[Ifeffit] Ifeffit Digest, Vol 174, Issue 8
Bruce Ravel
bravel at bnl.gov
Thu Aug 17 16:16:30 CDT 2017
That's a thumbs-up from me, Hiroyuki. Carmelo set out to use Larch
specifically to address the problem of processing many MANY files. I
think Athena and PrestoPronto could both have a good place in anyone's
toolbox.
B
On 08/17/2017 04:29 PM, Carmelo Prestipino wrote:
> Hi Hiroyuki,
> I done a small interface to Larch to work with a lot of files
> http://soonready.github.io/PrestoPronto/
> It is not nice as Athena and it has not all its possibility but if you
> are used to Athena you should not get lost (the name of parameter is
> the same).
> It is not fast how it should be but give a try, maybe could be useful
> Carmelo
>
>
> On Thu, Aug 17, 2017 at 7:00 PM,
> <ifeffit-request at millenia.cars.aps.anl.gov
> <mailto:ifeffit-request at millenia.cars.aps.anl.gov>> wrote:
>
> Send Ifeffit mailing list submissions to
> ifeffit at millenia.cars.aps.anl.gov
> <mailto:ifeffit at millenia.cars.aps.anl.gov>
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
> or, via email, send a message with subject or body 'help' to
> ifeffit-request at millenia.cars.aps.anl.gov
> <mailto:ifeffit-request at millenia.cars.aps.anl.gov>
>
> You can reach the person managing the list at
> ifeffit-owner at millenia.cars.aps.anl.gov
> <mailto:ifeffit-owner at 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: How to use Larch as backend for Athena and Artemis on
> Windows (Bruce Ravel)
> 2. Re: How to use Larch as backend for Athena and Artemis on
> Windows (ASAKURA, Hiroyuki)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 16 Aug 2017 13:17:13 -0400
> From: Bruce Ravel <bravel at bnl.gov <mailto:bravel at bnl.gov>>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov
> <mailto:ifeffit at millenia.cars.aps.anl.gov>>
> Subject: Re: [Ifeffit] How to use Larch as backend for Athena and
> Artemis on Windows
> Message-ID: <1956f39f-85f4-7a92-a989-24a5436df426 at bnl.gov
> <mailto:1956f39f-85f4-7a92-a989-24a5436df426 at bnl.gov>>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
> Hi Hiroyuki,
>
> Sorry I didn't respond yesterday. Yesterday was a bit of crazy day...
>
> I suppose that this is still a work in progress. I believe that Demeter
> works with Larch on Windows, but it is certainly not as easy or
> convenient yet as it should be.
>
> In the place where Demeter got installed on your computer, there is a
> folder called \perl\site\bin -- you can look at the properties of the
> Athena desktop icon to see where that is. In that folder is the
> "dathena.bat" file which the Athena desktop icon points at.
>
> You should also find a file called "lathena.bat". Try running that or
> pointing your desktop icon at it instead.
>
> The difference between "lathena.bat" and "dathena.bat" is line 25 that
> sets an environment variable that Demeter uses to decide which of
> ifeffit or larch to use.
>
> Obviously, there are number of other ways to get this environment
> variable set. The bottom line is, yes, there is a switch. The switch
> is the DEMETER_BACKEND environment variable.
>
> Unfortunately, that switch cannot be in the configuration files,
> although what you tired in item 2 of your email was a sensible guess.
> It turns out that the choice of larch/ifeffit has to made long before
> the configuration files are read.
>
> Do let me know how you get on. While Demeter + larch should work, there
> are still almost certainly problems. I need to get a new version of the
> Demeter installer out soon, so it would be nice to get some feedback in
> this area.
>
> As for using Demeter + larch + 100s of file -- it should work after a
> fashion. But I worry that Athena's performance might not be what you
> are hoping for. Athena does a lot of things that are more user-friendly
> than performance-friendly....
>
>
> Cheers,
> B
>
>
> On 08/15/2017 06:10 AM, ASAKURA, Hiroyuki wrote:
> > 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
> <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
> <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
> >
> >
>
>
> --
> Bruce Ravel ------------------------------------ bravel at bnl.gov
> <mailto:bravel at 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/
> <http://bruceravel.github.io/home/>
> Software: https://github.com/bruceravel
> Demeter: http://bruceravel.github.io/demeter/
> <http://bruceravel.github.io/demeter/>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 17 Aug 2017 18:21:51 +0900
> From: "ASAKURA, Hiroyuki" <asakura at moleng.kyoto-u.ac.jp
> <mailto:asakura at moleng.kyoto-u.ac.jp>>
> To: ifeffit at millenia.cars.aps.anl.gov
> <mailto:ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] How to use Larch as backend for Athena and
> Artemis on Windows
> Message-ID:
> <2d60a548-06bf-5cdf-02f7-154ab039924a at moleng.kyoto-u.ac.jp
> <mailto:2d60a548-06bf-5cdf-02f7-154ab039924a at moleng.kyoto-u.ac.jp>>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear Bruce,
>
> I do appreciate your prompt response!
>
> Now, I managed to run Athena with Larch backend on Windows 10 and
> handle about 100 XAS data at once.
> Athena with Ifeffit backend stalls when handling about 40 XAS
> spectra at least in my case.
> Unfortunately, there seems to be a bit severe performance issue with
> a large number of spectra, as noted.
>
> Here is what I did.
>
> 0. Install an official Git package
> 1-1. Download "64-bit Git for Windows Setup" via
> https://git-scm.com/download/win
> 1-2 <https://git-scm.com/download/win 1-2>. Install Git with default
> options except for "Use Git from the Windows Command Prompt" and
> "Use Windows' default console window"
> Note: You can use any options you want.
>
> 1. Install an official Demeter package
> 1-1. Download "Demeter 0.9.25 (32 bit)" via
> https://bruceravel.github.io/demeter/
> 1-2 <https://bruceravel.github.io/demeter/ 1-2>. Install Demeter
> with default options
> Note: I cannot run 64 bit version with Larch.
>
> 2. Install an official Python package
> 2-1. Download "Windows x86-64 web-based installer" via
> https://www.python.org/downloads/release/python-362/
> 2-2 <https://www.python.org/downloads/release/python-362/ 2-2>.
> Custom Install Python with default options except for "Add Python
> 3.6 to PATH" (checked)
>
> 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 <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
> <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.
>
> 5. Run Larch and Athena with Larch
> 5-1. Start a new command prompt
> 5-2. larch -rc
> 5-3. Start another new command prompt
> 5-4.cd <http://5-4.cd> %APPDATA%\DemeterPerl\perl\site\bin
> 5-5. lathena.bat
>
> It works.
> Athena is the most user-friendly XAS processing tool I have used.
>
> Thanks so much!
>
> Best regards,
>
> ASAKURA, Hiroyuki
>
>
> On 2017/08/17 2:17, Bruce Ravel wrote:
> >
> > Hi Hiroyuki,
> >
> > Sorry I didn't respond yesterday. Yesterday was a bit of crazy
> day...
> >
> > I suppose that this is still a work in progress. I believe that
> Demeter works with Larch on Windows, but it is certainly not as easy
> or convenient yet as it should be.
> >
> > In the place where Demeter got installed on your computer, there
> is a folder called \perl\site\bin -- you can look at the properties
> of the Athena desktop icon to see where that is. In that folder is
> the "dathena.bat" file which the Athena desktop icon points at.
> >
> > You should also find a file called "lathena.bat". Try running
> that or pointing your desktop icon at it instead.
> >
> > The difference between "lathena.bat" and "dathena.bat" is line 25
> that sets an environment variable that Demeter uses to decide which
> of ifeffit or larch to use.
> >
> > Obviously, there are number of other ways to get this environment
> variable set. The bottom line is, yes, there is a switch. The
> switch is the DEMETER_BACKEND environment variable.
> >
> > Unfortunately, that switch cannot be in the configuration files,
> although what you tired in item 2 of your email was a sensible
> guess. It turns out that the choice of larch/ifeffit has to made
> long before the configuration files are read.
> >
> > Do let me know how you get on. While Demeter + larch should
> work, there are still almost certainly problems. I need to get a
> new version of the Demeter installer out soon, so it would be nice
> to get some feedback in this area.
> >
> > As for using Demeter + larch + 100s of file -- it should work
> after a fashion. But I worry that Athena's performance might not be
> what you are hoping for. Athena does a lot of things that are more
> user-friendly than performance-friendly....
> >
> >
> > Cheers,
> > B
> >
> >
> > On 08/15/2017 06:10 AM, ASAKURA, Hiroyuki wrote:
> >> 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
> <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
> <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)
> Program-Specific Assistant Professor (ESICB)
> T. Tanaka Lab., ESICB, Kyoto University, Japan
> asakura at moleng.kyoto-u.ac.jp <mailto:asakura at moleng.kyoto-u.ac.jp>
> http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/
> <http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> <mailto:Ifeffit at millenia.cars.aps.anl.gov>
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
> Unsubscribe:
> http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
> <http://millenia.cars.aps.anl.gov/mailman/options/ifeffit>
>
>
> ------------------------------
>
> End of Ifeffit Digest, Vol 174, Issue 8
> ***************************************
>
>
>
>
> --
> Carmelo Prestipino
> Sciences Chimiques de Rennes, UMR 6226
> Solid State and Materials Chemistry group (CSM)
> Campus de Beaulieu, Bât 10B, bureau 123
> 263 avenue du Général Leclerc
> F-35042 RENNES
> France
> Tel: (+33) 22323 6531
> FAX: (+33) 22323 5959
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
--
Bruce Ravel ------------------------------------ bravel at 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/
More information about the Ifeffit
mailing list