fascicle.simulate

fascicle.simulate(save_V_mem=False, **kwargs) → fascicle_results[source]

Simulates the fascicle using neuron framework. Parallel computing friendly. Does not return results (possibly too large in memory and complex with parallel computing), but instead creates a folder and store fascicle configuration and all axons results. On the fly post processing is possible by specifying an additional script.

Parameters:

  • t_sim (float) – total simulation time (ms), by default 20 ms

  • record_V_mem (bool) – if true, the membrane voltage is recorded, set to True by default

  • record_I_mem (bool) – if true, the membrane current is recorded, set to False by default

  • record_I_ions (bool) – if true, the ionic currents are recorded, set to False by default

  • record_particules (bool) – if true, the marticule states are recorded, set to False by default

  • loaded_footprints (dict or bool) – Dictionnary composed of axon footprint dictionary, the keys are int value of the corresponding axon ID. if type is bool, fascicle footprints attribute is used if None, footprins calculated during the simulation, by default None

  • save_V_mem (bool) – if true, all membrane voltages values are stored in results whe basic postprocessing is applied. Can be heavy ! False by default

  • save_path (str) – name of the folder to store results of the fascicle simulation.

  • Unmyelinated_model (str) – model for unmyelinated fibers, by default ‘Rattay_Aberham’

  • Myelinated_model (str) – model for myelinated fibers, by default ‘MRG’

  • myelinated_seg_per_sec (int) – number of segment per section for myelinated axons

  • PostProc_Filtering (float, list, array, np.array) – value or iterable values for basic post proc filtering. If None specified, no filtering is performed

  • postproc_script (str) – path to a postprocessing file. If specified, the basic post processing is not performed, and all postprocessing have to be handled by user. The specified script can access global and local variables. Can also be key word (‘Vmem_plot’ or ‘scarter’) to use script saved in OTF_PP folder, use with caution

  • return_parameters_only (bool) – if True the results of axon simulations are integrated into fasc_sim return after simulation use with caution: can increase a lot computational memory

  • save_results (bool) – if False disable the result storage can only be False if return_parameters_only is False

Returns:

fasc_sim – results of the simulation

Return type:

sim_results