Re: [Ifeffit] unable to export xdi file in xas viewer
Hi Matt, Thanks for the explanation, I now see what you meant. George On Fri, May 1, 2020 at 6:28 PM Matt Newville wrote: > Hi George, > > > On Thu, Apr 30, 2020 at 11:39 PM George Sterbinsky < > georgesterbin...@u.northwestern.edu> wrote: > >> Hi Matt, >> >> Thank you, it is now working for me too. In your previous email, you >> said, "It probably should not even be trying to estimate the uncertainty in >> the model." Why do you say that? Having the uncertainty in the fit >> parameters, and therefore the centroid, could seemingly be useful. >> >> > Sorry for the delay in answering... > > I think the problem you were seeing was because uncertainties in fitted > parameters were not estimated. Sometimes that happens, say if some > parameter doesn't actually alter the fit or gets stuck at a boundary or > something like that. That case is not ideal, but it should be > acceptable - and definitely not cause problems. > > After a fit is done, the code tries to evaluate the uncertainties in the > best-fit, per point `delta_fit` so that one would be able to plot bands of > uncertainty (such as > https://lmfit.github.io/lmfit-py/examples/documentation/model_uncertainty.html). > Of course, to calculate that `delta_fit`, it needs uncertainties in the > parameters. The error you were seeing wat that it could not do this > calculation because, for some reason, it did not have those uncertainties. > So, what I meant was that the code should not be trying to estimate that > `delta_fit` if it doesn't have uncertainties in the parameters. > > --Matt > > > > > > > > > George >> >> On Wed, Apr 29, 2020 at 12:05 PM Matt Newville < >> newvi...@cars.uchicago.edu> wrote: >> >>> Hi George, >>> >>> Very sorry, that should have been >>> delta_fit = 0.0*result.best_fit >>> It's now fixed in github master, and I verified that I could actually >>> export a model from pre-edge peak fitting in XAS_Viewer. >>> >>> >>> >>> On Wed, Apr 29, 2020 at 10:31 AM George Sterbinsky < >>> georgesterbin...@u.northwestern.edu> wrote: >>> Hi Matt and all, Unfortunately, after a clean install of larch following the source installation instructions, I am not able export any fits to xdi files, and a different error, shown below, is now printed in the terminal. Please let me know if any additional information would be helpful in solving this issue. Thank you, George Traceback (most recent call last): File "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/wxxas/prepeak_panel.py", line 366, in onExportFitResult yerr=yerr, x=x) File "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/io/export_modelresult.py", line 59, in export_modelresult delta_fit = 0.0*result_best_fit NameError: name 'result_best_fit' is not defined On Tue, Apr 21, 2020 at 9:25 AM Matt Newville < newvi...@cars.uchicago.edu> wrote: > Hi George, > > Hm, sorry about that. It seems to be saying that the parameter > uncertainties weren't calculated correctly. It probably should not even > be > trying to estimate the uncertainty in the model. I believe it should be > fixed in git master for larch, and I'll see about looking for this in > lmfit > too. > > On Mon, Apr 20, 2020 at 4:00 PM George Sterbinsky < > georgesterbin...@u.northwestern.edu> wrote: > >> Hello, >> >> When attempting to export an xdi file for a pre-edge peak fit in XAS >> viewer, the error message below prints to the terminal and the xdi file >> is >> not generated. I can provide the project file and instructions for >> generating the error message if that would be helpful. >> >> Thank you, >> George >> >> >> Traceback (most recent call last): >> File >> "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", >> line >> 369, in onExportFitResult >> yerr=yerr, x=x) >> File >> "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py", >> line 60, in export_modelresult >> delta_fit = result.eval_uncertainty(result.params, **kwargs) >> File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line >> 1488, in eval_uncertainty >> dval = pars[pname].stderr/3.0 >> TypeError: unsupported operand type(s) for /: 'NoneType' and 'float' >> ___ >> 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 Newville 630-252-0431 > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov >
Re: [Ifeffit] unable to export xdi file in xas viewer
Hi George, On Thu, Apr 30, 2020 at 11:39 PM George Sterbinsky < georgesterbin...@u.northwestern.edu> wrote: > Hi Matt, > > Thank you, it is now working for me too. In your previous email, you said, > "It probably should not even be trying to estimate the uncertainty in the > model." Why do you say that? Having the uncertainty in the fit parameters, > and therefore the centroid, could seemingly be useful. > > Sorry for the delay in answering... I think the problem you were seeing was because uncertainties in fitted parameters were not estimated. Sometimes that happens, say if some parameter doesn't actually alter the fit or gets stuck at a boundary or something like that. That case is not ideal, but it should be acceptable - and definitely not cause problems. After a fit is done, the code tries to evaluate the uncertainties in the best-fit, per point `delta_fit` so that one would be able to plot bands of uncertainty (such as https://lmfit.github.io/lmfit-py/examples/documentation/model_uncertainty.html). Of course, to calculate that `delta_fit`, it needs uncertainties in the parameters. The error you were seeing wat that it could not do this calculation because, for some reason, it did not have those uncertainties. So, what I meant was that the code should not be trying to estimate that `delta_fit` if it doesn't have uncertainties in the parameters. --Matt George > > On Wed, Apr 29, 2020 at 12:05 PM Matt Newville > wrote: > >> Hi George, >> >> Very sorry, that should have been >> delta_fit = 0.0*result.best_fit >> It's now fixed in github master, and I verified that I could actually >> export a model from pre-edge peak fitting in XAS_Viewer. >> >> >> >> On Wed, Apr 29, 2020 at 10:31 AM George Sterbinsky < >> georgesterbin...@u.northwestern.edu> wrote: >> >>> Hi Matt and all, >>> >>> Unfortunately, after a clean install of larch following the source >>> installation instructions, I am not able export any fits to xdi files, and >>> a different error, shown below, is now printed in the terminal. Please let >>> me know if any additional information would be helpful in solving this >>> issue. >>> >>> Thank you, >>> George >>> >>> >>> Traceback (most recent call last): >>> File >>> "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/wxxas/prepeak_panel.py", >>> line 366, in onExportFitResult >>> yerr=yerr, x=x) >>> File >>> "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/io/export_modelresult.py", >>> line 59, in export_modelresult >>> delta_fit = 0.0*result_best_fit >>> NameError: name 'result_best_fit' is not defined >>> >>> >>> >>> >>> On Tue, Apr 21, 2020 at 9:25 AM Matt Newville < >>> newvi...@cars.uchicago.edu> wrote: >>> Hi George, Hm, sorry about that. It seems to be saying that the parameter uncertainties weren't calculated correctly. It probably should not even be trying to estimate the uncertainty in the model. I believe it should be fixed in git master for larch, and I'll see about looking for this in lmfit too. On Mon, Apr 20, 2020 at 4:00 PM George Sterbinsky < georgesterbin...@u.northwestern.edu> wrote: > Hello, > > When attempting to export an xdi file for a pre-edge peak fit in XAS > viewer, the error message below prints to the terminal and the xdi file is > not generated. I can provide the project file and instructions for > generating the error message if that would be helpful. > > Thank you, > George > > > Traceback (most recent call last): > File > "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", > line > 369, in onExportFitResult > yerr=yerr, x=x) > File > "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py", > line 60, in export_modelresult > delta_fit = result.eval_uncertainty(result.params, **kwargs) > File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line > 1488, in eval_uncertainty > dval = pars[pname].stderr/3.0 > TypeError: unsupported operand type(s) for /: 'NoneType' and 'float' > ___ > 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 Newville 630-252-0431 ___ 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 >>> ___ >>> Ifeffit mailing list >>> Ifeffit@millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> Unsubscribe:
Re: [Ifeffit] unable to export xdi file in xas viewer
Hi Matt, Thank you, it is now working for me too. In your previous email, you said, "It probably should not even be trying to estimate the uncertainty in the model." Why do you say that? Having the uncertainty in the fit parameters, and therefore the centroid, could seemingly be useful. George On Wed, Apr 29, 2020 at 12:05 PM Matt Newville wrote: > Hi George, > > Very sorry, that should have been > delta_fit = 0.0*result.best_fit > It's now fixed in github master, and I verified that I could actually > export a model from pre-edge peak fitting in XAS_Viewer. > > > > On Wed, Apr 29, 2020 at 10:31 AM George Sterbinsky < > georgesterbin...@u.northwestern.edu> wrote: > >> Hi Matt and all, >> >> Unfortunately, after a clean install of larch following the source >> installation instructions, I am not able export any fits to xdi files, and >> a different error, shown below, is now printed in the terminal. Please let >> me know if any additional information would be helpful in solving this >> issue. >> >> Thank you, >> George >> >> >> Traceback (most recent call last): >> File >> "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/wxxas/prepeak_panel.py", >> line 366, in onExportFitResult >> yerr=yerr, x=x) >> File >> "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/io/export_modelresult.py", >> line 59, in export_modelresult >> delta_fit = 0.0*result_best_fit >> NameError: name 'result_best_fit' is not defined >> >> >> >> >> On Tue, Apr 21, 2020 at 9:25 AM Matt Newville >> wrote: >> >>> Hi George, >>> >>> Hm, sorry about that. It seems to be saying that the parameter >>> uncertainties weren't calculated correctly. It probably should not even be >>> trying to estimate the uncertainty in the model. I believe it should be >>> fixed in git master for larch, and I'll see about looking for this in lmfit >>> too. >>> >>> On Mon, Apr 20, 2020 at 4:00 PM George Sterbinsky < >>> georgesterbin...@u.northwestern.edu> wrote: >>> Hello, When attempting to export an xdi file for a pre-edge peak fit in XAS viewer, the error message below prints to the terminal and the xdi file is not generated. I can provide the project file and instructions for generating the error message if that would be helpful. Thank you, George Traceback (most recent call last): File "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line 369, in onExportFitResult yerr=yerr, x=x) File "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py", line 60, in export_modelresult delta_fit = result.eval_uncertainty(result.params, **kwargs) File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line 1488, in eval_uncertainty dval = pars[pname].stderr/3.0 TypeError: unsupported operand type(s) for /: 'NoneType' and 'float' ___ 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 Newville 630-252-0431 >>> ___ >>> 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 >>> >> ___ >> 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 Newville 630-252-0431 > ___ > 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 > ___ 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
Re: [Ifeffit] unable to export xdi file in xas viewer
Hi George, Very sorry, that should have been delta_fit = 0.0*result.best_fit It's now fixed in github master, and I verified that I could actually export a model from pre-edge peak fitting in XAS_Viewer. On Wed, Apr 29, 2020 at 10:31 AM George Sterbinsky < georgesterbin...@u.northwestern.edu> wrote: > Hi Matt and all, > > Unfortunately, after a clean install of larch following the source > installation instructions, I am not able export any fits to xdi files, and > a different error, shown below, is now printed in the terminal. Please let > me know if any additional information would be helpful in solving this > issue. > > Thank you, > George > > > Traceback (most recent call last): > File > "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/wxxas/prepeak_panel.py", > line 366, in onExportFitResult > yerr=yerr, x=x) > File > "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/io/export_modelresult.py", > line 59, in export_modelresult > delta_fit = 0.0*result_best_fit > NameError: name 'result_best_fit' is not defined > > > > > On Tue, Apr 21, 2020 at 9:25 AM Matt Newville > wrote: > >> Hi George, >> >> Hm, sorry about that. It seems to be saying that the parameter >> uncertainties weren't calculated correctly. It probably should not even be >> trying to estimate the uncertainty in the model. I believe it should be >> fixed in git master for larch, and I'll see about looking for this in lmfit >> too. >> >> On Mon, Apr 20, 2020 at 4:00 PM George Sterbinsky < >> georgesterbin...@u.northwestern.edu> wrote: >> >>> Hello, >>> >>> When attempting to export an xdi file for a pre-edge peak fit in XAS >>> viewer, the error message below prints to the terminal and the xdi file is >>> not generated. I can provide the project file and instructions for >>> generating the error message if that would be helpful. >>> >>> Thank you, >>> George >>> >>> >>> Traceback (most recent call last): >>> File >>> "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line >>> 369, in onExportFitResult >>> yerr=yerr, x=x) >>> File >>> "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py", >>> line 60, in export_modelresult >>> delta_fit = result.eval_uncertainty(result.params, **kwargs) >>> File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line >>> 1488, in eval_uncertainty >>> dval = pars[pname].stderr/3.0 >>> TypeError: unsupported operand type(s) for /: 'NoneType' and 'float' >>> ___ >>> 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 Newville 630-252-0431 >> ___ >> 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 >> > ___ > 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 Newville 630-252-0431 ___ 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
Re: [Ifeffit] unable to export xdi file in xas viewer
Hi Matt and all, Unfortunately, after a clean install of larch following the source installation instructions, I am not able export any fits to xdi files, and a different error, shown below, is now printed in the terminal. Please let me know if any additional information would be helpful in solving this issue. Thank you, George Traceback (most recent call last): File "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/wxxas/prepeak_panel.py", line 366, in onExportFitResult yerr=yerr, x=x) File "/opt/anaconda3/lib/python3.7/site-packages/xraylarch-0.9.47-py3.7.egg/larch/io/export_modelresult.py", line 59, in export_modelresult delta_fit = 0.0*result_best_fit NameError: name 'result_best_fit' is not defined On Tue, Apr 21, 2020 at 9:25 AM Matt Newville wrote: > Hi George, > > Hm, sorry about that. It seems to be saying that the parameter > uncertainties weren't calculated correctly. It probably should not even be > trying to estimate the uncertainty in the model. I believe it should be > fixed in git master for larch, and I'll see about looking for this in lmfit > too. > > On Mon, Apr 20, 2020 at 4:00 PM George Sterbinsky < > georgesterbin...@u.northwestern.edu> wrote: > >> Hello, >> >> When attempting to export an xdi file for a pre-edge peak fit in XAS >> viewer, the error message below prints to the terminal and the xdi file is >> not generated. I can provide the project file and instructions for >> generating the error message if that would be helpful. >> >> Thank you, >> George >> >> >> Traceback (most recent call last): >> File >> "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line >> 369, in onExportFitResult >> yerr=yerr, x=x) >> File >> "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py", >> line 60, in export_modelresult >> delta_fit = result.eval_uncertainty(result.params, **kwargs) >> File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line >> 1488, in eval_uncertainty >> dval = pars[pname].stderr/3.0 >> TypeError: unsupported operand type(s) for /: 'NoneType' and 'float' >> ___ >> 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 Newville 630-252-0431 > ___ > 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 > ___ 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
Re: [Ifeffit] unable to export xdi file in xas viewer
Hi George, Hm, sorry about that. It seems to be saying that the parameter uncertainties weren't calculated correctly. It probably should not even be trying to estimate the uncertainty in the model. I believe it should be fixed in git master for larch, and I'll see about looking for this in lmfit too. On Mon, Apr 20, 2020 at 4:00 PM George Sterbinsky < georgesterbin...@u.northwestern.edu> wrote: > Hello, > > When attempting to export an xdi file for a pre-edge peak fit in XAS > viewer, the error message below prints to the terminal and the xdi file is > not generated. I can provide the project file and instructions for > generating the error message if that would be helpful. > > Thank you, > George > > > Traceback (most recent call last): > File > "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line > 369, in onExportFitResult > yerr=yerr, x=x) > File > "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py", > line 60, in export_modelresult > delta_fit = result.eval_uncertainty(result.params, **kwargs) > File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line 1488, > in eval_uncertainty > dval = pars[pname].stderr/3.0 > TypeError: unsupported operand type(s) for /: 'NoneType' and 'float' > ___ > 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 Newville 630-252-0431 ___ 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
[Ifeffit] unable to export xdi file in xas viewer
Hello, When attempting to export an xdi file for a pre-edge peak fit in XAS viewer, the error message below prints to the terminal and the xdi file is not generated. I can provide the project file and instructions for generating the error message if that would be helpful. Thank you, George Traceback (most recent call last): File "/anaconda3/lib/python3.7/site-packages/larch/wxxas/prepeak_panel.py", line 369, in onExportFitResult yerr=yerr, x=x) File "/anaconda3/lib/python3.7/site-packages/larch/io/export_modelresult.py", line 60, in export_modelresult delta_fit = result.eval_uncertainty(result.params, **kwargs) File "/anaconda3/lib/python3.7/site-packages/lmfit/model.py", line 1488, in eval_uncertainty dval = pars[pname].stderr/3.0 TypeError: unsupported operand type(s) for /: 'NoneType' and 'float' ___ 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
