neat.NeuronSimTree.run

NeuronSimTree.run(t_max, downsample=1, dt_rec=None, record_from_syns=False, record_from_iclamps=False, record_from_vclamps=False, record_from_channels=False, record_v_deriv=False, record_concentrations=[], record_currents=[], spike_rec_loc=None, spike_rec_thr=-20.0, pprint=False)[source]

Run the NEURON simulation. Records at all locations stored under the name ‘rec locs’ on self (see MorphTree.store_locs())

Parameters:

  • t_max (float) – Duration of the simulation

  • downsample (int (> 0)) – Records the state of the model every downsample time-steps

  • dt_rec (float or None) – recording time step (if None is given, defaults to the simulation time-step). Note that if running with coreneuron, this parameter is ignored and recording is done at every simulation time-step and downsampled according to the downsample argument.

  • record_from_syns (bool (default False)) – Record currents of synapstic point processes (in self.syns). Accessible as np.ndarray in the output dict under key ‘i_syn’

  • record_from_iclamps (bool (default False)) – Record currents of iclamps (in self.iclamps) Accessible as np.ndarray in the output dict under key ‘i_clamp’

  • record_from_vclamps (bool (default False)) – Record currents of vclamps (in self.vclamps) Accessible as np.ndarray in the output dict under key ‘i_vclamp’

  • record_from_channels (bool (default False)) – Record channel state variables from neat defined channels in self, at locations stored under ‘rec locs’ Accessible as np.ndarray in the output dict under key ‘chan’

  • record_v_deriv (bool (default False)) – Record voltage derivative at locations stored under ‘rec locs’ Accessible as np.ndarray in the output dict under key ‘dv_dt’

  • record_concentrations (list (default [])) – Record ion concentration at locations stored under ‘rec locs’ Accessible as np.ndarray in the output dict with as key the ion’s name

  • record_currents (list (default [])) – Record ion currents at locations stored under ‘rec locs’ Accessible as np.ndarray in the output dict with as key the ion’s name

  • spike_rec_loc (neat.MorphLoc (default None)) – Record the output spike times from this location

  • spike_rec_thr (float) – Spike threshold

  • pprint (bool (default False)) – Whether or not to print info on the NEURON simulation

Returns:

Dictionary with the results of the simulation. Contains time and voltage as np.ndarray at locations stored under the name ‘ rec locs’, respectively with keys ‘t’ and ‘v_m’. Also contains traces of other recorded variables if the option to record them was set to True

Return type:

dict