Index

A | B | C | D | E | F | G | H | I | J | K | L | M | N | P | R | S | T | U | W

A

A_em (fretbursts.burstlib.Data attribute)
alex_apply_period() (in module fretbursts.loader)
alex_jointplot() (in module fretbursts.burst_plot)
alex_period (fretbursts.burstlib.Data attribute)
and_gate() (fretbursts.phtools.burstsearch.Bursts method)
asym_gaussian() (in module fretbursts.mfit)
asymmetry() (in module fretbursts.burstlib_ext)

B

background_correction() (fretbursts.burstlib.Data method)
bg (fretbursts.burstlib.Data attribute)
bg_bs (fretbursts.burstlib.Data attribute)
bg_fun (fretbursts.burstlib.Data attribute)
bg_mean (fretbursts.burstlib.Data attribute)
bg_ph_sel (fretbursts.burstlib.Data attribute)
bound_check() (in module fretbursts.fit.gaussian_fitting)
bp (fretbursts.burstlib.Data attribute)
bridge_function() (in module fretbursts.mfit)
brightness() (in module fretbursts.select_bursts)
bsearch_py() (in module fretbursts.phtools.burstsearch)
Burst (class in fretbursts.phtools.burstsearch)
burst_data() (in module fretbursts.burstlib_ext)
burst_data_period_mean() (in module fretbursts.burstlib_ext)
burst_search() (fretbursts.burstlib.Data method)
burst_search_and_gate() (in module fretbursts.burstlib_ext)
burst_sizes() (fretbursts.burstlib.Data method)
burst_sizes_ich() (fretbursts.burstlib.Data method)
burst_widths (fretbursts.burstlib.Data attribute)
Bursts (class in fretbursts.phtools.burstsearch)
bursts_fitter() (in module fretbursts.burstlib_ext)
BurstsGap (class in fretbursts.phtools.burstsearch)

C

calc_bg() (fretbursts.burstlib.Data method)
calc_bg_brute() (in module fretbursts.burstlib_ext)
calc_bg_brute_cache() (in module fretbursts.burstlib_ext)
calc_fret() (fretbursts.burstlib.Data method)
calc_kde() (fretbursts.mfit.MultiFitter method)
calc_max_rate() (fretbursts.burstlib.Data method)
calc_mdelays_hist() (in module fretbursts.burstlib_ext)
calc_mean_lifetime() (in module fretbursts.burstlib_ext)
calc_ph_num() (fretbursts.burstlib.Data method)
calc_sbr() (fretbursts.burstlib.Data method)
chi_ch (fretbursts.burstlib.Data attribute)
clk_p (fretbursts.burstlib.Data attribute)
consecutive() (in module fretbursts.select_bursts)
copy() (fretbursts.burstlib.Data method)
(fretbursts.phtools.burstsearch.Bursts method)
correct_E_gamma_leak_dir() (in module fretbursts.fretmath)
correct_S() (in module fretbursts.fretmath)
count_ph_in_bursts() (in module fretbursts.phtools.burstsearch)
counts (fretbursts.phtools.burstsearch.Burst attribute)
(fretbursts.phtools.burstsearch.Bursts attribute)
(fretbursts.phtools.burstsearch.BurstsGap attribute)

D

D_em (fretbursts.burstlib.Data attribute)
Data (class in fretbursts.burstlib), [1], [2], [3], [4], [5], [6], [7]
dataframe (fretbursts.phtools.burstsearch.Bursts attribute)
dir_ex (fretbursts.burstlib.Data attribute)
dir_ex_correct_E() (in module fretbursts.fretmath)
dir_ex_uncorrect_E() (in module fretbursts.fretmath)
dither() (fretbursts.burstlib.Data method)

E

E (fretbursts.burstlib.Data attribute)
E() (in module fretbursts.select_bursts)
empty() (fretbursts.phtools.burstsearch.Bursts class method)
ES() (in module fretbursts.select_bursts)
ES_ellips() (in module fretbursts.select_bursts)
ES_rect() (in module fretbursts.select_bursts)
exp_cdf_fit() (in module fretbursts.background)
exp_fit() (in module fretbursts.background)
exp_hist_fit() (in module fretbursts.background)
expand() (fretbursts.burstlib.Data method)
expon_fit() (in module fretbursts.fit.exp_fitting), [1]
expon_fit_cdf() (in module fretbursts.fit.exp_fitting), [1]
expon_fit_hist() (in module fretbursts.fit.exp_fitting), [1]

F

F (fretbursts.burstlib.Data attribute)
factory_asym_gaussian() (in module fretbursts.mfit)
factory_gaussian() (in module fretbursts.mfit)
factory_three_gaussians() (in module fretbursts.mfit)
factory_two_asym_gaussians() (in module fretbursts.mfit)
factory_two_gaussians() (in module fretbursts.mfit)
find_kde_max() (fretbursts.mfit.MultiFitter method)
fit_bursts_kde_peak() (in module fretbursts.burstlib_ext)
fit_E_binom() (in module fretbursts.fret_fit)
fit_E_cdf() (in module fretbursts.fret_fit)
fit_E_E_size() (in module fretbursts.fret_fit)
fit_E_generic() (fretbursts.burstlib.Data method)
fit_E_hist() (in module fretbursts.fret_fit)
fit_E_m() (fretbursts.burstlib.Data method)
(in module fretbursts.fret_fit)
fit_E_minimize() (fretbursts.burstlib.Data method)
fit_E_ML_poiss() (fretbursts.burstlib.Data method)
fit_E_poisson_na() (in module fretbursts.fret_fit)
fit_E_poisson_nd() (in module fretbursts.fret_fit)
fit_E_poisson_nt() (in module fretbursts.fret_fit)
fit_E_slope() (in module fretbursts.fret_fit)
fit_E_two_gauss_EM() (fretbursts.burstlib.Data method)
fit_histogram() (fretbursts.mfit.MultiFitter method)
fname (fretbursts.burstlib.Data attribute)
fretbursts (module)
fretbursts.background (module), [1]
fretbursts.burst_plot (module), [1]
fretbursts.burstlib (module), [1], [2], [3]
fretbursts.burstlib_ext (module)
fretbursts.dataload (module)
fretbursts.fit (module)
fretbursts.fit.exp_fitting (module), [1]
fretbursts.fit.gaussian_fitting (module)
fretbursts.fret_fit (module)
fretbursts.fretmath (module)
fretbursts.loader (module), [1]
fretbursts.mfit (module)
fretbursts.ph_sel (module)
fretbursts.phtools (module)
fretbursts.phtools.burstsearch (module)
fretbursts.phtools.phrates (module)
fretbursts.select_bursts (module)
from_list() (fretbursts.phtools.burstsearch.Bursts class method)
(fretbursts.phtools.burstsearch.BurstsGap class method)
fuse (fretbursts.burstlib.Data attribute)
fuse_bursts() (fretbursts.burstlib.Data method)

G

gamma (fretbursts.burstlib.Data attribute), [1]
gamma_correct_E() (in module fretbursts.fretmath)
gamma_uncorrect_E() (in module fretbursts.fretmath)
gap (fretbursts.phtools.burstsearch.BurstsGap attribute)
gap_counts (fretbursts.phtools.burstsearch.BurstsGap attribute)
gaussian2d_fit() (in module fretbursts.fit.gaussian_fitting)
gaussian_fit_cdf() (in module fretbursts.fit.gaussian_fitting)
gaussian_fit_curve() (in module fretbursts.fit.gaussian_fitting)
gaussian_fit_hist() (in module fretbursts.fit.gaussian_fitting)
gaussian_fit_ml() (in module fretbursts.fit.gaussian_fitting)
gaussian_fit_pdf() (in module fretbursts.fit.gaussian_fitting)
get_burst_photons() (in module fretbursts.burstlib_ext)
get_dist_euclid() (in module fretbursts.fret_fit)
get_ecdf() (in module fretbursts.fit.exp_fitting), [1]
get_epdf() (in module fretbursts.fit.gaussian_fitting)
get_naa_corrected() (fretbursts.burstlib.Data method)
get_ph_mask() (fretbursts.burstlib.Data method)
get_ph_times() (fretbursts.burstlib.Data method)
get_residuals() (in module fretbursts.fit.exp_fitting), [1]
get_weights() (in module fretbursts.fret_fit)

H

hexbin_alex() (in module fretbursts.burst_plot)
hist2d_alex() (in module fretbursts.burst_plot)
hist_asymmetry() (in module fretbursts.burst_plot)
hist_bg() (in module fretbursts.burst_plot)
hist_bg_single() (in module fretbursts.burst_plot)
hist_brightness() (in module fretbursts.burst_plot)
hist_burst_data() (in module fretbursts.burst_plot)
hist_burst_delays() (in module fretbursts.burst_plot)
hist_burst_phrate() (in module fretbursts.burst_plot)
hist_fret() (in module fretbursts.burst_plot)
hist_interphoton() (in module fretbursts.burst_plot)
hist_interphoton_single() (in module fretbursts.burst_plot)
hist_S() (in module fretbursts.burst_plot)
hist_sbr() (in module fretbursts.burst_plot)
hist_size() (in module fretbursts.burst_plot)
hist_size_all() (in module fretbursts.burst_plot)
hist_width() (in module fretbursts.burst_plot)
histogram() (fretbursts.mfit.MultiFitter method)
histogram_mdelays() (in module fretbursts.burstlib_ext)

I

istart (fretbursts.phtools.burstsearch.Bursts attribute)
istop (fretbursts.phtools.burstsearch.Bursts attribute)
iter_bursts_ph() (fretbursts.burstlib.Data method)
iter_ph_masks() (fretbursts.burstlib.Data method)
iter_ph_times() (fretbursts.burstlib.Data method)

J

join() (fretbursts.phtools.burstsearch.Bursts method)
join_data() (in module fretbursts.burstlib_ext)

K

kde_gaussian() (in module fretbursts.phtools.phrates)
kde_laplace() (in module fretbursts.phtools.phrates)
kde_rect() (in module fretbursts.phtools.phrates)

L

L (fretbursts.burstlib.Data attribute)
leakage (fretbursts.burstlib.Data attribute), [1]
leakage_correct_E() (in module fretbursts.fretmath)
leakage_correction() (fretbursts.burstlib.Data method)
leakage_uncorrect_E() (in module fretbursts.fretmath)
Lim (fretbursts.burstlib.Data attribute)
log_likelihood_binom() (in module fretbursts.fret_fit)
log_likelihood_poisson_na() (in module fretbursts.fret_fit)
log_likelihood_poisson_nd() (in module fretbursts.fret_fit)
log_likelihood_poisson_nt() (in module fretbursts.fret_fit)

M

m (fretbursts.burstlib.Data attribute)
mburst (fretbursts.burstlib.Data attribute)
mch_count_ph_in_bursts_py() (in module fretbursts.phtools.burstsearch)
merge() (fretbursts.phtools.burstsearch.Bursts class method)
moving_window_chunks() (in module fretbursts.burstlib_ext)
moving_window_dataframe() (in module fretbursts.burstlib_ext)
moving_window_startstop() (in module fretbursts.burstlib_ext)
mtuple_delays() (in module fretbursts.phtools.phrates)
mtuple_delays_min() (in module fretbursts.phtools.phrates)
mtuple_rates() (in module fretbursts.phtools.phrates)
mtuple_rates_max() (in module fretbursts.phtools.phrates)
mtuple_rates_t() (in module fretbursts.phtools.phrates)
MultiFitter (class in fretbursts.mfit)

N

na() (in module fretbursts.select_bursts)
na_bg() (in module fretbursts.select_bursts)
na_bg_p() (in module fretbursts.select_bursts)
naa (fretbursts.burstlib.Data attribute)
naa() (in module fretbursts.select_bursts)
naa_bg() (in module fretbursts.select_bursts)
naa_bg_p() (in module fretbursts.select_bursts)
name (fretbursts.burstlib.Data attribute)
Name() (fretbursts.burstlib.Data method)
nch (fretbursts.burstlib.Data attribute)
nd() (in module fretbursts.select_bursts)
nd_bg() (in module fretbursts.select_bursts)
nd_bg_p() (in module fretbursts.select_bursts)
nda_percentile() (in module fretbursts.select_bursts)
normpdf() (in module fretbursts.fit.gaussian_fitting)
nperiods (fretbursts.burstlib.Data attribute)
nsalex() (in module fretbursts.loader)
nsalex_apply_period() (in module fretbursts.loader)
nt (fretbursts.burstlib.Data attribute)
nt_bg() (in module fretbursts.select_bursts)
nt_bg_p() (in module fretbursts.select_bursts)
num_bursts (fretbursts.burstlib.Data attribute)
(fretbursts.phtools.burstsearch.Bursts attribute)

P

P (fretbursts.burstlib.Data attribute)
peak_phrate() (in module fretbursts.select_bursts)
period() (in module fretbursts.select_bursts)
ph_burst_stats() (in module fretbursts.burstlib_ext)
ph_data_sizes (fretbursts.burstlib.Data attribute)
ph_in_bursts_ich() (fretbursts.burstlib.Data method)
ph_in_bursts_mask_ich() (fretbursts.burstlib.Data method)
Ph_p (fretbursts.burstlib.Data attribute)
ph_rate (fretbursts.phtools.burstsearch.Burst attribute)
(fretbursts.phtools.burstsearch.Bursts attribute)
Ph_sel (class in fretbursts.ph_sel)
ph_sel (fretbursts.burstlib.Data attribute)
ph_times_m (fretbursts.burstlib.Data attribute)
photon_hdf5() (in module fretbursts.loader)
plot_alternation_hist() (in module fretbursts.burst_plot)
plot_alternation_hist_nsalex() (in module fretbursts.burst_plot)
plot_ES_selection() (in module fretbursts.burst_plot)

R

ratetrace() (in module fretbursts.burst_plot)
ratetrace_single() (in module fretbursts.burst_plot)
recompute_index_expand() (fretbursts.phtools.burstsearch.Bursts method)
recompute_index_reduce() (fretbursts.phtools.burstsearch.Bursts method)
recompute_times() (fretbursts.phtools.burstsearch.Bursts method)
reorder_parameters() (in module fretbursts.fit.gaussian_fitting)
reorder_parameters_ab() (in module fretbursts.fit.gaussian_fitting)

S

S (fretbursts.burstlib.Data attribute)
sbr() (in module fretbursts.select_bursts)
scatter_alex() (in module fretbursts.burst_plot)
scatter_da() (in module fretbursts.burst_plot)
scatter_fret_nd_na() (in module fretbursts.burst_plot)
scatter_fret_size() (in module fretbursts.burst_plot)
scatter_fret_width() (in module fretbursts.burst_plot)
scatter_naa_nt() (in module fretbursts.burst_plot)
scatter_rate_da() (in module fretbursts.burst_plot)
scatter_width_size() (in module fretbursts.burst_plot)
select_bursts() (fretbursts.burstlib.Data method)
select_bursts_mask() (fretbursts.burstlib.Data method)
select_bursts_mask_apply() (fretbursts.burstlib.Data method)
separation (fretbursts.phtools.burstsearch.Bursts attribute)
set_weights_func() (fretbursts.mfit.MultiFitter method)
sim_nd_na() (in module fretbursts.fret_fit)
single() (in module fretbursts.select_bursts)
size (fretbursts.phtools.burstsearch.Bursts attribute)
size() (in module fretbursts.select_bursts)
slice_ph() (fretbursts.burstlib.Data method)
start (fretbursts.phtools.burstsearch.Bursts attribute)
status() (fretbursts.burstlib.Data method)
stop (fretbursts.phtools.burstsearch.Bursts attribute)
str_G() (in module fretbursts.select_bursts)

T

T (fretbursts.burstlib.Data attribute)
test_fretmath() (in module fretbursts.fretmath)
Th_us (fretbursts.burstlib.Data attribute)
time() (in module fretbursts.select_bursts)
time_max (fretbursts.burstlib.Data attribute)
time_min (fretbursts.burstlib.Data attribute)
timetrace() (in module fretbursts.burst_plot)
timetrace_b_rate() (in module fretbursts.burst_plot)
timetrace_bg() (in module fretbursts.burst_plot)
timetrace_single() (in module fretbursts.burst_plot)
topN_max_rate() (in module fretbursts.select_bursts)
topN_nda() (in module fretbursts.select_bursts)
topN_sbr() (in module fretbursts.select_bursts)
TT (fretbursts.burstlib.Data attribute)
two_gauss_mix_ab() (in module fretbursts.fit.gaussian_fitting)
two_gauss_mix_pdf() (in module fretbursts.fit.gaussian_fitting)
two_gaussian2d_fit() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_cdf() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_curve() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_EM() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_EM_b() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_hist() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_hist_min() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_hist_min_ab() (in module fretbursts.fit.gaussian_fitting)
two_gaussian_fit_KDE_curve() (in module fretbursts.fit.gaussian_fitting)

U

uncorrect_E_gamma_leak_dir() (in module fretbursts.fretmath)
uncorrect_S() (in module fretbursts.fretmath)
usalex() (in module fretbursts.loader)
usalex_apply_period() (in module fretbursts.loader)

W

width (fretbursts.phtools.burstsearch.Burst attribute)
(fretbursts.phtools.burstsearch.Bursts attribute)
(fretbursts.phtools.burstsearch.BurstsGap attribute)
width() (in module fretbursts.select_bursts)