NetworkMapper¶

class single_cell_parser.network.NetworkMapper(postCell, nwParam, simParam=None)¶

Map active presynaptic cells to a multi-compartmental neuron model.

See also

This is not the same class as singlecell_input_mapper.singlecell_input_mapper.network_embedding.NetworkMapper. This class is specialized for synapse activations and simulation control and re-creating already existing network realizations, not for creating such anatomical network realizations from empirical data.

Initialize NetworkMapper.

Parameters:¶

postCell : Cell¶

The cell to map synapses onto.

nwParam : NTParameterSet¶

The network parameter set (see Network parameters for more info).

simParam : NTParameterSet¶

The simulation parameter set. Default: None.

Attributes:¶

cells¶

dictionary holding all presynaptic cells ordered by cell type.

Type:¶

dict

connected_cells¶

dictionary holding indices of all active presynaptic cells ordered by cell type.

Type:¶

dict

postCell¶

reference to postsynaptic (multi-compartment) cell model.

Type:¶

Cell

nwParam¶

network parameter set (see Network parameters for more info).

Type:¶

NTParameterSet

simParam¶

simulation parameter set.

Type:¶

NTParameterSet

Methods:¶

create_network(synWeightName, change)	Set up a network from network parameters.
create_saved_network2(synWeightName, full_network)	Recreate a saved network embedding and activate it.
reconnect_saved_synapses(synInfoName, synWeightName, include_silent_synapses)	Set up a network from a saved Synapse activation file.
create_functional_realization()	Create a new functional connectivity realization from an existing network parameter file based on convergence.
re_init_network(replayMode)	Reinitialize the network for a new simulation run.
_assign_anatomical_synapses()	Assigns synapses to postsynaptic cell from .syn files.
_apply_network_modify_functions()	Apply network modify functions to the network.
_create_presyn_cells()	Creates presynaptic cells.
_activate_presyn_cells()	Create PointCell or SpikeTrain activation patters for each presynaptic cell.
_create_spiketrain_activities(preCellType, networkParameters)	Create spike train times based on the network parameters spiketrain keywords.
_create_pointcell_activities(preCellType, networkParameters)	Create point cell spike times based on the network parameters distribution keyword.
_connect_functional_synapses()	Connects anatomical synapses to spike generators (PointCells).
_create_functional_connectivity_map()	Connect functional anatomical synapses based on convergence.
_map_functional_realization(weights)	Connects anatomical synapses to spike generators (PointCells).
_map_complete_anatomical_realization(weights, full_network)	Connect synapses to active presynaptic cells.
_assign_synapse_weights(receptor, recepStr, syn)	Assign synapse weights according to distribution specified in network parameters.
_connect_spike_trains(weights, change)	Connects synapses with spike generators.
create_saved_network(synWeightName)	Recreate a saved network embedding and activate it.
reconnect_network()	Re-generate activity and connectivity patterns for a network.