Index

A

action_execution() (in module pysted.utils), [1] action_execution_2() (in module pysted.utils), [1] action_execution_g() (in module pysted.utils), [1] add_event() (in module pysted.utils), [1] add_flash_curve() (pysted.exp_data_gen.Nanodomain method), [1] add_nanodomains() (pysted.exp_data_gen.Synapse method), [1] add_node() (pysted.temporal.Fiber method) (pysted.temporal.Nodes method), [1] (pysted.temporal.Polygon method) add_object() (pysted.temporal.NodesCombiner method), [1] (pysted.temporal.Synapse method) add_to_pixel_bank() (pysted.base.Microscope method), [1] (pysted.microscopes.DyMINMicroscope method) (pysted.microscopes.DyMINRESCueMicroscope method) (pysted.microscopes.RESCueMicroscope method)

append() (pysted.temporal.Ensemble method), [1] apply_force() (pysted.temporal.Fiber method) (pysted.temporal.Nodes method), [1] (pysted.temporal.NodesCombiner method), [1] (pysted.temporal.Polygon method) (pysted.temporal.Synapse method) apply_jitter() (pysted.temporal.Fiber method) (pysted.temporal.Nodes method), [1] (pysted.temporal.NodesCombiner method), [1] (pysted.temporal.Polygon method) (pysted.temporal.Synapse method) approx_binomial() (in module pysted.utils), [1] area() (pysted.temporal.Polygon method), [1] array_padder() (in module pysted.utils), [1] array_unpadder() (in module pysted.utils), [1]

B

Beads (class in pysted.exp_data_gen) bleach_future() (pysted.base.TemporalDatamap method), [1] (pysted.base.TemporalSynapseDmap method), [1] (pysted.base.TestTemporalDmap method), [1]

bleach_future_proportional() (pysted.base.TemporalSynapseDmap method), [1]

C

cache() (pysted.base.Microscope method), [1] (pysted.microscopes.DyMINMicroscope method) (pysted.microscopes.DyMINRESCueMicroscope method) (pysted.microscopes.RESCueMicroscope method) calculate_amplitude() (in module pysted.cUtils), [1] cart2pol() (in module pysted.utils), [1] clear_cache() (pysted.base.Microscope method), [1] (pysted.microscopes.DyMINMicroscope method) (pysted.microscopes.DyMINRESCueMicroscope method) (pysted.microscopes.RESCueMicroscope method)

Clock (class in pysted.base), [1] complex_quadrature() (in module pysted.utils), [1] compute_time_correspondances() (in module pysted.utils), [1] create_t_stack_dmap() (pysted.base.TemporalDatamap method), [1] (pysted.base.TemporalSynapseDmap method), [1] (pysted.base.TestTemporalDmap method), [1] create_t_stack_dmap_sampled() (pysted.base.TemporalSynapseDmap method), [1] create_t_stack_dmap_smooth() (pysted.base.TemporalSynapseDmap method), [1] create_t_stack_dmap_smooth_2() (pysted.base.TemporalSynapseDmap method)

D

Datamap (class in pysted.base), [1] datamap_generator() (in module pysted.utils), [1] DatamapLoader (class in pysted.data.loader), [1] default_update_survival_probabilities() (in module pysted.bleach_funcs), [1] degrees_to_radians() (in module pysted.exp_data_gen)

Detector (class in pysted.base), [1] dict_write_func() (in module pysted.utils), [1] DonutBeam (class in pysted.base), [1] DyMINMicroscope (class in pysted.microscopes), [1] DyMINRESCueMicroscope (class in pysted.microscopes), [1]

E

empty_pixel_bank() (pysted.base.Microscope method), [1] (pysted.microscopes.DyMINMicroscope method) (pysted.microscopes.DyMINRESCueMicroscope method) (pysted.microscopes.RESCueMicroscope method)

Ensemble (class in pysted.temporal), [1] event_reader() (in module pysted.utils), [1] expand() (pysted.temporal.Polygon method), [1] exponential() (in module pysted.utils)

F

fatten_nanodomains() (pysted.exp_data_gen.Synapse method), [1] Fiber (class in pysted.temporal), [1] filter_valid_nanodomain_pos() (pysted.exp_data_gen.Synapse method), [1] flash_generator() (in module pysted.utils), [1] flash_nanodomains() (pysted.exp_data_gen.Synapse method), [1]

flash_routine() (in module pysted.utils), [1] float_to_array_verifier() (in module pysted.utils), [1] Fluorescence (class in pysted.base), [1] fwhm() (in module pysted.utils), [1] fwhm_donut() (in module pysted.utils), [1]

G

GaussianBeam (class in pysted.base), [1] generate_fiber_with_synapses() (in module pysted.utils), [1] generate_frame() (pysted.exp_data_gen.Beads method) generate_objects_dict() (pysted.temporal.Ensemble method), [1] generate_random() (pysted.temporal.Fiber method), [1] (pysted.temporal.Polygon method), [1] generate_raster_pixel_list() (in module pysted.utils), [1] generate_secondary_fibers() (in module pysted.utils), [1] generate_sequence() (pysted.temporal.Ensemble method), [1] generate_synapse_flash_dicts() (in module pysted.utils), [1] generate_synapses_on_fiber() (in module pysted.utils), [1] generate_synaptic_fibers() (in module pysted.utils), [1] get_avg_lightcurve() (in module pysted.utils), [1] get_detection_psf() (pysted.base.Detector method), [1] get_effective() (pysted.base.Microscope method), [1] (pysted.microscopes.DyMINMicroscope method) (pysted.microscopes.DyMINRESCueMicroscope method) (pysted.microscopes.RESCueMicroscope method)

get_intensity() (pysted.base.DonutBeam method), [1] (pysted.base.GaussianBeam method), [1] get_k_bleach() (pysted.base.Fluorescence method), [1] get_light_curve() (in module pysted.utils), [1] get_photons() (pysted.base.Fluorescence method), [1] get_psf() (pysted.base.Fluorescence method), [1] get_sigma_abs() (pysted.base.Fluorescence method), [1] get_sigma_ste() (pysted.base.Fluorescence method), [1] get_signal() (pysted.base.Detector method), [1] get_signal_and_bleach() (pysted.base.Microscope method), [1] (pysted.microscopes.DyMINMicroscope method), [1] (pysted.microscopes.DyMINRESCueMicroscope method), [1] (pysted.microscopes.RESCueMicroscope method), [1] get_transmission() (pysted.base.Objective method) grow() (pysted.temporal.Fiber method), [1] (pysted.temporal.Synapse method), [1]

H

hand_crafted_light_curve() (in module pysted.utils), [1]

I

inverse() (in module pysted.utils), [1] inverse_exponential() (in module pysted.utils), [1] is_cached() (pysted.base.Microscope method), [1] (pysted.microscopes.DyMINMicroscope method) (pysted.microscopes.DyMINRESCueMicroscope method) (pysted.microscopes.RESCueMicroscope method)

M

make_path_sane() (in module pysted.utils), [1] Microscope (class in pysted.base), [1] module pysted pysted.base pysted.bleach_funcs pysted.cUtils pysted.data pysted.data.loader pysted.exp_data_gen pysted.microscopes pysted.raster pysted.temporal pysted.utils

molecules_survival() (in module pysted.utils), [1] molecules_symmetry() (in module pysted.utils), [1] mse_calculator() (in module pysted.utils), [1]

N

Nanodomain (class in pysted.exp_data_gen), [1]

Nodes (class in pysted.temporal), [1] NodesCombiner (class in pysted.temporal), [1]

O

Objective (class in pysted.base), [1]

P

pad_values() (in module pysted.utils), [1] pinhole() (in module pysted.utils), [1] pixel_list_filter() (in module pysted.utils), [1] pixel_sampling() (in module pysted.utils), [1] play_action() (pysted.base.TemporalExperiment method), [1] Polygon (class in pysted.temporal), [1] pxsize_comp2() (in module pysted.utils), [1] pxsize_comp_array_maker() (in module pysted.utils), [1] pxsize_grid() (in module pysted.utils), [1] pxsize_ratio() (in module pysted.utils), [1] pysted module pysted.base module pysted.bleach_funcs module

pysted.cUtils module pysted.data module pysted.data.loader module pysted.exp_data_gen module pysted.microscopes module pysted.raster module pysted.temporal module pysted.utils module

R

RandomActionSelector (class in pysted.base), [1] raster_func_c_self_bleach_split_g() (in module pysted.raster), [1] raster_func_dymin() (in module pysted.raster), [1] raster_func_rescue() (in module pysted.raster), [1] rescale() (in module pysted.utils), [1] rescale_data() (in module pysted.utils), [1] RESCueMicroscope (class in pysted.microscopes), [1] reset() (pysted.base.Clock method), [1] reset_force() (pysted.temporal.Ensemble method), [1] (pysted.temporal.Fiber method) (pysted.temporal.Nodes method), [1] (pysted.temporal.NodesCombiner method), [1] (pysted.temporal.Polygon method) (pysted.temporal.Synapse method)

reset_prob() (in module pysted.raster), [1] reset_speed() (pysted.temporal.Ensemble method), [1] (pysted.temporal.Fiber method) (pysted.temporal.Nodes method), [1] (pysted.temporal.NodesCombiner method), [1] (pysted.temporal.Polygon method) (pysted.temporal.Synapse method) resize() (in module pysted.utils), [1] return_frame() (pysted.temporal.Ensemble method), [1] return_shape() (pysted.temporal.Fiber method), [1] (pysted.temporal.Nodes method), [1] (pysted.temporal.Polygon method), [1] (pysted.temporal.Synapse method), [1] rotate_and_translate() (pysted.exp_data_gen.Synapse method) rotate_nds() (in module pysted.exp_data_gen), [1]

S

sample_light_curve() (in module pysted.utils), [1] sample_molecules() (in module pysted.bleach_funcs), [1] sampled_flash_manipulations() (in module pysted.utils), [1] savitzky_golay() (in module pysted.utils), [1] select_action() (pysted.base.RandomActionSelector method), [1] set_bleached_datamap() (pysted.base.Datamap method), [1] (pysted.base.TemporalDatamap method) (pysted.base.TemporalSynapseDmap method) (pysted.base.TestTemporalDmap method) set_roi() (pysted.base.Datamap method), [1] (pysted.base.TemporalDatamap method) (pysted.base.TemporalSynapseDmap method) (pysted.base.TestTemporalDmap method)

set_starting_pixel() (in module pysted.utils), [1] shift_data() (in module pysted.utils), [1] show() (pysted.temporal.Ensemble method), [1] smooth_ramp_hand_crafted_light_curve() (in module pysted.utils), [1] smooth_ramp_hand_crafted_light_curve_2() (in module pysted.utils) spawn() (pysted.temporal.Ensemble method), [1] (pysted.temporal.Fiber method), [1] stack() (in module pysted.utils), [1] stack_btmod_definitive() (in module pysted.utils), [1] symmetry_verifier() (in module pysted.utils), [1] Synapse (class in pysted.exp_data_gen), [1] (class in pysted.temporal), [1]

T

take_from_pixel_bank() (pysted.base.Microscope method), [1] (pysted.microscopes.DyMINMicroscope method) (pysted.microscopes.DyMINRESCueMicroscope method) (pysted.microscopes.RESCueMicroscope method)

TemporalDatamap (class in pysted.base), [1] TemporalExperiment (class in pysted.base), [1] TemporalSynapseDmap (class in pysted.base), [1] TestTemporalDmap (class in pysted.base), [1] time_quantum_to_flash_tstep_correspondance() (in module pysted.utils), [1]

U

update() (pysted.temporal.Ensemble method), [1] (pysted.temporal.Fiber method), [1] (pysted.temporal.Nodes method), [1] (pysted.temporal.NodesCombiner method), [1] (pysted.temporal.Polygon method), [1] (pysted.temporal.Synapse method)

update_dicts() (pysted.base.TemporalDatamap method), [1] (pysted.base.TemporalSynapseDmap method), [1] (pysted.base.TestTemporalDmap method) update_time() (pysted.base.Clock method), [1] update_whole_datamap() (pysted.base.TemporalDatamap method), [1] (pysted.base.TemporalSynapseDmap method), [1] (pysted.base.TestTemporalDmap method)