The fretmath
module contains functions to compute corrected FRET efficiency
from the proximity ratio and viceversa.
For derivation see notebook: “Derivation of FRET and S correction formulas.ipynb” (link).
fretbursts.fretmath.
correct_E_gamma_leak_dir
(Eraw, gamma=1, leakage=0, dir_ex_t=0)¶Compute corrected FRET efficiency from proximity ratio Eraw
.
For the inverse function see uncorrect_E_gamma_leak_dir()
.
Parameters: 


fretbursts.fretmath.
correct_S
(Eraw, Sraw, gamma, leakage, dir_ex_t)¶Correct S values for gamma, leakage and direct excitation.
Parameters: 


Sraw
.fretbursts.fretmath.
dir_ex_correct_E
(Eraw, dir_ex_t)¶Apply direct excitation correction to the uncorrected FRET Eraw
.
The coefficient dir_ex_t
expresses the direct excitation as
n_dir = dir_ex_t * (na + gamma*nd). In terms of physical
parameters it is the ratio of acceptor over donor absorption
crosssections at the donorexcitation wavelength.
For the inverse see dir_ex_uncorrect_E()
.
fretbursts.fretmath.
dir_ex_uncorrect_E
(E, dir_ex_t)¶Reverse direct excitation correction and return uncorrected FRET.
For the inverse see dir_ex_correct_E()
.
fretbursts.fretmath.
gamma_correct_E
(Eraw, gamma)¶Apply gamma correction to the uncorrected FRET Eraw
.
For the inverse see gamma_uncorrect_E()
.
fretbursts.fretmath.
gamma_uncorrect_E
(E, gamma)¶Reverse gamma correction and return uncorrected FRET.
For the inverse see gamma_correct_E()
.
fretbursts.fretmath.
leakage_correct_E
(Eraw, leakage)¶Apply leakage correction to the uncorrected FRET Eraw
.
For the inverse see leakage_uncorrect_E()
.
fretbursts.fretmath.
leakage_uncorrect_E
(E, leakage)¶Reverse leakage correction and return uncorrected FRET.
For the inverse see leakage_correct_E()
.
fretbursts.fretmath.
test_fretmath
()¶Run a few consistency checks for the correction functions.
fretbursts.fretmath.
uncorrect_E_gamma_leak_dir
(E, gamma=1, leakage=0, dir_ex_t=0)¶Compute proximity ratio from corrected FRET efficiency E
.
This function is the inverse of correct_E_gamma_leak_dir()
.
Parameters: 


fretbursts.fretmath.
uncorrect_S
(E_R, S, gamma, L_k, d_dirT)¶Function used to test correct_S()
.