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whats_new.rst

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What's new?

hnn_core

Current

Changelog

  • Store all connectivity information under ~hnn_core.Network.connectivity before building the network, by Nick Tolley in #276
  • Add new function ~hnn_core.viz.plot_cell_morphology to visualize cell morphology, by Mainak Jas in #319
  • Compute dipole component in z-direction automatically from cell morphology instead of hard coding, by Mainak Jas in #327
  • Store ~hnn_core.Cell instances in ~hnn_core.Network's ~/hnn_core.Network.cells attribute by Ryan Thorpe in #321

Bug

API

  • New API for defining cell-cell connections. Custom connections can be added with ~hnn_core.Network.add_connection, by Nick Tolley in #276
  • Remove ~hnn_core.L2Pyr, ~hnn_core.L5Pyr, ~hnn_core.L2Basket, and ~hnn_core.L5Basket classes in favor of instantation through functions and a more consistent ~hnn_core.Cell class by Mainak Jas in #322
  • Remove parameter distribution in ~hnn_core.Network.add_bursty_drive. The distribution is now Gaussian by default, by Mainak Jas in #330
  • New API for accessing and modifying ~hnn_core.Cell attributes (e.g., synapse and biophysics parameters) as cells are now instantiated from template cells specified in a ~hnn_core.Network instance's ~/hnn_core.Network.cell_types attribute by Ryan Thorpe in #321

0.1

Changelog

  • Add ability to simulate multiple trials in parallel using joblibs, by Mainak Jas in #44
  • Rhythmic inputs can now be turned off by setting their conductance weights to 0 instead of setting their start times to exceed the simulation stop time, by Ryan Thorpe in #105
  • Reader for parameter files, by Blake Caldwell in #80
  • Add plotting of voltage at soma to inspect firing pattern of cells, by Mainak Jas in #86
  • Add ability to simulate a single trial in parallel across cores using MPI, by Blake Caldwell in #79
  • Modify ~hnn_core.viz.plot_dipole to accept both lists and individual instances of Dipole object, by Nick Tolley in #145
  • Update plot_hist_input to ~hnn_core.viz.plot_spikes_hist which can plot histogram of spikes for any cell type, by Nick Tolley in #157
  • Add function to compute mean spike rates with user specified calculation type, by Nick Tolley and Mainak Jas in #155
  • Add ability to record somatic voltages from all cells, by Nick Tolley in #190
  • Add ability to instantiate external feed event times of a network prior to building it, by Christopher Bailey in #191
  • Add ability to record somatic currents from all cells, by Nick Tolley in #199
  • Add option to turn off dipole postprocessing, by Carmen Kohl in #188
  • Add ability to add tonic inputs to cell types with ~hnn_core.Network.add_tonic_bias, by Mainak Jas in #209
  • Modify ~hnn_core.viz.plot_spikes_raster to display individual cells, by Nick Tolley in #231
  • Add ~hnn_core.Network.copy method for cloning a Network instance, by Christopher Bailey in #221
  • Add methods for creating input drives and biases to network: ~hnn_core.Network.add_evoked_drive, ~hnn_core.Network.add_poisson_drive, ~hnn_core.Network.add_bursty_drive and ~hnn_core.Network.add_tonic_bias, by Christopher Bailey in #221
  • Add functions for plotting power spectral density (~hnn_core.viz.plot_psd) and Morlet time-frequency representations (~hnn_core.viz.plot_tfr_morlet), by Christopher Bailey in #264
  • Add y-label units (nAm) to all visualisation functions involving dipole moments, by Christopher Bailey in #264
  • Add Savitzky-Golay filtering method ~hnn_core.dipole.Dipole.savgol_filter to Dipole; copied from mne-python ~mne.Evoked.savgol_filter, by Christopher Bailey in #264

Bug

  • Fix missing autapses in network construction, by Mainak Jas in #50
  • Fix rhythmic input feed, by Ryan Thorpe in #98
  • Fix bug introduced into rhythmic input feed and add test, by Christopher Bailey in #102
  • Fix bug in amplitude of delay (for connection between L2 Basket and Gaussian feed) being passed incorrectly, by Mainak Jas in #146
  • Connections now cannot be removed by setting the weights to 0., by Mainak Jas and Ryan Thorpe in #162
  • MPI and Joblib backends now apply jitter across multiple trials identically, by Ryan Thorpe in #171
  • Fix bug in Poisson input where the first spike was being missed after the start time, by Mainak Jas in #204
  • Fix bug in network to add empty spike when empty file is read in, by Samika Kanekar and Ryan Thorpe in #207

API

  • Make a context manager for Network class, by Mainak Jas and Blake Caldwell in #86
  • Create Spikes class, add write methods and read functions for Spikes and Dipole classes, by Ryan Thorpe in #96
  • Only specify n_jobs when instantiating the JoblibBackend, by Blake Caldwell in #79
  • Make a context manager for parallel backends (JoblibBackend, MPIBackend), by Blake Caldwell in #79
  • Add ~hnn_core.dipole.average_dipoles function, by Blake Caldwell in #156
  • New API for defining external drives and biases to network. By default, a ~hnn_core.Network is created without drives, which are added using class methods. The argument add_drives_from_params controls this behaviour, by Christopher Bailey in #221
  • Examples apply random state seeds that reproduce the output of HNN GUI documentation, by Christopher Bailey in #221
  • Force conversion to nAm (from fAm) for output of ~hnn_core.dipole.simulate_dipole regardless of postproc-argument, which now only controls parameter file-based smoothing and scaling, by Christopher Bailey in #264

People who contributed to this release (in alphabetical order):