single_cell_parser ❭ network ❭ NetworkMapper

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:
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:

ParameterSet

simParam

simulation parameter set.

Type:

ParameterSet

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.