New subject: Ifeffit Digest, Vol 174, Issue 8

17 Aug 2017


      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, 
wrote:
...
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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 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] How to use Larch as backend for Athena and
        Artemis on Windows
Message-ID: <1956f39f-85f4-7a92-a989-24a5436df426@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
...
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
--
  Bruce Ravel  ------------------------------------ bravel@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/
------------------------------
Message: 2
Date: Thu, 17 Aug 2017 18:21:51 +0900
From: "ASAKURA, Hiroyuki" 
To: ifeffit@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@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. 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. 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. 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. 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.
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 %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
...
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)
Program-Specific Assistant Professor (ESICB)
T. Tanaka Lab., ESICB, Kyoto University, Japan
asakura@moleng.kyoto-u.ac.jp
http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/
------------------------------
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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

Re: [Ifeffit] Ifeffit Digest, Vol 174, Issue 8

Carmelo Prestipino

Bruce Ravel

Bruce Ravel

ASAKURA, Hiroyuki

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participants (3)