hnn_core.CellResponse¶
- class hnn_core.CellResponse(spike_times=None, spike_gids=None, spike_types=None, times=None)¶
The CellResponse class.
- Parameters
- spike_timeslist (n_trials,) of list (n_spikes,) of float, shape | None
Each element of the outer list is a trial. The inner list contains the time stamps of spikes.
- spike_gidslist (n_trials,) of list (n_spikes,) of float, shape | None
Each element of the outer list is a trial. The inner list contains the cell IDs of neurons that spiked.
- spike_typeslist (n_trials,) of list (n_spikes,) of float, shape | None
Each element of the outer list is a trial. The inner list contains the type of spike (e.g., evprox1 or L2_pyramidal) that occured at the corresonding time stamp. Each gid corresponds to a type via Network().gid_ranges.
- Attributes
- spike_timeslist (n_trials,) of list (n_spikes,) of float, shape
Each element of the outer list is a trial. The inner list contains the time stamps of spikes.
- spike_gidslist (n_trials,) of list (n_spikes,) of float, shape
Each element of the outer list is a trial. The inner list contains the cell IDs of neurons that spiked.
- spike_typeslist (n_trials,) of list (n_spikes,) of float, shape
Each element of the outer list is a trial. The inner list contains the type of spike (e.g., evprox1 or L2_pyramidal) that occured at the corresonding time stamp. Each gid corresponds to a type via Network::gid_ranges.
- vsomalist (n_trials,) of dict, shape
Each element of the outer list is a trial. Dictionary indexed by gids containing somatic voltages.
- isomalist (n_trials,) of dict, shape
Each element of the outer list is a trial. Dictionary indexed by gids containing somatic currents.
- timesnumpy array
Array of time points for samples in continuous data. This includes vsoma and isoma.
Methods
update_types(gid_ranges)
Update spike types in the current instance of CellResponse.
plot(ax=None, show=True)
Plot and return a matplotlib Figure object showing the aggregate network spiking activity according to cell type.
mean_rates(tstart, tstop, gid_ranges, mean_type=’all’)
Calculate mean firing rate for each cell type. Specify averaging method with mean_type argument.
write(fname)
Write spiking activity to a collection of spike trial files.
- __getitem__(gid_item)¶
Returns a CellResponse object with a copied subset filtered by gid.
- Parameters
- gid_itemint | slice
Subset of gids .
- Returns
- cell_responseinstance of CellResponse
See below for use cases.
- __repr__()¶
Return repr(self).
- mean_rates(tstart, tstop, gid_ranges, mean_type='all')¶
Mean spike rates (Hz) by cell type.
- Parameters
- tstartint | float | None
Value defining the start time of all trials.
- tstopint | float | None
Value defining the stop time of all trials.
- gid_rangesdict of lists or range objects
Dictionary with keys ‘evprox1’, ‘evdist1’ etc. containing the range of Cell or input IDs of different cell or input types.
- mean_typestr
- ‘all’Average over trials and cells
Returns mean rate for cell types
- ‘trial’Average over cell types
Returns trial mean rate for cell types
- ‘cell’Average over individual cells
Returns trial mean rate for individual cells
- Returns
- spike_ratedict
Dictionary with keys ‘L5_pyramidal’, ‘L5_basket’, etc.
- plot_spikes_hist(ax=None, spike_types=None, show=True)¶
Plot the histogram of spiking activity across trials.
- Parameters
- axinstance of matplotlib axis | None
An axis object from matplotlib. If None, a new figure is created.
- spike_types: string | list | dictionary | None
- String input of a valid spike type is plotted individually.
Ex: ‘common’, ‘evdist’, ‘evprox’, ‘extgauss’, ‘extpois’
- List of valid string inputs will plot each spike type individually.
Ex: [‘common’, ‘evdist’]
- Dictionary of valid lists will plot list elements as a group.
Ex: {‘Evoked’: [‘evdist’, ‘evprox’], ‘External’: [‘extpois’]}
If None, all input spike types are plotted individually if any are present. Otherwise spikes from all cells are plotted. Valid strings also include leading characters of spike types
Example: ‘ext’ is equivalent to [‘extgauss’, ‘extpois’]
- showbool
If True, show the figure.
- Returns
- figinstance of matplotlib Figure
The matplotlib figure handle.
- plot_spikes_raster(ax=None, show=True)¶
Plot the aggregate spiking activity according to cell type.
- Parameters
- axinstance of matplotlib axis | None
An axis object from matplotlib. If None, a new figure is created.
- showbool
If True, show the figure.
- Returns
- figinstance of matplotlib Figure
The matplotlib figure object.
- update_types(gid_ranges)¶
Update spike types in the current instance of CellResponse.
- Parameters
- gid_rangesdict of lists or range objects
Dictionary with keys ‘evprox1’, ‘evdist1’ etc. containing the range of Cell or input IDs of different cell or input types.
- write(fname)¶
Write spiking activity per trial to a collection of files.
- Parameters
- fnamestr
String format (e.g., ‘<pathname>/spk_%d.txt’) of the path to the output spike file(s).