bmtk.simulator package

Subpackages

• bmtk.simulator.bionet package
  • Subpackages
    • bmtk.simulator.bionet.default_setters package
      • Submodules
      • bmtk.simulator.bionet.default_setters.cell_models module
      • bmtk.simulator.bionet.default_setters.synapse_models module
      • bmtk.simulator.bionet.default_setters.synaptic_weights module
      • Module contents
    • bmtk.simulator.bionet.modules package
      • Submodules
      • bmtk.simulator.bionet.modules.comsol module
      • bmtk.simulator.bionet.modules.ecephys_module module
      • bmtk.simulator.bionet.modules.ecp module
      • bmtk.simulator.bionet.modules.iclamp module
      • bmtk.simulator.bionet.modules.record_cellvars module
      • bmtk.simulator.bionet.modules.record_clamp module
      • bmtk.simulator.bionet.modules.record_netcons module
      • bmtk.simulator.bionet.modules.record_spikes module
      • bmtk.simulator.bionet.modules.save_synapses module
      • bmtk.simulator.bionet.modules.sim_module module
      • bmtk.simulator.bionet.modules.xstim module
      • bmtk.simulator.bionet.modules.xstim_waveforms module
      • Module contents
  • Submodules
  • bmtk.simulator.bionet.biocell module
    • BioCell
      • BioCell.build_morphology()
      • BioCell.connections()
      • BioCell.get_connection_info()
      • BioCell.get_im()
      • BioCell.get_section()
      • BioCell.get_sections()
      • BioCell.get_sections_id()
      • BioCell.init_connections()
      • BioCell.morphology
      • BioCell.morphology_file
      • BioCell.print_synapses()
      • BioCell.seg_coords
      • BioCell.set_e_extracellular()
      • BioCell.set_im_ptr()
      • BioCell.set_ptr2e_extracellular()
      • BioCell.set_sec_array()
      • BioCell.set_spike_detector()
      • BioCell.set_syn_connection()
      • BioCell.setup_ecp()
      • BioCell.setup_xstim()
    • BioCellSpontSyn
    • ConnectionStruct
      • ConnectionStruct.is_gap_junc
      • ConnectionStruct.is_virtual
      • ConnectionStruct.source_node
      • ConnectionStruct.syn_weight
  • bmtk.simulator.bionet.bionetwork module
    • BioNetwork
      • BioNetwork.add_nodes()
      • BioNetwork.add_spike_trains()
      • BioNetwork.build_nodes()
      • BioNetwork.build_recurrent_edges()
      • BioNetwork.build_replay_inputs()
      • BioNetwork.cell_type_maps()
      • BioNetwork.find_edges()
      • BioNetwork.get_cell_gid()
      • BioNetwork.get_cell_node_id()
      • BioNetwork.get_disconnected_cell()
      • BioNetwork.get_gj_id()
      • BioNetwork.get_local_cells()
      • BioNetwork.get_node_id()
      • BioNetwork.get_virtual_cells()
      • BioNetwork.gid_pool
      • BioNetwork.local_gids
      • BioNetwork.model_type_col
      • BioNetwork.py_function_caches
      • BioNetwork.set_spont_syn_activity()
  • bmtk.simulator.bionet.biosimulator module
    • BioSimulator
      • BioSimulator.add_mod()
      • BioSimulator.attach_se_voltage_clamp()
      • BioSimulator.biophysical_gids
      • BioSimulator.cell_var_output
      • BioSimulator.cell_variables
      • BioSimulator.celsius
      • BioSimulator.dt
      • BioSimulator.from_config()
      • BioSimulator.h
      • BioSimulator.local_gids
      • BioSimulator.n_steps
      • BioSimulator.nsteps_block
      • BioSimulator.post_fadvance()
      • BioSimulator.report_load_balance()
      • BioSimulator.run()
      • BioSimulator.set_spikes_recording()
      • BioSimulator.simulation_time()
      • BioSimulator.spikes_table
      • BioSimulator.tstop
      • BioSimulator.v_init
  • bmtk.simulator.bionet.cell module
    • Cell
      • Cell.get_connection_info()
      • Cell.gid
      • Cell.group_id
      • Cell.hobj
      • Cell.init_connections()
      • Cell.netcons
      • Cell.network_name
      • Cell.node
      • Cell.node_id
      • Cell.scale_weights()
      • Cell.set_soma_position()
      • Cell.set_syn_connections()
      • Cell.soma_position
  • bmtk.simulator.bionet.config module
    • Config
      • Config.build_env()
      • Config.create_output_dir()
      • Config.load_nrn_modules()
  • bmtk.simulator.bionet.gids module
    • GidPool
      • GidPool.add_pool()
      • GidPool.get_gid()
      • GidPool.get_pool_id()
    • PopulationID
      • PopulationID.node_id
      • PopulationID.population
  • bmtk.simulator.bionet.iclamp module
    • FileIClamp
      • FileIClamp.attach_current()
    • IClamp
      • IClamp.attach_current()
  • bmtk.simulator.bionet.io_tools module
    • NEURONIOUtils
      • NEURONIOUtils.barrier()
  • bmtk.simulator.bionet.morphology module
    • Morphology
      • Morphology.choose_sections()
      • Morphology.find_sections()
      • Morphology.get_coords()
      • Morphology.get_section()
      • Morphology.get_swc_id()
      • Morphology.load()
      • Morphology.move_and_rotate()
      • Morphology.n_sections
      • Morphology.nseg
      • Morphology.sec_type_swc
      • Morphology.sections
      • Morphology.seg_coords
      • Morphology.seg_props
      • Morphology.segments
      • Morphology.set_segment_dl()
      • Morphology.soma_position
      • Morphology.swc_map
    • rotation_matrix()
  • bmtk.simulator.bionet.nml_reader module
    • ChannelDensity
      • ChannelDensity.element_tag()
    • ChannelDensityNernst
      • ChannelDensityNernst.element_tag()
    • ConcentrationModel
      • ConcentrationModel.element_tag()
    • NMLElement
      • NMLElement.element_tag()
    • NMLTree
      • NMLTree.common_name()
      • NMLTree.element_registry
      • NMLTree.nml_ns
      • NMLTree.ns_name()
      • NMLTree.parse_value()
      • NMLTree.register_module()
    • Resistivity
      • Resistivity.element_tag()
    • SpecificCapacitance
      • SpecificCapacitance.element_tag()
  • bmtk.simulator.bionet.nrn module
    • clear_gids()
    • load_neuron_modules()
    • load_templates()
    • quit_execution()
    • reset()
  • bmtk.simulator.bionet.pointprocesscell module
    • ConnectionStruct
      • ConnectionStruct.is_virtual
      • ConnectionStruct.source_node
      • ConnectionStruct.syn_weight
    • PointProcessCell
      • PointProcessCell.connections()
      • PointProcessCell.get_connection_info()
      • PointProcessCell.print_synapses()
      • PointProcessCell.set_im_ptr()
      • PointProcessCell.set_spike_detector()
      • PointProcessCell.set_syn_connection()
    • PointProcessCellSpontSyns
      • PointProcessCellSpontSyns.set_syn_connection()
  • bmtk.simulator.bionet.pointsomacell module
    • PointSomaCell
  • bmtk.simulator.bionet.pyfunction_cache module
  • bmtk.simulator.bionet.seclamp module
    • SEClamp
      • SEClamp.attach_current()
  • bmtk.simulator.bionet.sonata_adaptors module
    • BioEdge
      • BioEdge.afferent_section_id
      • BioEdge.afferent_section_pos
      • BioEdge.load_synapses()
    • BioEdgeAdaptor
      • BioEdgeAdaptor.get_edge()
      • BioEdgeAdaptor.patch_adaptor()
    • BioNode
      • BioNode.load_cell()
      • BioNode.morphology_file
      • BioNode.position
      • BioNode.rotation_angle_xaxis
      • BioNode.rotation_angle_yaxis
      • BioNode.rotation_angle_zaxis
      • BioNode.rotations
      • BioNode.rotations_quaternion
    • BioNodeAdaptor
      • BioNodeAdaptor.get_node()
      • BioNodeAdaptor.patch_adaptor()
    • aff_sec_id()
    • aff_sec_id_old()
    • aff_sec_pos()
    • aff_sec_pos_old()
    • position()
    • position_x()
    • position_xy()
    • position_xyz()
    • positions()
    • positions_default()
    • ret_none_function()
    • rotation_angle_default()
    • rotation_angle_x()
    • rotation_angle_y()
    • rotation_angle_z()
    • rotations()
    • value_none()
  • bmtk.simulator.bionet.utils module
    • edge_converter_csv()
    • rotation_matrix()
  • bmtk.simulator.bionet.virtualcell module
    • VirtualCell
      • VirtualCell.hobj
      • VirtualCell.node_id
      • VirtualCell.set_stim()
  • Module contents
• bmtk.simulator.core package
  • Subpackages
    • bmtk.simulator.core.modules package
      • Submodules
      • bmtk.simulator.core.modules.ecephys_module module
      • bmtk.simulator.core.modules.iclamp module
      • bmtk.simulator.core.modules.simulator_module module
      • Module contents
    • bmtk.simulator.core.sonata_reader package
      • Submodules
      • bmtk.simulator.core.sonata_reader.edge_adaptor module
      • bmtk.simulator.core.sonata_reader.network_reader module
      • bmtk.simulator.core.sonata_reader.node_adaptor module
      • Module contents
  • Submodules
  • bmtk.simulator.core.edge_population module
    • EdgePopulation
      • EdgePopulation.initialize()
      • EdgePopulation.source_nodes
      • EdgePopulation.target_nodes
    • SimEdge
      • SimEdge.gid
      • SimEdge.node_id
  • bmtk.simulator.core.graph module
    • SimGraph
      • SimGraph.add_component()
      • SimGraph.add_edges()
      • SimGraph.add_nodes()
      • SimGraph.build_nodes()
      • SimGraph.build_recurrent_edges()
      • SimGraph.external_edge_populations()
      • SimGraph.from_config()
      • SimGraph.get_component()
      • SimGraph.get_node_population()
      • SimGraph.get_node_populations()
      • SimGraph.get_node_set()
      • SimGraph.io
      • SimGraph.model_type_col
      • SimGraph.node_populations
  • bmtk.simulator.core.io_tools module
    • IOUtils
      • IOUtils.barrier()
      • IOUtils.log_debug()
      • IOUtils.log_error()
      • IOUtils.log_exception()
      • IOUtils.log_info()
      • IOUtils.log_to_console
      • IOUtils.log_warning()
      • IOUtils.logger
      • IOUtils.quiet_simulator()
      • IOUtils.set_log_format()
      • IOUtils.set_log_level()
      • IOUtils.setup_output_dir()
  • bmtk.simulator.core.network_reader module
    • EdgesReader
      • EdgesReader.initialize()
      • EdgesReader.mixed
      • EdgesReader.mixed_connections
      • EdgesReader.recurrent
      • EdgesReader.recurrent_connections
      • EdgesReader.set_connection_type()
      • EdgesReader.source_nodes
      • EdgesReader.target_nodes
      • EdgesReader.unknown
      • EdgesReader.virtual
      • EdgesReader.virtual_connections
    • NodesReader
      • NodesReader.initialize()
      • NodesReader.internal_nodes_only
      • NodesReader.load()
      • NodesReader.mixed_nodes
      • NodesReader.name
      • NodesReader.virtual_nodes_only
  • bmtk.simulator.core.node_population module
    • NodePopulation
      • NodePopulation.initialize()
      • NodePopulation.internal_nodes_only
      • NodePopulation.load()
      • NodePopulation.mixed_nodes
      • NodePopulation.name
      • NodePopulation.virtual_nodes_only
    • SimNode
      • SimNode.gid
      • SimNode.node_id
  • bmtk.simulator.core.node_sets module
    • NodeSet
      • NodeSet.gids()
      • NodeSet.node_ids
      • NodeSet.nodes()
      • NodeSet.population_names()
      • NodeSet.populations()
    • NodeSetAll
    • to_list()
  • bmtk.simulator.core.pyfunction_cache module
    • add_cell_model()
    • add_cell_processor()
    • add_synapse_model()
    • add_weight_function()
    • cell_model()
    • load_py_modules()
    • synapse_model()
    • synaptic_weight()
  • bmtk.simulator.core.simulation_config module
    • SimulationConfig
      • SimulationConfig.build_env()
      • SimulationConfig.copy_to_output()
      • SimulationConfig.io
      • SimulationConfig.validate()
      • SimulationConfig.validator
    • from_dict()
    • from_json()
  • bmtk.simulator.core.simulation_config_validator module
    • SimulationConfigValidator
      • SimulationConfigValidator.is_type()
  • bmtk.simulator.core.simulator module
    • Simulator
      • Simulator.add_mod()
      • Simulator.run()
  • bmtk.simulator.core.simulator_network module
    • SimNetwork
      • SimNetwork.add_component()
      • SimNetwork.add_edges()
      • SimNetwork.add_node_set()
      • SimNetwork.add_nodes()
      • SimNetwork.build()
      • SimNetwork.build_nodes()
      • SimNetwork.build_recurrent_edges()
      • SimNetwork.build_virtual_connections()
      • SimNetwork.from_builder()
      • SimNetwork.from_config()
      • SimNetwork.from_manifest()
      • SimNetwork.get_component()
      • SimNetwork.get_edge_adaptor()
      • SimNetwork.get_node_adaptor()
      • SimNetwork.get_node_groups()
      • SimNetwork.get_node_population()
      • SimNetwork.get_node_populations()
      • SimNetwork.get_node_set()
      • SimNetwork.get_node_sets()
      • SimNetwork.has_component()
      • SimNetwork.io
      • SimNetwork.load_gap_junc_files()
      • SimNetwork.node_populations
      • SimNetwork.node_properties()
      • SimNetwork.py_function_caches
      • SimNetwork.recurrent_edges
  • Module contents
• bmtk.simulator.filternet package
  • Subpackages
    • bmtk.simulator.filternet.default_setters package
      • Submodules
      • bmtk.simulator.filternet.default_setters.cell_loaders module
      • Module contents
    • bmtk.simulator.filternet.lgnmodel package
      • Submodules
      • bmtk.simulator.filternet.lgnmodel.cellmetrics module
      • bmtk.simulator.filternet.lgnmodel.cellmodel module
      • bmtk.simulator.filternet.lgnmodel.cursor module
      • bmtk.simulator.filternet.lgnmodel.fitfuns module
      • bmtk.simulator.filternet.lgnmodel.gaborfilter module
      • bmtk.simulator.filternet.lgnmodel.kernel module
      • bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor module
      • bmtk.simulator.filternet.lgnmodel.lgnmodel1 module
      • bmtk.simulator.filternet.lgnmodel.linearfilter module
      • bmtk.simulator.filternet.lgnmodel.lnunit module
      • bmtk.simulator.filternet.lgnmodel.make_cell_list module
      • bmtk.simulator.filternet.lgnmodel.movie module
      • bmtk.simulator.filternet.lgnmodel.poissongeneration module
      • bmtk.simulator.filternet.lgnmodel.singleunitcell module
      • bmtk.simulator.filternet.lgnmodel.spatialfilter module
      • bmtk.simulator.filternet.lgnmodel.temporalfilter module
      • bmtk.simulator.filternet.lgnmodel.transferfunction module
      • bmtk.simulator.filternet.lgnmodel.util_fns module
      • bmtk.simulator.filternet.lgnmodel.utilities module
      • Module contents
    • bmtk.simulator.filternet.modules package
      • Submodules
      • bmtk.simulator.filternet.modules.base module
      • bmtk.simulator.filternet.modules.create_spikes module
      • bmtk.simulator.filternet.modules.record_rates module
      • Module contents
  • Submodules
  • bmtk.simulator.filternet.cell module
    • Cell
      • Cell.build()
      • Cell.default_jitter
      • Cell.get()
      • Cell.gid
      • Cell.lgn_cell_obj
      • Cell.population
  • bmtk.simulator.filternet.cell_models module
  • bmtk.simulator.filternet.config module
    • Config
      • Config.io
      • Config.jitter
  • bmtk.simulator.filternet.filternetwork module
    • FilterNetwork
      • FilterNetwork.build()
      • FilterNetwork.build_nodes()
      • FilterNetwork.cells()
      • FilterNetwork.jitter
      • FilterNetwork.set_default_processing()
  • bmtk.simulator.filternet.filters module
  • bmtk.simulator.filternet.filtersimulator module
    • FilterSimulator
      • FilterSimulator.add_movie()
      • FilterSimulator.dt
      • FilterSimulator.find_params()
      • FilterSimulator.from_config()
      • FilterSimulator.io
      • FilterSimulator.local_cells()
      • FilterSimulator.run()
  • bmtk.simulator.filternet.io_tools module
    • FilterNetIOUtils
      • FilterNetIOUtils.barrier()
      • FilterNetIOUtils.log_debug()
      • FilterNetIOUtils.log_info()
  • bmtk.simulator.filternet.pyfunction_cache module
    • add_cell_processor()
    • cell_processor()
    • load_py_modules()
  • bmtk.simulator.filternet.sonata_adaptors module
    • FilterNode
      • FilterNode.delays
      • FilterNode.delays_non_dom
      • FilterNode.jitter
      • FilterNode.kpeaks
      • FilterNode.kpeaks_non_dom
      • FilterNode.non_dom_params
      • FilterNode.predefined_jitter
      • FilterNode.sf_sep
      • FilterNode.tuning_angle
      • FilterNode.weights
      • FilterNode.weights_non_dom
    • FilterNodeAdaptor
      • FilterNodeAdaptor.get_node()
      • FilterNodeAdaptor.patch_adaptor()
      • FilterNodeAdaptor.preprocess_node_types()
    • find_delays_params()
    • find_kpeaks_params()
    • find_nondom_delays_params()
    • find_nondom_kpeaks_params()
    • find_nondom_weight_params()
    • find_weight_params()
    • non_dom_params()
    • return_none()
    • tuning_angle_preset()
    • tuning_angle_rand()
    • weights()
  • bmtk.simulator.filternet.transfer_functions module
  • bmtk.simulator.filternet.utils module
  • Module contents
• bmtk.simulator.pointnet package
  • Subpackages
    • bmtk.simulator.pointnet.default_setters package
      • Submodules
      • bmtk.simulator.pointnet.default_setters.synapse_models module
      • bmtk.simulator.pointnet.default_setters.synaptic_weights module
      • Module contents
    • bmtk.simulator.pointnet.modules package
      • Submodules
      • bmtk.simulator.pointnet.modules.ecephys_module module
      • bmtk.simulator.pointnet.modules.iclamp module
      • bmtk.simulator.pointnet.modules.multimeter_reporter module
      • bmtk.simulator.pointnet.modules.record_spikes module
      • Module contents
  • Submodules
  • bmtk.simulator.pointnet.config module
    • Config
      • Config.io
    • from_dict()
    • from_json()
  • bmtk.simulator.pointnet.gids module
    • GidPool
      • GidPool.add()
      • GidPool.add_gids()
      • GidPool.add_nestids()
      • GidPool.create_pool()
      • GidPool.get_gid()
      • GidPool.get_gids()
      • GidPool.get_nestids()
      • GidPool.get_pool_id()
      • GidPool.gids
      • GidPool.populations
    • PopulationID
      • PopulationID.node_id
      • PopulationID.population
    • ids2list()
    • ids2list_nest2()
    • ids2list_nest3()
  • bmtk.simulator.pointnet.glif_utils module
    • convert_aibs2nest()
    • converter_builtin()
    • converter_modules()
    • lif_aibs_converter()
    • lif_asc_aibs_converter()
    • lif_asc_psc_aibs_converter()
    • lif_psc_aibs_converter()
    • lif_r_aibs_converter()
    • lif_r_asc_a_aibs_converter()
    • lif_r_asc_a_psc_aibs_converter()
    • lif_r_asc_aibs_converter()
    • lif_r_asc_psc_aibs_converter()
    • lif_r_psc_aibs_converter()
  • bmtk.simulator.pointnet.io_tools module
    • NestIOUtils
      • NestIOUtils.barrier()
      • NestIOUtils.quiet_simulator()
      • NestIOUtils.setup_output_dir()
  • bmtk.simulator.pointnet.nest_utils module
    • get_version()
  • bmtk.simulator.pointnet.pointnetwork module
    • PointNetwork
      • PointNetwork.add_spike_trains()
      • PointNetwork.add_weight_function()
      • PointNetwork.build_nodes()
      • PointNetwork.build_recurrent_edges()
      • PointNetwork.find_edges()
      • PointNetwork.get_node_id()
      • PointNetwork.get_nodes_df()
      • PointNetwork.get_weight_function()
      • PointNetwork.gid_map
      • PointNetwork.gid_pool
      • PointNetwork.py_function_caches
      • PointNetwork.set_default_weight_function()
    • set_spikes()
    • set_spikes_nest2()
    • set_spikes_nest3()
  • bmtk.simulator.pointnet.pointsimulator module
    • PointSimulator
      • PointSimulator.add_mod()
      • PointSimulator.dt
      • PointSimulator.from_config()
      • PointSimulator.get_spike_generator_params()
      • PointSimulator.gid_map
      • PointSimulator.n_steps
      • PointSimulator.net
      • PointSimulator.run()
      • PointSimulator.set_spike_generator_params()
      • PointSimulator.simulation_time()
      • PointSimulator.tstart
      • PointSimulator.tstop
  • bmtk.simulator.pointnet.property_map module
    • EdgePropertyMap
      • EdgePropertyMap.build_map()
      • EdgePropertyMap.synaptic_model()
      • EdgePropertyMap.synpatic_params()
    • NodePropertyMap
      • NodePropertyMap.build_map()
      • NodePropertyMap.load_cell()
    • gid()
    • group_dynamics_params()
    • model_params()
    • model_params_batched()
    • model_type()
    • model_type_batched()
    • no_syns()
    • node_id()
    • nsyns()
    • syn_weight()
    • types_dynamics_params()
    • weight_function()
  • bmtk.simulator.pointnet.pyfunction_cache module
  • bmtk.simulator.pointnet.sonata_adaptors module
    • PointEdge
      • PointEdge.nest_params
      • PointEdge.source_node_ids
      • PointEdge.target_node_ids
    • PointEdgeAdaptor
      • PointEdgeAdaptor.batch_process
      • PointEdgeAdaptor.get_batches()
      • PointEdgeAdaptor.get_edge()
      • PointEdgeAdaptor.patch_adaptor()
      • PointEdgeAdaptor.preprocess_edge_types()
      • PointEdgeAdaptor.synaptic_params()
    • PointEdgeBatched
      • PointEdgeBatched.nest_params
      • PointEdgeBatched.source_node_ids
      • PointEdgeBatched.target_node_ids
    • PointNode
      • PointNode.build()
      • PointNode.gids
      • PointNode.n_nodes
      • PointNode.nest_ids
      • PointNode.nest_model
      • PointNode.nest_params
      • PointNode.node_ids
    • PointNodeAdaptor
      • PointNodeAdaptor.batch_process
      • PointNodeAdaptor.get_batches()
      • PointNodeAdaptor.get_node()
      • PointNodeAdaptor.patch_adaptor()
      • PointNodeAdaptor.preprocess_node_types()
    • PointNodeBatched
      • PointNodeBatched.build()
      • PointNodeBatched.gids
      • PointNodeBatched.model_type
      • PointNodeBatched.n_nodes
      • PointNodeBatched.nest_ids
      • PointNodeBatched.nest_model
      • PointNodeBatched.nest_params
      • PointNodeBatched.node_ids
    • all_null()
    • point_syn_weight()
  • bmtk.simulator.pointnet.utils module
    • gen_recurrent_csv()
    • gen_recurrent_h5()
    • load_conns()
    • load_params()
    • read_LGN_activity()
    • read_conns()
  • Module contents
• bmtk.simulator.popnet package
  • Submodules
  • bmtk.simulator.popnet.config module
    • Config
    • from_json()
  • bmtk.simulator.popnet.popedge module
    • PopEdge
      • PopEdge.delay
      • PopEdge.nsyns
      • PopEdge.params
      • PopEdge.source
      • PopEdge.target
      • PopEdge.weight
    • SimEdge
      • SimEdge.edge_type_id
  • bmtk.simulator.popnet.popnetwork module
    • ExtPopulation
      • ExtPopulation.build()
      • ExtPopulation.firing_rate
      • ExtPopulation.record
    • PopConnection
      • PopConnection.add_edge()
      • PopConnection.build()
      • PopConnection.dipde_obj
    • PopEdge
      • PopEdge.delay
      • PopEdge.nsyns
      • PopEdge.weight
    • PopNetwork
      • PopNetwork.add_rates()
      • PopNetwork.add_spike_trains()
      • PopNetwork.build_nodes()
      • PopNetwork.build_recurrent_edges()
      • PopNetwork.connections
      • PopNetwork.edges_table()
      • PopNetwork.find_edges()
      • PopNetwork.get_edges()
      • PopNetwork.get_population()
      • PopNetwork.get_populations()
      • PopNetwork.internal_populations
      • PopNetwork.populations
      • PopNetwork.rebuild()
    • Population
      • Population.add_node()
      • Population.build()
      • Population.dipde_obj
      • Population.get_gids()
      • Population.pop_id
      • Population.record
  • bmtk.simulator.popnet.popnode module
    • ExternalPopulation
      • ExternalPopulation.firing_rate
      • ExternalPopulation.is_firing_rate_set
      • ExternalPopulation.is_internal
    • InternalNode
      • InternalNode.dv
      • InternalNode.is_internal
      • InternalNode.tau_m
      • InternalNode.v_max
      • InternalNode.v_min
    • PopNode
      • PopNode.add_gid()
      • PopNode.dynamics_params
      • PopNode.get_gids()
      • PopNode.is_internal
      • PopNode.network
      • PopNode.node_id
      • PopNode.pop_id
    • SimNode
      • SimNode.model_params
      • SimNode.network
      • SimNode.node_id
      • SimNode.node_type_id
  • bmtk.simulator.popnet.popsimulator module
    • PopSimulator
      • PopSimulator.add_rate_hz()
      • PopSimulator.add_rates_nwb()
      • PopSimulator.build_populations()
      • PopSimulator.connections
      • PopSimulator.dt
      • PopSimulator.from_config()
      • PopSimulator.populations
      • PopSimulator.rates_file
      • PopSimulator.run()
      • PopSimulator.set_external_connections()
      • PopSimulator.set_logging()
      • PopSimulator.set_recurrent_connections()
      • PopSimulator.tstop
  • bmtk.simulator.popnet.sonata_adaptors module
    • PopEdgeAdaptor
      • PopEdgeAdaptor.get_edge()
    • PopNetEdge
      • PopNetEdge.syn_weight
  • bmtk.simulator.popnet.utils module
    • KeyDefaultDict
    • assert_model_known()
    • create_firing_rate_server()
    • create_instance()
    • create_nwb_server_file_path()
    • create_population_list()
    • df_to_csv()
    • get_firing_rate_from_nwb()
    • get_firing_rates()
    • get_mesoscale_connectivity_dict()
    • list_of_dicts_to_dict_of_lists()
    • network_dict_to_target_adjacency_dict()
    • population_list_to_csv()
    • population_list_to_dataframe()
    • population_to_dict_for_dataframe()
    • reorder_columns_in_frame()
  • Module contents
• bmtk.simulator.utils package
  • Submodules
  • bmtk.simulator.utils.simulation_inputs module
    • SimInput
      • SimInput.build()
      • SimInput.node_set
      • SimInput.register_module()
      • SimInput.registry
    • from_config()
  • bmtk.simulator.utils.simulation_reports module
    • ClampReport
      • ClampReport.avail_modules()
      • ClampReport.node_set
    • ECPReport
      • ECPReport.avail_modules()
      • ECPReport.build()
    • MembraneReport
      • MembraneReport.add_variables()
      • MembraneReport.avail_modules()
      • MembraneReport.build()
      • MembraneReport.can_combine()
    • MultimeterReport
      • MultimeterReport.avail_modules()
    • NetconReport
      • NetconReport.avail_modules()
    • SEClampReport
      • SEClampReport.avail_modules()
    • SaveSynapses
      • SaveSynapses.avail_modules()
    • SimReport
      • SimReport.avail_modules()
      • SimReport.build()
      • SimReport.default_dir
      • SimReport.node_set
      • SimReport.register_module()
      • SimReport.registry
    • SpikesReport
      • SpikesReport.avail_modules()
      • SpikesReport.build()
      • SpikesReport.from_output_dict()
    • from_config()
  • Module contents

Module contents