API Documentation

Simulation (hnn_core):

simulate_dipole(net, tstop[, dt, n_trials, ...])	Simulate a dipole given the experiment parameters.
Network(params[, add_drives_from_params, ...])	The Network class.
Cell(name, pos, sections, synapses, ...[, gid])	Create a cell object.
CellResponse([spike_times, spike_gids, ...])	The CellResponse class.
pick_connection(net[, src_gids, ...])	Returns indices of connections that match search parameters.

Network Models (hnn_core):

jones_2009_model([params, ...])	Instantiate the network model described in Jones et al. J.
law_2021_model([params, ...])	Instantiate the expansion of Jones 2009 model to study beta modulated ERPs as described in Law et al. Cereb.
calcium_model([params, ...])	Instantiate the Jones 2009 model with improved calcium dynamics in L5 pyramidal neurons.

Optimization (hnn_core.optimization):

optimize_evoked(net, tstop, n_trials, ...[, ...])

Optimize drives to generate evoked response.

Dipole (hnn_core.dipole):

Dipole(times, data[, nave])	Dipole class.
average_dipoles(dpls)	Compute dipole averages over a list of Dipole objects.

ExtracellularArray (hnn_core.extracellular):

ExtracellularArray(positions, *[, ...])

Class for recording extracellular potential fields with electrode array

Visualization (hnn_core.viz):

plot_dipole(dpl[, tmin, tmax, ax, layer, ...])	Simple layer-specific plot function.
plot_spikes_hist(cell_response[, trial_idx, ...])	Plot the histogram of spiking activity across trials.
plot_spikes_raster(cell_response[, ...])	Plot the aggregate spiking activity according to cell type.
plot_cells(net[, ax, show])	Plot the cells using Network.pos_dict.
plot_cell_morphology(cell, ax[, show])	Plot the cell morphology.
plot_psd(dpl, *[, fmin, fmax, tmin, tmax, ...])	Plot power spectral density (PSD) of dipole time course
plot_tfr_morlet(dpl, freqs, *[, n_cycles, ...])	Plot Morlet time-frequency representation of dipole time course
plot_cell_connectivity(net, conn_idx[, ...])	Plot synaptic weight of connections.
plot_connectivity_matrix(net, conn_idx[, ...])	Plot connectivity matrix with color bar for synaptic weights
plot_laminar_lfp(times, data, contact_labels)	Plot laminar extracellular electrode array voltage time series.
plot_laminar_csd(times, data, contact_labels)	Plot laminar current source density (CSD) estimation from LFP array.

Parallel backends (hnn_core.parallel_backends):

MPIBackend([n_procs, mpi_cmd])	The MPIBackend class.
JoblibBackend([n_jobs])	The JoblibBackend class.

Input and Output:

read_params(params_fname)	Read param values from a file (.json or .param).
read_dipole(fname)	Read dipole values from a file and create a Dipole instance.
read_spikes(fname[, gid_ranges])	Read spiking activity from a collection of spike trial files.

GUI (hnn_core.gui):

HNNGUI([theme_color, total_height, ...])

HNN GUI class