Description of the files¶
Here a brief descriprion of the main FRETBursts files.
This module contains all the main FRETBursts analysis functions.
burstslib.py defines the fundamental object
Data() that contains both the
experimental data (attributes) and the high-level analysis routines (methods).
Furthermore it loads all the remaining FRETBursts modules (except for
For usage example see the IPython Notebooks in sub-folder “notebooks”.
loader module contains functions to load each supported data format.
The loader functions load data from a specific format and
return a new
fretbursts.burstlib.Data() object containing the data.
This module contains the high-level function to load a data-file and
to return a
Data() object. The low-level functions that perform the binary
loading and preprocessing can be found in the
This module defines all the plotting functions for the
The main plot function is
dplot() that takes, as parameters, a
object and a 1-ch-plot-function and creates a subplot for each channel.
The 1-ch plot functions are usually called through
dplot but can also be
called directly to make a single channel plot.
The 1-ch plot functions names all start with the plot type (
Example 1 - Plot the timetrace for all ch:
dplot(d, timetrace, scroll=True)
Example 2 - Plot a FRET histogramm for each ch with a fit overlay:
dplot(d, hist_fret, show_model=True)
For more examples refer to FRETBurst notebooks.
Routines to compute the background from an array of timestamps. This module
is normally imported as
bg when fretbursts is imported.
The important functions are
provide two (fast) algorithms to estimate the background without binning.
These functions are not usually called directly but passed to
Data.calc_bg() to compute the background of a measurement.
exp_hist_fit() for background estimation using an histogram fit.
This folder contains the core functions to manipulate timestamps, including burst search and photon rates computations. Additionally, data structures for storing and manipulating bursts data are provided.
Burst search and photon counting functions (to count number of donor and acceptor
photons in each burts) are provided both as a pure python implementation and as
an optimized Cython (compiled) version. The cython version is usually 10 or 20
burstlib.py will load the Cython functions, falling back to the
pure python version if the compiled version is not found.
This folder contains one file per each supported data file.
Each file contains the binary load and preprocessing functions needed for
the specific format. Functions defined here are used by loader functions
loaders.py to properly initialize a
This folder contains generic fit functions for Gaussian and exponential fit of a sample.
See Fit framework.