[Ifeffit] Ifeffit Digest, Vol 174, Issue 8

Fri Aug 18 02:38:44 CDT 2017

Hi Carmelo,

I know your PrestoPronto, and had tried it when hosted at Google Code.
It must be a good time to try it again.
Thank you very much.

Best,

ASAKURA, Hiroyuki

On 2017/08/18 5:29, 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>
> 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 <bravel at bnl.gov>
>> To: XAFS Analysis using Ifeffit <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>
>> 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 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/
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 17 Aug 2017 18:21:51 +0900
>> From: "ASAKURA, Hiroyuki" <asakura at moleng.kyoto-u.ac.jp>
>> To: 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>
>> 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 at moleng.kyoto-u.ac.jp
>> http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/
>>
>>
>> ------------------------------
>>
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>>
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>> ------------------------------
>>
>> End of Ifeffit Digest, Vol 174, Issue 8
>> ***************************************
>>
>
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-- 
ASAKURA, Hiroyuki (Ph.D)
Program-Specific Assistant Professor (ESICB)
T. Tanaka Lab., ESICB, Kyoto University, Japan
asakura at moleng.kyoto-u.ac.jp
http://www.moleng.kyoto-u.ac.jp/~moleng_04/asakura/