On Jan 13, 2021, at 12:51 PM, Matt Newville <newville@cars.uchicago.edu> wrote:

Hi Rachita, 

On Wed, Jan 13, 2021 at 2:00 PM Rachita Rana <racrana@ucdavis.edu> wrote:

Hi Everyone, 

I am using Larch for reading and fitting EXAFS data and I get the autobk and Fourier transforms working. But when I try to generate the fefffpaths and fit the data I get an error from the feffit function. I am using the developer version of Larch on MC OS Catalina. Below is the error and the sample script-

runfile('/Users/rachita/Box/Larch/Feff_Try2/001.py', wdir='/Users/rachita/Box/Larch/Feff_Try2')

Traceback (most recent call last):

  File "/Users/rachita/Box/Larch/Feff_Try2/001.py", line 27, in <module>

    fit   = feffit(params, dset)

  File "/Users/rachita/opt/anaconda3/lib/python3.8/site-packages/xraylarch-0.9.50-py3.8.egg/larch/xafs/feffit.py", line 534, in feffit

    ds.prepare_fit(params=params)

  File "/Users/rachita/opt/anaconda3/lib/python3.8/site-packages/xraylarch-0.9.50-py3.8.egg/larch/xafs/feffit.py", line 265, in prepare_fit

    ikmax = int(1.01 + max(self.data.k)/trans.kstep)

AttributeError: 'AthenaGroup' object has no attribute ‘k’ #tried this with xdi format data and got the same error

I think this is because your script actually did not do the background subtraction.  The "read_xdi()" command reads in the raw data, which probably contains "energy" and "mu" arrays, but not "k" and "chi" arrays.   You said you got autobk and ffts working, you probably want to just add a

    

   autobk(data, rbkg=1.0)

command  (maybe with other options).  That will add "k" and "chi" arrays to the "data" group, which feffit() is expecting.   

I guess the error message could be clearer there....

Below is the script -

#!/usr/bin/env python3

# -*- coding: utf-8 -*-

from larch.fitting import param_group, Parameter

from larch.io import read_xdi

from larch.xafs import feffpath, feffit_dataset, feffit_transform, feffit, feffit_report

data = read_xdi('cu_metal_rt.xdi’)   #I tried importing Athena project file too 

path1 = feffpath('feff0001.dat', s02='amplitude', e0='del_e0',

                 sigma2='sigma2', deltar='del_r')

trans = feffit_transform(kmin=3, kmax=16, kw=(2,1,3),

                         dk=1, window='hanning', rmin=1.7, rmax=3.1)

params = param_group(amplitude= Parameter(1, vary=True),

                     del_e0   = Parameter(1e-7,  vary=True),

                     del_r    = Parameter(1e-7,  vary=True),

                     sigma2   = Parameter(0.003, vary=True))

dset  = feffit_dataset(data=data, pathlist=[path1], transform=trans)

fit   = feffit(params, dset)

print(feffit_report(fit))

By printing path groups and transform fit, I confirmed that the data is read correctly.

Please let me know if there are ways to fix this or if there is an error in my script. 

Thank You!

Rachita

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--Matt 

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