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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. Note
also that the previous import
will 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: