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NaN values detected in your input data or the output of your objective/model function #13

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opened 2020-10-20 11:10:50 +02:00 by usov_i · 1 comment
usov_i commented 2020-10-20 11:10:50 +02:00 (Migrated from gitlab.psi.ch)
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Created by: ivan-usov

Trying to fit the measurement 75 in zebra2020n000039.ccl with all default fitting parameters fails with:

File "/das/home/usov_i/pyzebra/pyzebra/fit2.py", line 132, in fitccl
    y, params, weights=[np.abs(1 / y_err[i]) for i in range(len(y_err))], x=x, calc_covar=True
  File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/model.py", line 1013, in fit
    output.fit(data=data, weights=weights)
  File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/model.py", line 1366, in fit
    _ret = self.minimize(method=self.method)
  File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 2285, in minimize
    return function(**kwargs)
  File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 1646, in leastsq
    lsout = scipy_leastsq(self.__residual, variables, **lskws)
  File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/scipy/optimize/minpack.py", line 410, in leastsq
    shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
  File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/scipy/optimize/minpack.py", line 24, in _check_func
    res = atleast_1d(thefunc(*((x0[:numinputs],) + args)))
  File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 591, in __residual
    nan_policy=self.nan_policy)
  File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 2366, in _nan_policy
    raise ValueError(msg)
ValueError: NaN values detected in your input data or the output of your objective/model function - fitting algorithms cannot handle this! Please read https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-what-can-i-do for more information.

Some error handling needs to be done here.

*Created by: ivan-usov* Trying to fit the measurement 75 in `zebra2020n000039.ccl` with all default fitting parameters fails with: ``` File "/das/home/usov_i/pyzebra/pyzebra/fit2.py", line 132, in fitccl y, params, weights=[np.abs(1 / y_err[i]) for i in range(len(y_err))], x=x, calc_covar=True File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/model.py", line 1013, in fit output.fit(data=data, weights=weights) File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/model.py", line 1366, in fit _ret = self.minimize(method=self.method) File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 2285, in minimize return function(**kwargs) File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 1646, in leastsq lsout = scipy_leastsq(self.__residual, variables, **lskws) File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/scipy/optimize/minpack.py", line 410, in leastsq shape, dtype = _check_func('leastsq', 'func', func, x0, args, n) File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/scipy/optimize/minpack.py", line 24, in _check_func res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 591, in __residual nan_policy=self.nan_policy) File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 2366, in _nan_policy raise ValueError(msg) ValueError: NaN values detected in your input data or the output of your objective/model function - fitting algorithms cannot handle this! Please read https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-what-can-i-do for more information. ``` Some error handling needs to be done here.
usov_i commented 2020-10-20 11:19:06 +02:00 (Migrated from gitlab.psi.ch)
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Created by: JakHolzer

This happens when constraints are not applied on the fitting
parameters when fitting something that doesent fit the model. Often no peak
scenario when one tries to fit a gaussian on it. Do you suggest:
Try:
fit
except ValueError:
print("select appropriate constraints")
..?

út 20. 10. 2020 v 11:11 odesílatel Ivan Usov notifications@github.com
napsal:

Trying to fit the measurement 75 in zebra2020n000039.ccl with all default
fitting parameters fails with:

File "/das/home/usov_i/pyzebra/pyzebra/fit2.py", line 132, in fitccl
y, params, weights=[np.abs(1 / y_err[i]) for i in range(len(y_err))], x=x, calc_covar=True
File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/model.py", line 1013, in fit
output.fit(data=data, weights=weights)
File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/model.py", line 1366, in fit
_ret = self.minimize(method=self.method)
File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 2285, in minimize
return function(**kwargs)
File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 1646, in leastsq
lsout = scipy_leastsq(self.__residual, variables, **lskws)
File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/scipy/optimize/minpack.py", line 410, in leastsq
shape, dtype = _check_func('leastsq', 'func', func, x0, args, n)
File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/scipy/optimize/minpack.py", line 24, in _check_func
res = atleast_1d(thefunc(*((x0[:numinputs],) + args)))
File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 591, in __residual
nan_policy=self.nan_policy)
File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 2366, in _nan_policy
raise ValueError(msg)
ValueError: NaN values detected in your input data or the output of your objective/model function - fitting algorithms cannot handle this! Please read https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-what-can-i-do for more information.

Some error handling needs to be done here.

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*Created by: JakHolzer* This happens when constraints are not applied on the fitting parameters when fitting something that doesent fit the model. Often no peak scenario when one tries to fit a gaussian on it. Do you suggest: Try: fit except ValueError: print("select appropriate constraints") ..? út 20. 10. 2020 v 11:11 odesílatel Ivan Usov <notifications@github.com> napsal: > Trying to fit the measurement 75 in zebra2020n000039.ccl with all default > fitting parameters fails with: > > File "/das/home/usov_i/pyzebra/pyzebra/fit2.py", line 132, in fitccl > y, params, weights=[np.abs(1 / y_err[i]) for i in range(len(y_err))], x=x, calc_covar=True > File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/model.py", line 1013, in fit > output.fit(data=data, weights=weights) > File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/model.py", line 1366, in fit > _ret = self.minimize(method=self.method) > File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 2285, in minimize > return function(**kwargs) > File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 1646, in leastsq > lsout = scipy_leastsq(self.__residual, variables, **lskws) > File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/scipy/optimize/minpack.py", line 410, in leastsq > shape, dtype = _check_func('leastsq', 'func', func, x0, args, n) > File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/scipy/optimize/minpack.py", line 24, in _check_func > res = atleast_1d(thefunc(*((x0[:numinputs],) + args))) > File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 591, in __residual > nan_policy=self.nan_policy) > File "/das/work/p15/p15876/miniconda3/envs/pyz/lib/python3.6/site-packages/lmfit/minimizer.py", line 2366, in _nan_policy > raise ValueError(msg) > ValueError: NaN values detected in your input data or the output of your objective/model function - fitting algorithms cannot handle this! Please read https://lmfit.github.io/lmfit-py/faq.html#i-get-errors-from-nan-in-my-fit-what-can-i-do for more information. > > Some error handling needs to be done here. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <https://github.com/paulscherrerinstitute/pyzebra/issues/13>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AM2BBRQMTLGWXD4EAIGCZVLSLVH2VANCNFSM4SX5HEKA> > . >
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Reference: zebra/pyzebra#13