Antonino Ingargiola edited smFRET data analysis.tex  over 9 years ago

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\section{smFRET data analysis}  In the following we provide a high-level description of FRETbursts usage. Normally, especially when FRETbursts is combined with other packages, In general,  we suggest to import FRETBursts with: FRETbursts with the expression:  \verb|import fretbursts as fb|  that will make available all the FRETBursts functions with a concise `fb.` prefix.  In this article, however,to save some typing  we assume that FRETBursts is imported with: with the shortcut form:  \verb|from fretbursts import *|  In this way we can avoid to use skip  the \verb|fb.| prefix to access FRETBursts functions. prefix.  Notealso  that the previous importwill  also import numpy, imports common numeric libraries (numpy,  pandas, matplotlib.pyplot (as as  \verb|np|, \verb|pd| and \verb|plt| respectively). \subsection{Loading the data}  Currently Currently,  FRETBursts supports loading data from a few file formats: SM files (a binary format saved by a common LabVIEW program used in smFRET setups), SPC a (a  binary format used by TCSPC Becker & Hickl cards cards)  and HDF5-Ph-Data an open binary format single-molecule data based on HDF5. We encourage adopting HDF5-Ph-Data format beacuse it is relatively  simple, scalable, well documented, space efficient and very fast. fast[Link].  All the FRETBursts example data files are in HDF5-Ph-Data. An additional file-set can be found here[multi-spot paper data files]. Functions to load data files are defined in the \verb|loader| module. In particular, to load an HDF5-Ph-Data file use: