this is for holding javascript data
Antonino Ingargiola renamed Loading data.tex to dataload.tex
over 9 years ago
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\section{smFRET burst analysis}
\subsection{Loading the data}
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 binary format used by TCSPC Becker \& Hickl cards) and \href{http://photon-hdf5.readthedocs.org/}{Photon-HDF5} an open binary format single-molecule data based on HDF5.
We encourage adopting \href{http://photon-hdf5.readthedocs.org/}{Photon-HDF5} as a fast and space efficient format that assure long-term accessibility to the data and ease data sharing between different programs. All the FRETBursts example data files are in Photon-HDF5 and can be opened with standard viewers such as \href{http://www.hdfgroup.org/products/java/hdfview/}{HDFView}. An additional data file can be found here[multi-spot paper data files].
The \href{http://fretbursts.readthedocs.org/en/latest/loader.html}{\texttt{loader} module}
contains all the functions to load the different file formats. In particular, to load a Photon-HDF5 file use:
\begin{verbatim}
d = loader.hdf5(file_name)
\end{verbatim}
where \verb|file_name| is a string containing the file path. The function \verb|load.hdf5| returns an object \verb|d| of type \href{http://fretbursts.readthedocs.org/en/latest/data_class.html}{\texttt{Data}}) containing all the measurement info (see section~\ref{sec:data_intro}).
Similar functions in the \href{http://fretbursts.readthedocs.org/en/latest/loader.html}{\texttt{loader} module} allows to load the other supported file formats.
\begin{quote}
On MS Windows, it is good practice to use \href{https://docs.python.org/2/tutorial/introduction.html#strings}{RAW strings} for file names (for example: \verb|r'C:\Data\smFRET\example.hdf5'|, note the prepending \textit{r}) in order to avoid substitutions of special escape sequences like \verb|\t| (that would be replaced with TAB in a normal string).
\end{quote}
\subsubsection{Load data manually}
In case the data is available in a format not directly supported by FRETBursts it is possible to manually create a \verb|Data| variable. For example, for non-ALEX smFRET data, two arrays of same length are needed: the timestamps and the acceptor-mask. The timestamps needs to be an int64 numpy array containing the recorded photon timestamps in arbitrary units (usually dictated by the acquisition hardware clock period). The acceptor-mask needs to be a numpy boolean array that is \verb|True| when the corresponding timestamps comes from the acceptor channel and \verb|False| when it comes from the donor channel. Having these arrays a \verb|Data| object can be manually created with:
\begin{verbatim}
d = Data(ph_times_m=[timestamps], A_em=[acceptor_mask],
clk_p=10e-9, ALEX=False, nch=1, fname='file_name')
\end{verbatim}
In the previous example, we set the timestamp unit (\verb|clk_p|) to 10~ns and we specify that the data is not from an ALEX measurements. Creating Data objects for ALEX and nsALEX measurements follows the same lines. We point the interested readers to the \href{https://github.com/tritemio/FRETBursts/blob/master/fretbursts/loader.py}{loader module source code} for other examples.
