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
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
- 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_current_clamp()
BioSimulator.attach_file_current_clamp()
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
- 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
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
- 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
BioEdge
BioEdgeAdaptor
BioNode
BioNodeAdaptor
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
- 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
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
- 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
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
- 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
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.add_step_currents()
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
- 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
ExtPopulation
PopConnection
PopEdge
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
- bmtk.simulator.popnet.popnode module
- 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
- 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