[Ifeffit] Larch as python library

Tue Nov 1 19:56:18 CDT 2016

Hi Sean,

On Tue, Nov 1, 2016 at 5:35 PM, Sean Fackler <swfackler at lbl.gov> wrote:

> Hi Matt,
>
> On Nov 1, 2016, at 2:00 PM, Matt Newville <newville at cars.uchicago.edu>
> wrote:
>
> Hi Sean,
>
> On Tue, Nov 1, 2016 at 1:39 PM, Sean Fackler <swfackler at lbl.gov> wrote:
>
>> Dear Matt,
>>
>> I’ve been working to implement Larch functions as a Python library.
>> During the implementation I found a number of things I needed to do
>> including:
>>
>>
> You can use Larch functions from Python, of course.   Normally, you'd do
> something like
>
>     import larch
>     from larch_plugins.xafs import pre_edge, mback
>
>
>
>> 1. Identifiying a functions’ python callable name, i.e. _group as a
>> python callable function instead of group as the larch function.
>>
>
> I'm not sure I understand.  You shouldn't need "a function's python
> callable name", you should just need the function.  Maybe I misunderstand.
>
> If you need a larch Group, you should be able to do
>     import larch
>     agroup = larch.Group(name='mygroupname', xdata = range(100),
> label='hello')
>
>
> Thanks for showing me the precise command.
>
>
>
>
>
>>
>> 2. The need to pass '_larch = mylarch’ in the said function or I get the
>> 'AttributeError: 'NoneType' object has no attribute ‘symtable’ ‘
>>
>>
> Yes, many of the larch plugin functions either require or are much happier
> with an instance of a larch session passed in as the '_larch' argument.
> It's kind of a feature ;).
>
>
>> 3. The need to run the script through the Python console as oppose to
>> running as a script.
>>
>>
> I'm not sure I understand what this means.  You should be able to run a
> python program from any environment.
>
>
>> You can see my sample script with data attached. Keep in mind I am a
>> Python novice. So for point 3 in particular *I don’t understand the
>> difference between running some selected code in the Python console and
>> running the whole script in the shell *(I am using PyCharm CE). I
>> checked my Python interpreter with sys.executable (path) and
>> sys.version_info (version) which are the same between the console and
>> interpreter which were initial issues I found online. Is the interpreter
>> somehow not seeing the xraylarch library?
>>
>
> Hmm, that doesn't make a lot of sense to me either.  What errors do you
> get when you run your script?
>
> I don't use PyCharm, so maybe that's not seeing all of the modules from
> anaconda?   Is PyCharm seeing your  anaconda distribution?
>
>
> When I run the script I get the following error from the same script
> “import_fit.py":
>
>  "Traceback (most recent call last):
>   File "/Users/SeanFackler/PycharmProjects/msp_sean/import_fit.py", line
> 10, in <module>
>     from larch_plugins.lineshapes import gaussian
> ImportError: No module named larch_plugins.lineshapes
>
> Process finished with exit code 1”
>

I think that should be

     from larch_plugins.math.lineshapes import gaussian

with "math"

>
> Somehow it can’t load the module lineshapes. But selecting all the code
> and running it in the Python console works fine. I checked as before and it
> appears to be seeing the same anaconda Python interpreter. Pycharm also
> appears to see the anaconda distribution.
>
>
Hm, are you sure that's the same version of "import_fit.py"?

>
> A few comments on your script:
>    a) there should be no need to do a os.chdir() to any folder, especially
> not to source code folders.
>    b) doing   from xxx import *  is bound to lead to confusion.  Import
> what you need, and don't import what you don't need.
>
>
> Thanks for those helpful comments. The asterisks was an attempt to get
> plotter working on my system :)
>
>
>
> Finally: 1. Is there an easier way to use the larch functions as a python
>> library?
>>
>
> Is the above suggestion better?
>
>
>> 2. Is a larch group basically a python dictionary?
>>
>
> Actually, it's basically an empty class:
>
>     class Group:
>         def __init__(self, **kws):
>              ....
>
>     mygroup = Group()
>     mygroup.x = 1
>     mygroup.y = 'a string'
>
> even in more detail, it's an empty class.  In most cases it would probably
> be OK to substitute almost any class instance as a Group.
>
> In Larch, I tend to make as many things as possible "group-like" so that
> accessing elements is easy.
>
>
> Indeed I had no problem replacing larch groups as dictionaries so the
> group-like accessing of elements is more general than a dictionary I guess.
> That’s useful!
>

OK, great!

>
>
>> If so, this could be made clearer in the documentation. I am interested
>> to contribute to the documentation if that’s of interest/help.
>>
>>
> Sure!  The docs are definitely in need of some serious work.
>
>
> Let me know how best I could contribute. For starters I can help with
> typos and the like.
>
>
Any work or suggestions on the docs would be greatly appreciated!

>
>
>
>> I am running MacOS Sierra 10.12.1 on a mid-2015 15" MacBook Pro with
>> Python 2.7.
>>
>> Ron and Alpha: Maybe you have some ideas to the above points?
>>
>> Thanks everyone for any help.
>>
>> Sean
>>
>>
> The attached modified version of your script works for me from a Terminal
> (The fit's not very good, yet, but it did run).   On Mac OSX with anaconda,
> you probably have to run this as "pythonw import_fit.py"  (note: pythonw,
> not python).
>
> Hope that helps,
>
>
> That works perfectly! I just ran it in the Interpreter normally (no
> pythonw). I guess it’s just the way I was importing things.
>
> Thank you,
>
> Sean
>
>
> --Matt
> <import_fitMN.py>_______________________________________________
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--Matt
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