nerve

class nrv.nmod.nerve(length=10000, diameter=100, Outer_D=5, ID=0, **kwargs)

A nerve in NRV is defined as:

• a list of fascicle

• an analytical stimulation or a FEM_stimulation context

A nerve can be instrumented by adding couples of electrodes+stimulus

The extracellular context of the nerve is automatically generated from the context of its fascicles and an optional context added directly to the nerve.

See also

Simulables users guide, Fascicle-class, Axon-class

Customizable Attributes:

Attributes	Type	Default	Description
ID	int	0	Identification number of the nerve.
L	float	None	Length of the nerve.
D	float	None	Diameter of the nerve.
y_grav_center	float	0	y-position of the nerve center.
z_grav_center	float	0	z-position of the nerve center.
postproc_label	str	None	Label of the axon postprocessing funtion, used for the buildin postproc functions.
postproc_function	function	None	Axon postprocessing funtion, used for the custom postproc functions.
postproc_script	str | function	None	Either postprocessing funtion or postprocessing funtion label, automatically set depending on the type
postproc_kwargs	dict	None	key arguments of the postporcessing function
save_results	bool	False	If True, nerve configuration and all axon simulations results are saved in save_path directory.
save_path	str	“”	Path of the directory where simulation results should be saved.
return_parameters_only	bool	False	If True (and save_results also True), only the parameters should be returned from the simulation.
loaded_footprints	bool	False	If False, the footprints already computed are favored over new footprint computation.
verbose	bool	False	Plot or not.

Note

Customizable attributes can either be set using nerve.set_parameters() or simply by reafecting the value of the attribute.

Tip

Additional simulation parameters can be changed using (nerve.set_axons_parameters(), nerve.change_stimulus_from_electrode(), …).

Parameters:

• length (float) – Nerve length, in um

• diameter (float) – Nerve diameter, in um

• Outer_D (float) – Outer saline box diameter, in mm

• ID (int) – Nerve unique identifier

Attributes

nerve.has_FEM_extracel
nerve.n_ax	Number of axons in the nerves
nerve.n_fasc	Number of fascicles in the nerves

Methods

nerve.__init__([length, diameter, Outer_D, ID])	Instanciates an empty nerve.
nerve.add_fascicle(fascicle[, ID, y, z, ...])	Add a fascicle to the list of fascicles
nerve.attach_extracellular_recorder(rec)	attach an extracellular recorder to the axon
nerve.attach_extracellular_stimulation(...)	attach a extracellular context of simulation for an axon.
nerve.change_stimulus_from_electrode(...)	Change the stimulus of the ID_elec electrods
nerve.clear_I_clamp()	Clear any I-clamp attached to the nerve
nerve.clear_context([extracel_context, ...])	Clear all stimulation and recording mecanism
nerve.compute_electrodes_footprints(**kwargs)	compute electrodes footprints
nerve.define_circular_contour(D[, y_c, z_c])	Define a circular countour to the nerve
nerve.define_ellipsoid_contour(a, b[, y_c, ...])	Define ellipsoidal contour
nerve.define_length(L)	Set the length over the x axis of the nerve
nerve.extracel_status()	Check if an extracellular context is attached to the instance
nerve.fit_circular_contour([y_c, z_c, ...])	Define a circular countour to the nerve
nerve.get_axons_parameters([...])	get parameters of axons in the nerve
nerve.get_circular_contour()	Returns the properties of the nerve contour considered as a circle (y and z center and diameter)
nerve.get_fascicles([ID_only])	Return a _fascicle.fascicle object from it ID in the nerve
nerve.get_n_ax([id_fasc])	Returns the number of axons in a given fascicle or in all the nerve
nerve.get_parameters()	Generic method returning all the atributes of an NRV_class instance
nerve.import_contour(smthing_else)	Define contour from a file
nerve.insert_I_Clamp(position, t_start, ...)	Insert a IC clamp stimulation
nerve.intracel_status()	Check if an intracellular context is attached to the instance
nerve.load(data[, extracel_context, ...])	Load a fascicle configuration from a json file
nerve.plot(axes[, contour_color, ...])	plot the nerve in the Y-Z plane (transverse section)
nerve.rec_status()	Check if a recording context is attached to the instance
nerve.save([fname, extracel_context, ...])	Save a fascicle in a json file
nerve.set_ID(ID)	set the ID of the nerve
nerve.set_axons_parameters([...])	set parameters of axons in the nerve
nerve.set_parameters(**kawrgs)	Generic method to set any attribute of NRV_class instance
nerve.shut_recorder_down()	Shuts down the recorder locally
nerve.simulate(**kwargs)	Simulate the nerve with the proposed extracellular context.