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`):¶

Optimizer(initial_net, tstop, constraints, ...)

Methods

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[, color, pos, ...])	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.
`NetworkPlotter`(net[, ax, vmin, vmax, ...])	Helper class to visualize full morphology of HNN model.

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[, file_contents])	Read param values from a file (.json or .param).
`read_dipole`(fname)	Read dipole values from a txt or hdf5 file and
`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