by default using most installation mechanisms, and you may see a notice to update if running xas_viewer. The updates are described in some at https://github.com/xraypy/xraylarch/releases/tag/0.9.57 and in the github commit history. This includes adding support for reading RIXS data files from ESRF BM16, better support for de-glitching in XAS_Viewer, and fixing of reading of many Athena Project Files that were saved in the "old style" and have non-ASCII characters (the code now correctly reads the 78 Project files at https://github.com/xraypy/xraylarch/tree/master/examples/xafsdata/AthenaPro… ). Much of the work for this release has come from Mauro Rovezzi. In a conversation we had yesterday about this release, we talked about several potential changes going forward, especially for XAS_Viewer, about saving processing history, how to improve the concept of "reference spectrum" for a measurement, and other topics related to keeping track of analysis history and provenance. Some of these ideas are encapsulated in Github Issues at https://github.com/xraypy/xraylarch/issues, and the plan is to work on this. One possibility would be to be able to read and export to Athena Project files but use a different format (probably HDF5) as a new default "Larch Project File" so that more complexly nested data and some sort of "journal" per data set could be saved, displayed, edited, and so on. If anyone here has some thoughts on how such topics could or should be handled, please let us know. If you have other ideas on what might be added or improved, also don't hesitate to speak up, either in conversations here or on Github. Cheers, --Matt Newville

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XEOL
by Eugenio Otal 25 Nov '21

25 Nov '21

Hi all, I am planning XEOL measurements and I have a doubt. My system is Nd coordinated to Eosin, tetrabromofluorescein. I want to measure XEOL exciting on the Br K-edge (13.4keV) and the Nd L3-edge(6.2keV) and measure the emission spectra of the dye and the Nd. I just measured the emission of the Nd exciting at 530nm and it worked perfectly. My question is, I have access to Nd K-edge, is it worthy to measure XEOL at the K-edge? I am in the time limit to request an extra shift. I would appreciate some bibliography. Best regards.

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PostDoc position at Northeastern University
by NUCRET 23 Nov '21

23 Nov '21

Northeastern University Center for Renewable Energy Technology is currently looking for highly qualified candidate to fill a Post-Doctoral Research Associate position with hands-on experience in the area of in situ and operando XAS, XANES, EXAFS spectroscopy, high-energy XRD as applicable to batteries (especially solid-state), fuel cells and electrolyzers. Familiarity with Brookhaven synchrotron facility (or other US-based light source facilities, e.g. ANL, SLAC) is a plus. Candidates should be in the US and authorized to work in the US (visa is _not_ offered). To apply, please use Northeastern University Career Portal: https://careers.hrm.northeastern.edu/cw/en-us/job/508477/postdoctoral-resea…

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Postdoctoral beamline scientist position at Illinois Tech/MRCAT
by Carlo Segre 22 Nov '21

22 Nov '21

Please find attached the advertisement for a postdoctoral position at MRCAT (Sector 10) at the Advanced Photon Source. The position is with Illinois Institute of Technology, which operates MRCAT for its institutional membership. Feel free to share this with any appropriate individuals. Carlo -- Carlo U. Segre (he/him) -- Duchossois Leadership Professor of Physics Professor of Materials Science & Engineering Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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