ALLEN INSTITUTE

# bmtk.simulator.popnet package

## Submodules

## bmtk.simulator.popnet.config module

class bmtk.simulator.popnet.config.Config(*args, **kwargs)

  Bases: `SimulationConfig`

bmtk.simulator.popnet.config.from_json(config_file, validate=False)

## bmtk.simulator.popnet.popedge module

class bmtk.simulator.popnet.popedge.PopEdge(source_pop, target_pop, edge_params, dynamics_params)

  Bases: `SimEdge`

  property delay
  property nsyns
  property params
  property source
  property target
  property weight

class bmtk.simulator.popnet.popedge.SimEdge(original_params, dynamics_params)

  Bases: `object`

  property edge_type_id

## bmtk.simulator.popnet.popnetwork module

class bmtk.simulator.popnet.popnetwork.ExtPopulation(pop_id)

  Bases: `Population`

  build(firing_rate)
  property firing_rate
  property record

class bmtk.simulator.popnet.popnetwork.PopConnection(src_pop, trg_pop)

  Bases: `object`

  add_edge(edge)
  build()
  property dipde_obj

class bmtk.simulator.popnet.popnetwork.PopEdge(edge, property_map, graph)

  Bases: `object`

  property delay
  property nsyns
  property weight

class bmtk.simulator.popnet.popnetwork.PopNetwork(group_by='node_type_id', **properties)

  Bases: `SimNetwork`

  add_rates(rates, node_set)
  add_spike_trains(spike_trains, node_set)
  build_nodes()
  build_recurrent_edges()
  property connections
  edges_table(target_network, source_network)
  find_edges(source_nodes=None, target_nodes=None)
  get_edges(source_network)
  get_population(node_set, gid)
  get_populations(network)
  property internal_populations
  property populations
  rebuild()

class bmtk.simulator.popnet.popnetwork.Population(pop_id)

  Bases: `object`

  add_node(pnode)
  build()
  property dipde_obj
  get_gids()
  property pop_id
  property record

## bmtk.simulator.popnet.popnode module

class bmtk.simulator.popnet.popnode.ExternalPopulation(node_id, graph, network, params)

  Bases: `PopNode`

  property firing_rate
  property is_firing_rate_set
  property is_internal

class bmtk.simulator.popnet.popnode.InternalNode(node_id, graph, network, params)

  Bases: `PopNode`

  property dv
  property is_internal
  property tau_m
  property v_max
  property v_min

class bmtk.simulator.popnet.popnode.PopNode(node_id, graph, network, params)

  Bases: `SimNode`

  add_gid(gid)
  property dynamics_params
  get_gids()
  property is_internal
  property network

    Name of network node belongs too.

  property node_id
  property pop_id

class bmtk.simulator.popnet.popnode.SimNode(node_id, graph, network, params)

  Bases: `object`

  property model_params

    Parameters (json file, nml, dictionary) that describe a specific node

  property network

    Name of network node belongs too.

  property node_id
  property node_type_id

## bmtk.simulator.popnet.popsimulator module

class bmtk.simulator.popnet.popsimulator.PopSimulator(graph, dt=0.0001, tstop=0.0, overwrite=True)

  Bases: `Simulator`

  add_rate_hz(network, pop_id, rate, force=False)

    Set the firing rate of an external population.

    This should be done before calling build_cells(). If a population has already been assigned a firing rate an error will occur unless force=True.

    Parameters:

      - network – name of network with wanted exteranl population

      - pop_id – name/id of external population

      - rate – firing rate in Hz.

      - force – will overwrite existing firing rates

  add_rates_nwb(network, nwb_file, trial, force=False)

    Creates external population firing rates from an NWB file.

    Will iterate through a processing trial of an NWB file by assigning gids the population it belongs too and taking the average firing rate.

    This should be done before calling build_cells(). If a population has already been assigned a firing rate an error will occur unless force=True.

    Parameters:

      - network – Name of network with external populations.

      - nwb_file – NWB file with spike rates.

      - trial – trial id in NWB file

      - force – will overwrite existing firing rates

  build_populations()

    Build dipde Population objects from graph nodes.

    To calculate external populations firing rates, it first see if a population’s firing rate has been manually set in the graph. Otherwise it attempts to calulate the firing rate from the call to add_rate_hz, add_rates_NWB, etc. (which should be called first).

  property connections
  property dt
  classmethod from_config(configure, graph)
  property populations
  property rates_file
  run(tstop=None)
  set_external_connections(network_name)

    Sets the external connections for populations in a given network.

    Parameters:

      network_name – name of external network with External Populations to connect to internal pops.

  set_logging(log_file)
  set_recurrent_connections()

    Initialize internal connections.

  property tstop

## bmtk.simulator.popnet.sonata_adaptors module

class bmtk.simulator.popnet.sonata_adaptors.PopEdgeAdaptor(network)

  Bases: `EdgeAdaptor`

  get_edge(sonata_edge)

class bmtk.simulator.popnet.sonata_adaptors.PopNetEdge(sonata_edge, edge_adaptor)

  Bases: `SonataBaseEdge`

  property syn_weight

## bmtk.simulator.popnet.utils module

class bmtk.simulator.popnet.utils.KeyDefaultDict

  Bases: `defaultdict`

bmtk.simulator.popnet.utils.assert_model_known(model, model_dict)

  Test if a model in in the model_dict; if not, raise UnknownModelError

bmtk.simulator.popnet.utils.create_firing_rate_server(t, y)

bmtk.simulator.popnet.utils.create_instance(data_dict)

  Helper function to create an object from a dictionary containing:

  “module”: The name of the module containing the class “class”: The name of the class to be used to create the object

bmtk.simulator.popnet.utils.create_nwb_server_file_path(nwb_file_name, nwb_path)

bmtk.simulator.popnet.utils.create_population_list(node_table, model_table)

  Create a population list from the node and model pandas tables

bmtk.simulator.popnet.utils.df_to_csv(df, save_file_name, index=False, sep=' ', na_rep='None')

bmtk.simulator.popnet.utils.get_firing_rate_from_nwb(populations, nwb_file, trial)

  Calculates firing rates for an external population

bmtk.simulator.popnet.utils.get_firing_rates(populations, spike_trains)

  Calculates firing rates for an external population

bmtk.simulator.popnet.utils.get_mesoscale_connectivity_dict()

bmtk.simulator.popnet.utils.list_of_dicts_to_dict_of_lists(list_of_dicts, default=None)

bmtk.simulator.popnet.utils.network_dict_to_target_adjacency_dict(network_dict)

bmtk.simulator.popnet.utils.population_list_to_csv(population_list, save_file_name)

bmtk.simulator.popnet.utils.population_list_to_dataframe(population_list)

bmtk.simulator.popnet.utils.population_to_dict_for_dataframe(p)

bmtk.simulator.popnet.utils.reorder_columns_in_frame(frame, var)

## Module contents