bmtk.simulator package¶
Subpackages¶
- bmtk.simulator.bionet package
- Subpackages
- bmtk.simulator.bionet.default_setters package
- bmtk.simulator.bionet.modules package
- Submodules
- bmtk.simulator.bionet.modules.ecp 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
BioCellBioCell.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.morphologyBioCell.morphology_fileBioCell.print_synapses()BioCell.seg_coordsBioCell.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()
BioCellSpontSynConnectionStruct
- bmtk.simulator.bionet.bionetwork module
BioNetworkBioNetwork.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_poolBioNetwork.local_gidsBioNetwork.model_type_colBioNetwork.py_function_cachesBioNetwork.set_spont_syn_activity()
- bmtk.simulator.bionet.biosimulator module
BioSimulatorBioSimulator.add_mod()BioSimulator.attach_current_clamp()BioSimulator.attach_file_current_clamp()BioSimulator.attach_se_voltage_clamp()BioSimulator.biophysical_gidsBioSimulator.cell_var_outputBioSimulator.cell_variablesBioSimulator.celsiusBioSimulator.dtBioSimulator.from_config()BioSimulator.hBioSimulator.local_gidsBioSimulator.n_stepsBioSimulator.nsteps_blockBioSimulator.post_fadvance()BioSimulator.report_load_balance()BioSimulator.run()BioSimulator.set_spikes_recording()BioSimulator.simulation_time()BioSimulator.spikes_tableBioSimulator.tstopBioSimulator.v_init
- bmtk.simulator.bionet.cell module
- bmtk.simulator.bionet.config module
- bmtk.simulator.bionet.gids module
- bmtk.simulator.bionet.iclamp module
- bmtk.simulator.bionet.io_tools module
- bmtk.simulator.bionet.morphology module
MorphologyMorphology.choose_sections()Morphology.find_sections()Morphology.get_coords()Morphology.get_section()Morphology.get_swc_id()Morphology.load()Morphology.move_and_rotate()Morphology.n_sectionsMorphology.nsegMorphology.sec_type_swcMorphology.sectionsMorphology.seg_coordsMorphology.seg_propsMorphology.segmentsMorphology.set_segment_dl()Morphology.soma_positionMorphology.swc_map
rotation_matrix()
- bmtk.simulator.bionet.nml_reader module
- bmtk.simulator.bionet.nrn module
- bmtk.simulator.bionet.pointprocesscell module
- bmtk.simulator.bionet.pointsomacell module
- bmtk.simulator.bionet.pyfunction_cache module
- bmtk.simulator.bionet.seclamp module
- bmtk.simulator.bionet.sonata_adaptors module
BioEdgeBioEdgeAdaptorBioNodeBioNodeAdaptoraff_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
- bmtk.simulator.bionet.virtualcell module
- Module contents
- Subpackages
- bmtk.simulator.core package
- Subpackages
- Submodules
- bmtk.simulator.core.edge_population module
- bmtk.simulator.core.graph module
SimGraphSimGraph.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.ioSimGraph.model_type_colSimGraph.node_populations
- bmtk.simulator.core.io_tools module
- bmtk.simulator.core.network_reader module
- bmtk.simulator.core.node_population module
- bmtk.simulator.core.node_sets module
- bmtk.simulator.core.pyfunction_cache module
- bmtk.simulator.core.simulation_config module
- bmtk.simulator.core.simulation_config_validator module
- bmtk.simulator.core.simulator module
- bmtk.simulator.core.simulator_network module
SimNetworkSimNetwork.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.ioSimNetwork.load_gap_junc_files()SimNetwork.node_populationsSimNetwork.node_properties()SimNetwork.py_function_cachesSimNetwork.recurrent_edges
- Module contents
- bmtk.simulator.filternet package
- Subpackages
- bmtk.simulator.filternet.default_setters package
- 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.cell module
- bmtk.simulator.filternet.cell_models module
- bmtk.simulator.filternet.config module
- bmtk.simulator.filternet.filternetwork module
- bmtk.simulator.filternet.filters module
- bmtk.simulator.filternet.filtersimulator module
- bmtk.simulator.filternet.io_tools module
- bmtk.simulator.filternet.pyfunction_cache module
- bmtk.simulator.filternet.sonata_adaptors module
- bmtk.simulator.filternet.transfer_functions module
- bmtk.simulator.filternet.utils module
- Module contents
- Subpackages
- bmtk.simulator.pointnet package
- Subpackages
- Submodules
- bmtk.simulator.pointnet.config module
- bmtk.simulator.pointnet.gids module
- 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
- bmtk.simulator.pointnet.nest_utils module
- bmtk.simulator.pointnet.pointnetwork module
PointNetworkPointNetwork.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_mapPointNetwork.gid_poolPointNetwork.py_function_cachesPointNetwork.set_default_weight_function()
set_spikes()set_spikes_nest2()set_spikes_nest3()
- bmtk.simulator.pointnet.pointsimulator module
PointSimulatorPointSimulator.add_mod()PointSimulator.add_step_currents()PointSimulator.dtPointSimulator.from_config()PointSimulator.get_spike_generator_params()PointSimulator.gid_mapPointSimulator.n_stepsPointSimulator.netPointSimulator.run()PointSimulator.set_spike_generator_params()PointSimulator.simulation_time()PointSimulator.tstartPointSimulator.tstop
- bmtk.simulator.pointnet.property_map module
- bmtk.simulator.pointnet.pyfunction_cache module
- bmtk.simulator.pointnet.sonata_adaptors module
- bmtk.simulator.pointnet.utils module
- Module contents
- bmtk.simulator.popnet package
- Submodules
- bmtk.simulator.popnet.config module
- bmtk.simulator.popnet.popedge module
- bmtk.simulator.popnet.popnetwork module
ExtPopulationPopConnectionPopEdgePopNetworkPopNetwork.add_rates()PopNetwork.add_spike_trains()PopNetwork.build_nodes()PopNetwork.build_recurrent_edges()PopNetwork.connectionsPopNetwork.edges_table()PopNetwork.find_edges()PopNetwork.get_edges()PopNetwork.get_population()PopNetwork.get_populations()PopNetwork.internal_populationsPopNetwork.populationsPopNetwork.rebuild()
Population
- bmtk.simulator.popnet.popnode module
- bmtk.simulator.popnet.popsimulator module
PopSimulatorPopSimulator.add_rate_hz()PopSimulator.add_rates_nwb()PopSimulator.build_populations()PopSimulator.connectionsPopSimulator.dtPopSimulator.from_config()PopSimulator.populationsPopSimulator.rates_filePopSimulator.run()PopSimulator.set_external_connections()PopSimulator.set_logging()PopSimulator.set_recurrent_connections()PopSimulator.tstop
- bmtk.simulator.popnet.sonata_adaptors module
- bmtk.simulator.popnet.utils module
KeyDefaultDictassert_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