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tritemio / FRETBursts

Burst analysis software for smFRET. **Moved to OpenSMFS organization**
https://github.com/OpenSMFS/FRETBursts
GNU General Public License v2.0
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Consider using lmfit for fitting #5

Closed tritemio closed 10 years ago

tritemio commented 10 years ago

Currently all the fitting are performed using the standard scipy functions.

In particular, 2-Gaussiam mixture fit of the FRET histogram is currently implemented using scipy.optimize.minimize. The only methods supporting boundaries (constrains) are SLSQP and L-BFGS-B.

Lmfit is a nice pythonic wrapper for non-linear least squares and other methods. Moreover lmfit displays nice fit summaries with several goodness-of-fit statistics.

Using lmfit instead of "home made" functions would make the fitting infrastructure more flexible and easy to use while reducing the maintenance burden.

tritemio commented 10 years ago

This is already working on branch fit_experim. Greatly improved fitting for E and S histograms.

tritemio commented 10 years ago

Branch fit_experim is stable. A PR is ready (#18). Will be merged once the notebook in https://github.com/tritemio/FRETBursts_notebooks will be updated.

tritemio commented 10 years ago

Branch merged. Closing.