[Ifeffit] Scripting - Python

Thu Jul 21 10:09:21 CDT 2011

Seems you hit the nail on the head. I reinstalled everything and all
appears to be working now. Thanks for all the help.

Andy Korinda

On Thu, Jul 14, 2011 at 10:08 PM, Andrew Korinda
<a-korinda at northwestern.edu> wrote:
> Ya, I can go back and do that, just glad to have a viable lead. I'll
> get back to everyone next week about how it goes but this sounds
> promising.
>
> Andy K.
>
> On Thu, Jul 14, 2011 at 10:03 PM, Matt Newville
> <newville at cars.uchicago.edu> wrote:
>> Hi Andrew,
>>
>> Ah, I believe the problem is due to using 64-bit version of Python.
>> That is, the ifeffit_12.dll *was* found, but it couldn't be loaded
>> because it is built for 32-bit.   I was testing with a 32-bit Python
>> on a Win7 64-bit machine...
>>
>> I'm pretty sure the ifeffit_12.dll would have to be rebuilt to work
>> with Enthought's EPD 7.1-1 (64-bit).  That might be possible, but I
>> haven't tried doing this, and can't guarantee it will happen quickly.
>>  That dll would also need to be kept separately from the rest of the
>> ifeffit/bin, as Athena, Artemis, etc are all built for 32-bit systems.
>>
>> Is using a 32-bit Python a viable alternative?
>> Sorry for the trouble,
>>
>> --Matt
>>
>>
>> On Thu, Jul 14, 2011 at 9:43 PM, Andrew Korinda
>> <a-korinda at northwestern.edu> wrote:
>>> So I went through and double checked the use_ifeffit, no change. I
>>> then entered the bin path directly and tried again, again with the
>>> same results. Following your code, I just have one difference when I
>>> import Ifeffit:
>>> "Forcing DISTUTILS_USE_SDK=1"
>>> Do I need to install a version of Visual Studio?
>>>
>>> The full text from the command shell is attached to spare others
>>> following this including an output of my paths.
>>>
>>> Andy K.
>>>
>>> On Thu, Jul 14, 2011 at 12:50 PM, Matt Newville
>>> <newville at cars.uchicago.edu> wrote:
>>>> Hi Andrew,
>>>>
>>>> Just as a follow-up, loading the Ifeffit library from python worked
>>>> for me on a separate Win7 machine (64bit).  I even had Ifeffit
>>>> installed to the non-default location. With Ifeffit installed to
>>>> C:\apps\Ifeffit, I edited C:\apps\Ifeffit\bin\use_ifeffit.bat to read
>>>>
>>>>   @echo off
>>>>   SET IFEFFIT_DIR=C:\apps\Ifeffit\
>>>>   SET IFEFFIT_BIN=C:\apps\Ifeffit\bin
>>>>   SET PATH=%PATH%;%IFEFFIT_BIN%
>>>>   SET PGPLOT_DIR=%IFEFFIT_BIN%
>>>>   SET PGPLOT_DEV=/GW
>>>>
>>>> Then from a command prompt:
>>>>    C:\>C:\apps\Ifeffit\bin\use_ifeffit
>>>>    C:\>python
>>>>    Python 2.7.1 (r271:86832, Nov 27 2010, 18:30:46) [MSC v.1500 32
>>>> bit (Intel)] on win32
>>>>    Type "help", "copyright", "credits" or "license" for more information.
>>>>    >>> import Ifeffit
>>>>    >>> x  = Ifeffit.Ifeffit()
>>>>    >>> x.ifeffit('show $&build')
>>>>     $&build        = 1.2.11c Copyright (c) 2008 Matt Newville, Univ of Chicago
>>>>
>>>> Does that work for you?  If not, can you send a more complete report
>>>> of your environmental variables?
>>>>
>>>> Sorry for the trouble,
>>>>
>>>> --Matt
>>>>
>>>> On Thu, Jul 14, 2011 at 9:58 AM, Andrew Korinda
>>>> <a-korinda at northwestern.edu> wrote:
>>>>> Thanks Matt. That new binary was a great help. The install appears to
>>>>> have gone fine. I made the appropriate path changes in
>>>>> use_ifeffit.bat, ifeffit_config.py and ifeffit.py to reflect where I
>>>>> have installed Ifeffit. I noticed this when I was trying to debug an
>>>>> import error I get when I call ifeffit but this didn't solve the
>>>>> problem. The error I am getting is: ('failed to load ifeffit library
>>>>> ', 'C:\\Program Files (x86)\\Ifeffit\\bin\\ifeffit_12.dll') which is
>>>>> fatal. It's from line 125 of ifeffit.py. I've double check and the dll
>>>>> is there so I'm not sure why it is failing.
>>>>>
>>>>> I saw Joel.Brugger had the same issue on his Mac but I didn't see an
>>>>> email about that being resolved. Matt or anyone have another
>>>>> suggestion where I can look to debug this?
>>>>>
>>>>> Andy K.
>>>>>
>>>>> On Wed, Jul 13, 2011 at 2:53 PM, Matt Newville
>>>>> <newville at cars.uchicago.edu> wrote:
>>>>>> Hi Andrew,
>>>>>>
>>>>>> Sorry for not keeping these more up-to-date.  I posted windows
>>>>>> installers for Python 2.6 and Python 2.7 (sorry, no Python 3 support
>>>>>> yet) at
>>>>>>   http://cars.uchicago.edu/~ifeffit/src/PythonWrapper/
>>>>>>
>>>>>> I'll update the links on the wiki.
>>>>>>
>>>>>> Note that to use these well (especially for plotting fonts and colors
>>>>>> to work), you may have to run C:\Program
>>>>>> Files\Ifeffit\bin\use_ifeffit.bat, or otherwise set the environmental
>>>>>> variables given in that file.
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> --Matt
>>>>>>
>>>>>>
>>>>>> On Wed, Jul 13, 2011 at 10:41 AM, Andrew Korinda
>>>>>> <a-korinda at northwestern.edu> wrote:
>>>>>>> After a reprieve from XAS work, I'm back at it with a new laptop. In
>>>>>>> rebuilding the Ifeffit python package I realized I did not properly
>>>>>>> compile all the instructions which would explain why I wasn't getting
>>>>>>> things to return to the python shell such as echo messages. I am
>>>>>>> currently trying to properly install the Ifeffit wrapper from within
>>>>>>> ifeffit-1.2.11c.tar.gz onto Windows 7 and Python 2.7.2. Of course this
>>>>>>> has required some tweaks but when I get to "gcc.exe -mno-cygwin
>>>>>>> -shared -s build" the install crashes. I believe this has to do with
>>>>>>> site_install.py being writing for redhat and I'm not sure how to
>>>>>>> modify the directories for windows.
>>>>>>>
>>>>>>> Is there a way around this? I realize I could go back and install
>>>>>>> Python 2.5 and run Ifeffit-1.2.win32-py2.5.exe but that does mean
>>>>>>> going back and reinstalling every package (numpy, scipy, matplotlib,
>>>>>>> etc.) Is there maybe a way to rework Ifeffit-1.2.win32-py2.5.exe so it
>>>>>>> can be used on a machine with Python 2.7.2?
>>>>>>>
>>>>>>> Andy Korinda
>>>>>>>
>>>>>>> On Mon, Nov 8, 2010 at 12:36 AM, Andrew Korinda
>>>>>>> <a-korinda at northwestern.edu> wrote:
>>>>>>>> Thanks for the help. Sorry it took so long to report back but I can only do
>>>>>>>> must of my work on this on weekends. The corrected code worked great and I'm
>>>>>>>> moving forward again. No message was given when the code wasn't working.
>>>>>>>>
>>>>>>>> Andy Korinda
>>>>>>>>
>>>>>>>> On Nov 1, 2010 1:55 PM, "Matt Newville" <newville at cars.uchicago.edu> wrote:
>>>>>>>>
>>>>>>>> Hi Andrew,
>>>>>>>>
>>>>>>>> On Mon, Nov 1, 2010 at 12:01 PM, Andrew Korinda
>>>>>>>> <a-korinda at northwestern.edu> wrote:
>>>>>>>>> I'm looking t...
>>>>>>>>
>>>>>>>> This is almost certainly due to space in the filename, and is really
>>>>>>>> more of a problem with the fortran than python (or perl for that
>>>>>>>> matter).  That is, with a space in the file name, you should
>>>>>>>> explicitly use
>>>>>>>>    read_data(file=...., group=...)
>>>>>>>>
>>>>>>>> This should work better::
>>>>>>>>    import Ifeffit
>>>>>>>>    iff = Ifeffit.Ifeffit()
>>>>>>>>
>>>>>>>>    ret = iff.ifeffit("read_data(file=C:\Program
>>>>>>>> Files\Ifeffit\examples\Ifeffit\data\cu.xmu, group=c)")
>>>>>>>>
>>>>>>>> If it doesn't, let use know.
>>>>>>>>
>>>>>>>>> >From this experience I have some questions:
>>>>>>>>>
>>>>>>>>> ~First does anyone have some debugging tips for ...
>>>>>>>>
>>>>>>>> There should have been a printed message that might have altered you
>>>>>>>> that the file hadn't been read in correctly:
>>>>>>>>   *** read_data: no file name given!
>>>>>>>>
>>>>>>>> was that message not given?
>>>>>>>>
>>>>>>>>> ~Secondly, Does anyone have any example Python scripts for Ifeffit
>>>>>>>>> that they would like to shar...
>>>>>>>>
>>>>>>>> I sort of deliberately have left the base Ifeffit python module
>>>>>>>> bare-bones.  It would certainly be possible to add more functionality
>>>>>>>> to that, or distribute add-on packages.  It sort of depends what
>>>>>>>> people would find desirable.
>>>>>>>>
>>>>>>>> I have many example scripts using Ifeffit + Python, mostly scripts,
>>>>>>>> not documented, reliable code.  Of course, there is also sixpack.  I
>>>>>>>> had some older GUIs as well.  Would it be helpful to add some small
>>>>>>>> examples on a wiki page?
>>>>>>>>
>>>>>>>>> ~Finally, would I be better off coding in Perl and using Demeter?
>>>>>>>>
>>>>>>>> That's a difficult question.  The relative merits of Perl v Python are
>>>>>>>> sort of a topic all on their own.  For what it's worth, I believe
>>>>>>>> (far) more people have used Python than Perl, but several very notable
>>>>>>>> Ifeffit programs are written in Perl ;).
>>>>>>>>
>>>>>>>> --Matt
>>>>>>>>
>>>>>>>> PS: The next version of Ifeffit will be in python.   Progress is slow,
>>>>>>>> and when it will start to look like an EXAFS analysis program is a
>>>>>>>> fair question.  It probably shouldn't sway your decision much.
>>>>>>>>
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>>>>>>>
>>>>>>
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>>>>>
>>>>
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