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

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:

Send Ifeffit mailing list submissions to ifeffit@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@millenia.cars.aps.anl.gov

You can reach the person managing the list at ifeffit-owner@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 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/

------------------------------

Subject: Digest Footer

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: 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