bmtk.simulator.popnet package¶
Submodules¶
bmtk.simulator.popnet.config module¶
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class
bmtk.simulator.popnet.config.
Config
(*args, **kwargs)[source]¶ Bases:
bmtk.simulator.core.simulation_config.SimulationConfig
bmtk.simulator.popnet.popedge module¶
bmtk.simulator.popnet.popnetwork module¶
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class
bmtk.simulator.popnet.popnetwork.
ExtPopulation
(pop_id)[source]¶ Bases:
bmtk.simulator.popnet.popnetwork.Population
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firing_rate
¶
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record
¶
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class
bmtk.simulator.popnet.popnetwork.
PopConnection
(src_pop, trg_pop)[source]¶ Bases:
object
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dipde_obj
¶
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class
bmtk.simulator.popnet.popnetwork.
PopEdge
(edge, property_map, graph)[source]¶ Bases:
object
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delay
¶
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nsyns
¶
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weight
¶
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bmtk.simulator.popnet.popnode module¶
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class
bmtk.simulator.popnet.popnode.
ExternalPopulation
(node_id, graph, network, params)[source]¶ Bases:
bmtk.simulator.popnet.popnode.PopNode
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firing_rate
¶
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is_firing_rate_set
¶
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is_internal
¶
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class
bmtk.simulator.popnet.popnode.
InternalNode
(node_id, graph, network, params)[source]¶ Bases:
bmtk.simulator.popnet.popnode.PopNode
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dv
¶
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is_internal
¶
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tau_m
¶
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v_max
¶
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v_min
¶
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bmtk.simulator.popnet.popsimulator module¶
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class
bmtk.simulator.popnet.popsimulator.
PopSimulator
(graph, dt=0.0001, tstop=0.0, overwrite=True)[source]¶ Bases:
bmtk.simulator.core.simulator.Simulator
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add_rate_hz
(network, pop_id, rate, force=False)[source]¶ 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
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add_rates_nwb
(network, nwb_file, trial, force=False)[source]¶ 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
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build_populations
()[source]¶ 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).
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connections
¶
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dt
¶
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populations
¶
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rates_file
¶
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set_external_connections
(network_name)[source]¶ 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.
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tstop
¶
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bmtk.simulator.popnet.sonata_adaptors module¶
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class
bmtk.simulator.popnet.sonata_adaptors.
PopEdgeAdaptor
(network)[source]¶ Bases:
bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor
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class
bmtk.simulator.popnet.sonata_adaptors.
PopNetEdge
(sonata_edge, edge_adaptor)[source]¶ Bases:
bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge
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syn_weight
¶
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bmtk.simulator.popnet.utils module¶
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bmtk.simulator.popnet.utils.
assert_model_known
(model, model_dict)[source]¶ Test if a model in in the model_dict; if not, raise UnknownModelError
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bmtk.simulator.popnet.utils.
create_instance
(data_dict)[source]¶ 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
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bmtk.simulator.popnet.utils.
create_population_list
(node_table, model_table)[source]¶ Create a population list from the node and model pandas tables
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bmtk.simulator.popnet.utils.
df_to_csv
(df, save_file_name, index=False, sep=' ', na_rep='None')[source]¶
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bmtk.simulator.popnet.utils.
get_firing_rate_from_nwb
(populations, nwb_file, trial)[source]¶ Calculates firing rates for an external population