[Ifeffit] Larch python instructions

[Matt Newville]

Hi Imad,


On Sun, Apr 15, 2018 at 7:15 PM, Imad Ahmed <imad.ahmed at earth.ox.ac.uk>
wrote:

> Dear Matt,
>
> I am looking for some proper instructions on how to use Larch from python.
> I have larch installed on Anaconda2 and trying to run the
> /examples/feffit/doc_feffdat1.lar script from python.
> I tried the python code below but still having issues to run it,
> especially with Feffpath and some larch plugins. Could you please help?
>
> Best wishes, Imad
>
>
> import sys, os
> import numpy as np
> from scipy.optimize import leastsq as scipy_leastsq
> import larch
> from larch import Group, Parameter
> from larch_plugins.io import read_ascii
> from larch_plugins.xafs import FeffPathGroup
> from larch_plugins.xafs.feffit import (TransformGroup,
> FeffitDataSet,feffit, feffit_report)
>
> fname = ‘~/xraylarch/examples/feffit/feff0001.dat'
> path1 = FeffPathGroup(fname)
> path2chi(path1)
> show(path1)
> newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$',
> ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True,
> title=r'$\chi(k)$ from %s' % fname)
> path1.sigma2 = 0.002
> path2chi(path1)
> plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$')
>
>
>
Well, there are some differences between Larch and Python.

With some small modifications, your scaript can become a valid Larch script
like this:
      # larch
from os.path import join, expanduser
fname = join(expanduser(‘~'), '/xraylarch/examples/feffit/feff0001.dat')
path1 = feffpath(fname)

 path2chi(path1)
show(path1)
newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$',
ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True,
title=r'$\chi(k)$ from %s' % fname)
path1.sigma2 = 0.002
path2chi(path1)
plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$')


To do that from Python is a bit more involved.

Each of the functions "feffpath", "path2chi", "show", "newplot", and
"plot"  need to be translated.  As you probably say, "feffpath" is
effectively `FeffPathGroup'.   The others are less obvious, and many of the
larch functions really want to be passed a "larch session" so that they can
find other larch function or data sources.  For example, FeffPathGroup
needs a larch session in order to be able to look up atomic information.

So in pure python that would be approximately:

    import os
    import os.path
    import matplotlib.pyplot as plt   # using pyplot instead of build in
plot commmands

    from larch import Interpreter
    from larch_plugins.xafs.feffdat import FeffPathGroup, _path2chi

   # need to create a Larch interpreter for each "session"
   _larch = Interpreter()

    fname = os.path.join(os.path.expanduser("~"),
"Codes/xraylarch/examples/feffit/feff0001.dat")

    # note that many of the Larch functions will want a `_larch` instance
passed in.
    path1 = FeffPathGroup(fname, _larch=_larch)

   _path2chi(path1, _larch=_larch)

    # show, approximately
    for attr in dir(path1):
        print(attr, getattr(path1, attr))

    # plot, approximately
    plt.plot(path1.k, path1.chi*path1.k**2, label= r'$\sigma^2 = 0$')

    path1.sigma2 = 0.002
   _path2chi(path1, _larch=_larch)

    plt.plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$')

    plt.xlabel(r' $ k \rm\, (\AA^{-1})$')
    plt.ylabel(r'$ k^2\chi(k)$')
    plt.title(r'$\chi(k)$ from %s' % fname)

    plt.legend()
    plt.show()


But also, since you have to build a Larch Interpreter, you could simply use
it to execute the previous Larch script:


    from larch import Interpreter

   text = '''
      # larch
from os.path import join, expanduser
fname = join(expanduser(‘~'), '/xraylarch/examples/feffit/feff0001.dat')
path1 = feffpath(fname)

 path2chi(path1)
show(path1)
newplot(path1.k, path1.chi*path1.k**2, xlabel=r' $ k \rm\, (\AA^{-1})$',
ylabel=r'$ k^2\chi(k)$', label = r'$\sigma^2 = 0$', show_legend=True,
title=r'$\chi(k)$ from %s' % fname)
path1.sigma2 = 0.002
path2chi(path1)
plot(path1.k, path1.chi*path1.k**2, label = r'$\sigma^2 = 0.002$')
'''
    _larch = Interpreter()
    _larch.run(text)

The latter approach is highly recommended.

--Matt Newville
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