Single channel burst calculations

A collection of functions for single channel burst calculations.

scburst.endBurst(mec)

Calculate the end vector for a burst (Eq. 3.4, CH82).

\bs{e}_\text{b} = (\bs{I}-\bs{G}_\cl{AB} \bs{G}_\cl{BA}) \bs{u}_\cl{A}

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

Returns :

eB : array_like, shape (kA, 1)

scburst.first_opening_length_pdf_components(mec)

Calculate time constants and amplitudes for an ideal (no missed events) pdf of first opening in a burst with 2 or more openings.

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

Returns :

eigs : ndarray, shape(k, 1)

Time constants.

w : ndarray, shape(k, 1)

Component amplitudes.

scburst.length_cond_pdf(mec, t)

The distribution of burst length coditional on starting state.

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

t : float

Length.

Returns :

vec : array_like, shape (kA, 1)

Probability of seeing burst length t depending on starting state.

scburst.length_mean(mec)

Calculate the mean burst length (Eq. 3.19, CH82). m = PhiB * (I - GAB * GBA)^(-1) * (-QAA^(-1)) * (I - QAB * (QBB^(-1)) * GBA) * uA

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

Returns :

m : float

The mean burst length.

scburst.length_pdf(mec, t)

Probability density function of the burst length (Eq. 3.17, CH82). f(t) = phiB * [PEE(t)]AA * (-QAA) * eB, where PEE(t) = exp(QEE * t)

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

Returns :

f : float

scburst.length_pdf_components(mec)

Calculate time constants and areas for an ideal (no missed events) exponential burst length probability density function.

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

Returns :

eigs : ndarray, shape(k, 1)

Time constants.

w : ndarray, shape(k, 1)

Component amplitudes.

scburst.open_time_mean(mec)

Calculate the mean total open time per burst (Eq. 3.26, CH82).

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

Returns :

m : float

The mean total open time per burst.

scburst.openings_cond_distr_depend_on_start_state(mec, r)

The distribution of openings per burst coditional on starting state.

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

r : int

Number of openings per burst.

Returns :

vecPr : array_like, shape (kA, 1)

Probability of seeing r openings per burst depending on starting state.

scburst.openings_distr(mec, r)

The distribution of openings per burst (Eq. 3.5, CH82). P(r) = phiB * (GAB * GBA)^(r-1) * eB

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

r : int

Number of openings per burst.

Returns :

Pr : float

Probability of seeing r openings per burst.

scburst.openings_distr_components(mec)

Calculate coeficients for geometric ditribution P(r)- probability of seeing r openings (Eq. 3.9 CH82): P(r) = sum(W * rho^(r-1)) where w wm = phiB * Am * endB (Eq. 3.10 CH82) and rho- eigenvalues of GAB * GBA.

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

r : int

Number of openings per burst.

Returns :

rho : ndarray, shape (kA,)

w : ndarray, shape (kA,)

scburst.openings_mean(mec)

Calculate the mean number of openings per burst (Eq. 3.7, CH82). mu = phiB * (I - GAB * GBA)^(-1) * uA

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

Returns :

mu : float

The mean number ofopenings per burst.

scburst.phiBurst(mec)

Calculate the start probabilities of a burst (Eq. 3.2, CH82). phiB = (pCinf * (QCB * GBA + QCA)) / (pCinf * (QCB * GBA + QCA) * uA)

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

Returns :

phiB : array_like, shape (1, kA)

scburst.printout(mec, output=<open file '<stdout>', mode 'w' at 0x2b971dd501e0>, eff='c')

Output burst calculations into selected device (sys.stdout, printer, file, text field.

Parameters :

mec : dcpyps.Mechanism

The mechanism to be analysed.

output : output device

Default device: sys.stdout

eff : string

Effector; e.g. ‘c’- concentration.

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