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Antonino Ingargiola edited Fitting.tex
about 8 years ago
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(\href{http://fretbursts.readthedocs.org/en/latest/plugins.html#fretbursts.burstlib\_ext.bursts\_fitter}{link}).
\paragraph{Python details}
Under the hood, histogram
fit fits in FRETBursts
is are performed using the
\href{http://lmfit.github.io/lmfit-py/}{lmfit} library~\cite{lmfit}.
Every fit model is, in fact, an Models returned by FRETBursts's factory functions (\verb|mfit.factory_*|)
are \verb|lmfit.Model|
object, and these object objects (\href{https://lmfit.github.io/lmfit-py/model.html}{link}).
Custom models can be created
and modified by calling
directly \verb|lmfit| functions.
Fitting \verb|lmfit.Model| directly.
When an
lmfit \verb|Model| \verb|lmfit.Model| is fitted, it returns
an a \verb|ModelResults| object
with (\href{https://lmfit.github.io/lmfit-py/model.html#the-modelresult-class}{link})
which contains all the
results.
FRETBursts appends information related to the fit
result (model, data,
parameters with best values and uncertainties) and useful methods to operate on fit results.
FRETBursts puts \verb|ModelResults| of each channel in the list
\verb|ds.E_fitter.fit_res|.
As an example, to get the reduced $\chi^2$ value of the E histogram fit in a
single-spot measurement \verb|d|, we use:
\begin{lstlisting}
d.E_fitter.fit_res[0].redchi
\end{lstlisting}
Other useful attributes are \verb|aic| and \verb|bic| which contain the
Akaike information criterion (AIC) and the Bayes Information criterion (BIC)
quantities respectively. AIC and BIC allow to compare different models and
to select the most approriate for the data at hand.
Example of defining and modifying models for fitting are provided in
the μs-ALEX FRETBursts tutorial (\href{http://nbviewer.jupyter.org/github/tritemio/FRETBursts_notebooks/blob/master/notebooks/FRETBursts%20-%20us-ALEX%20smFRET%20burst%20analysis.ipynb}{link}).
Interested users should also refer to the
excellent lmfit comprehensive lmfit's documentation
(\href{http://lmfit.github.io/lmfit-py/}{link}).