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 Below is the script - #!/usr/bin/env python3 # -*- coding: utf-8 -*- from larch.fitting import param_group, Parameter from larch.io http://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
Hi Rachita,
On Wed, Jan 13, 2021 at 2:00 PM Rachita Rana
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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
--Matt
That worked! Thank you for catching the error in my code. Regards, Rachita
On Jan 13, 2021, at 12:51 PM, Matt Newville
wrote: Hi Rachita,
On Wed, Jan 13, 2021 at 2:00 PM Rachita Rana
mailto: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 http://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 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
--Matt _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
participants (2)
-
Matt Newville
-
Rachita Rana