nrv.ui

Description

User Interface - ui: end user pre- or post processing code

ui provides classes and functions for pre- (meshing for instance) or post-processing computations. Basic or recurent simulation encapuslated as function are also accessible.

Functions

search_threshold_dispatcher(search_func, ...)	Automatically dispatches any search threshold callable object on available cpu cores.
axon_AP_threshold(axon, amp_max, update_func)	Find the activation threshold of an axon with arbitrary stimulation settings.
axon_block_threshold(axon, amp_max, ...[, ...])	Find the block threshold of an axon with arbitrary stimulation settings.
firing_threshold_point_source(diameter, L, ...)	Find the firing threshold with point source approximation using binary search.
firing_threshold_from_axon(axon[, ...])	Find the firing threshold from a specified axon using binary search
para_firing_threshold(diameter, L, material, ...)
blocking_threshold_point_source(diameter, L, ...)	Find the blocking threshold with point source approximation using binary search.
blocking_threshold_from_axon(axon[, ...])	Find the blocking threshold with point source approximation using binary search.
para_blocking_threshold(diameter, L, ...[, ...])
remove_key(my_dict, key[, verbose])	Remove an item from a dictionary, usefull before saving files, as some results maybe heavy and are potentially useless after some steps of postprocessing.
remove_non_NoR_zones(my_dict, key)	Automatically remove values out of nodes of Ranvier for membrane voltage and associated quantities.
generate_axon_from_results(results)	generate a blank axon with the same dimensions as in the results
filter_freq(my_dict, my_key, freq[, Q])	Basic Filtering of quantities.
rasterize(my_dict, my_key[, t_start, ...])	Rasterize a membrane potential (or filtered or any quantity processed from membrane voltage), with spike detection.
AP_detection(Voltage, t, x, list_to_parse, ...)	Internal use only, spike detection just in time compiled to speed up the process
speed(my_dict[, position_key, t_start, ...])	Compute the velocity of a spike from rasterized data in a dictionary.
block(my_dict[, position_key, t_start, t_stop])	check if an axon is blocked or not.
max_spike_position(...[, spike_begin])
count_spike(onset_position)	spike counting, just in time compiled.
check_test_AP(results_sim)	Check if a test AP is correctely triggered during an axon simulation and if so return the trigger time
detect_start_extrastim(results_sim[, threshold])	Returns the starting time of extracellular stimulation from axon simulation results
extra_stim_properties(results_sim)	Return elect caracteristics (blocked, Onset response, ...)
axon_state(results_sim[, save, saving_file])	Return axon caracteristics (blocked, Onset response, ...) from axon simulation results
get_index_myelinated_sequence(results, n)	Returns the sequence
find_central_node_index(results)	Returns the index of the closer node from the center from a dictionnary results
compute_f_mem(results)	compute the cutoff frequency of the axon's membrane and add it to the simulation results dictionnary NB: The frequency is computed in [kHz]
get_myelin_properties(results)	compute the cutoff frequency of the axon's membrane and add it to the simulation results dictionnary NB: The frequency is computed in [kHz]
plot_Nav_states(ax, values[, title])	Plot the state machine for kinetic (Markov) Nav 1.1 to 1.9 values
default_PP(results)	Default postprocessing function.
rmv_keys(results[, keys_to_remove, keys_to_keep])	remove most of the results key to save computing memory.
is_recruited(results)	Evaluate if each fibre is recruited by a stimulation (see axon_results.is_recruited) and remove most of the axon_results keys to alliviate RAM usage.
is_blocked(results[, AP_start, freq, ...])	Evaluate the impact od a blocking stimulation on axon (see axon_results.block_summary) and remove most of the axon_results keys to alliviate RAM usage.
sample_g_mem(results[, t_start_rec, ...])	Undersample the membrane coductivity (results["g_mem"]) key and remove most of the axon_results keys to alliviate RAM usage.
vmem_plot(results[, freq, save, fdir])	Plot and save the membrane potential along each axon of the fascicle
raster_plot(results[, freq, save, fdir])	Plot and save the raster plot along each axon of the fascicle.
ls_axons_results(dir_path)	return list of axons simulation result files
ls_csv(dir_path)	return list of axons simulation result files
rm_file(file_path[, verbose])	Delete file
rm_sim_dir(dir_path[, verbose])	Delete directory Warning: use with caution deleted files cannot be recovered
rm_sim_dir_from_results(results[, verbose])	Delete directory Warning: use with caution deleted files cannot be recovered
CAP_time_detection(Voltage, t[, t_stim, ...])	internal use, Return index in the time scale or time of the start and stop of a Compound Action Potentiel
fascicular_state(dir_path[, save, ...])	Return each axon caracteristics (blocked, Onset response, ...)
plot_fasc_state(facsicular_state, axes[, ...])	plot the fascicle in the Y-Z plane (transverse section)
mesh_from_electrode(elec[, mesh, Length, ...])	returns the corresponding mesh from a nrv.facsicle
mesh_from_extracellular_context(extracel_context)	returns the corresponding mesh from a nrv.facsicle
mesh_from_fascicle(fascicle[, mesh, Length, ...])	returns the corresponding mesh from a nrv.facsicle
mesh_from_nerve(nerve[, length, add_axons, ...])