EIT2DProblem

class nrv.eit.EIT2DProblem(nervefile: str, res_dname: str | None = None, label: str = '2deit_1', **parameters)

End-used class for Electrical Impedance Tomography (EIT) forward simulation in neural contexts solved with a 2D approximation.

This class extends eit_forward to provide specialized methods for setting up, meshing, and solving EIT problems in a 2D (Oyz) plan. It supports:

• mesh generation with axons

• physical domain assignment

• finite element method (FEM) initialization

• conductivity updates during the simulation.

Warning

For now the 2D approximation isn’t well documented. Further explaination will be added to the doc in the future.

Note

• Mesh generation and FEM setup rely on GMSH and FEniCS/Dolfinx libraries with interface integrated into this class classes.

• Conductivity calculations support various methods, including myelinated and unmyelinated axons.

Attributes

EIT2DProblem.dim	Spatial dimension of the FEM problem.
EIT2DProblem.fem_res_file	File where the fem results are saved
EIT2DProblem.i_drive_A	Injected current in A
EIT2DProblem.inj_protocol	Injection protocole.
EIT2DProblem.is_multi_patern	Check if the injection protocol contains more than one pattern.
EIT2DProblem.n_e	Number of electrodes.
EIT2DProblem.n_f	Number of frequency step in the EIT simulation.
EIT2DProblem.n_p	Number of injection paterns in the protocol.
EIT2DProblem.n_t	Number of time step in the EIT simulation.
EIT2DProblem.nerve_mesh_file	File where the nerve mesh is saved
EIT2DProblem.nerve_res_file	File where the nerve simulation results are saved
EIT2DProblem.timers_dict	Duration of all the simulations
EIT2DProblem.x_bounds_fem	Axial bounds used to sample axonal properties for the 2D model.
EIT2DProblem.i_drive	current amplitude injected in uA.
EIT2DProblem.use_backup	if true simulation resutls are save on the fligth

Methods

EIT2DProblem.__init__(nervefile[, ...])	Create a 2D EIT forward problem from a nerve description.
EIT2DProblem.build_mesh([with_axons])	creation of mesh file
EIT2DProblem.clear()	Clear all simulations outputs.
EIT2DProblem.clear_fem_res()	Clear FEM results and reset result file.
EIT2DProblem.get_info([verbose])	Return basic mesh statistics from the current Gmsh model.
EIT2DProblem.get_nproc([which])	return the number of process of a given simualtion step
EIT2DProblem.get_parameters()	Generic method returning all the atributes of an NRV_class instance
EIT2DProblem.load(data[, blacklist])	Generic loading method for NRV_class instance
EIT2DProblem.rerun_failed_steps([...])	Rerun failed FEM simulation steps.
EIT2DProblem.run_all_fem(task_info)	Run the FEM simulation for all time step of a given task (process).
EIT2DProblem.run_and_savefem(sfile[, ...])	Compute only a few time step of the EIT simulation and save the computed electric field in the whole domain
EIT2DProblem.run_fem(task_info)	Run the FEM simulation for all time step of a given task (process).
EIT2DProblem.run_fem_1core(task_info)
EIT2DProblem.save([save, fname, blacklist])	Generic saving method for NRV_class instance.
EIT2DProblem.set_ncore_gmsh(ncore_meshing)	Configure the number of Gmsh meshing threads.
EIT2DProblem.set_parameters(**kawrgs)	Generic method to set any attribute of NRV_class instance
EIT2DProblem.simulate_eit([save, sim_list])	Run the eit problem for all time steps
EIT2DProblem.simulate_nerve([t_start, ...])	Simulate the neural context: fibres conductivity and extracellular context.
EIT2DProblem.simulate_recording([t_start, ...])	Simulate the neural context: fibres conductivity and extracelullar context.
EIT2DProblem.v_shape()	Get the shape of the voltage results array.