Index

A

adaptor (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes property) add() (bmtk.simulator.pointnet.gids.GidPool method) (bmtk.utils.reports.spike_trains.spike_trains.GammaSpikeGenerator method) (bmtk.utils.reports.spike_trains.spike_trains.PoissonSpikeGenerator method) add_audio() (bmtk.simulator.filternet.filtersimulator.FilterSimulator method) add_bio_conn() (bmtk.simulator.bionet.modules.save_synapses.ConnectionWriter method) (bmtk.simulator.bionet.modules.save_synapses.ConnectionWriter.H5Index method) add_cell() (bmtk.utils.io.cell_vars.CellVarRecorder method) (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) add_cell_model() (in module bmtk.simulator.core.pyfunction_cache) add_cell_processor() (in module bmtk.simulator.core.pyfunction_cache) (in module bmtk.simulator.filternet.pyfunction_cache) add_component() (bmtk.simulator.core.graph.SimGraph method) (bmtk.simulator.core.simulator_network.SimNetwork method) add_edges() (bmtk.builder.network_adaptors.network.Network method) (bmtk.builder.network_builder.BioNetBuilder method) (bmtk.builder.network_builder.NetworkBuilder method) (bmtk.builder.network_builder.PointNetBuilder method) (bmtk.builder.network_builder.PopNetBuilder method) (bmtk.simulator.core.graph.SimGraph method) (bmtk.simulator.core.simulator_network.SimNetwork method) add_gap_junctions() (bmtk.builder.network_adaptors.network.Network method) add_gids() (bmtk.simulator.pointnet.gids.GidPool method) (bmtk.utils.sonata.population.NodePopulation method) add_hdf5_attrs() (in module bmtk.builder.builder_utils) (in module bmtk.builder.network_adaptors.dm_network) (in module bmtk.builder.network_adaptors.dm_network_orig) add_hdf5_magic() (in module bmtk.utils.sonata.utils) add_hdf5_version() (in module bmtk.utils.sonata.utils) add_mod() (bmtk.simulator.bionet.biosimulator.BioSimulator method) (bmtk.simulator.core.simulator.Simulator method) (bmtk.simulator.pointnet.pointsimulator.PointSimulator method) add_movie() (bmtk.simulator.filternet.filtersimulator.FilterSimulator method) add_nest_module() (bmtk.simulator.pointnet.pointnetwork.PointNetwork method) add_nestids() (bmtk.simulator.pointnet.gids.GidPool method) add_node_set() (bmtk.simulator.core.simulator_network.SimNetwork method) add_nodes() (bmtk.builder.network_adaptors.network.Network method) (bmtk.builder.network_builder.BioNetBuilder method) (bmtk.builder.network_builder.NetworkBuilder method) (bmtk.builder.network_builder.PointNetBuilder method) (bmtk.builder.network_builder.PopNetBuilder method) (bmtk.simulator.bionet.bionetwork.BioNetwork method) (bmtk.simulator.core.graph.SimGraph method) (bmtk.simulator.core.simulator_network.SimNetwork method) add_point_conn() (bmtk.simulator.bionet.modules.save_synapses.ConnectionWriter method) (bmtk.simulator.bionet.modules.save_synapses.ConnectionWriter.H5Index method) add_pool() (bmtk.simulator.bionet.gids.GidPool method) add_positions() (bmtk.builder.auxi.node_params.CellLocations method) add_positions_columnar() (bmtk.builder.auxi.node_params.CellLocations method) add_positions_ellipsoid() (bmtk.builder.auxi.node_params.CellLocations method) add_positions_nrrd() (bmtk.builder.auxi.node_params.CellLocations method) add_positions_rect_prism() (bmtk.builder.auxi.node_params.CellLocations method) add_properties() (bmtk.builder.connection_map.ConnectionMap method) add_rates() (bmtk.utils.io.firing_rates.RatesWriter method) add_spike() (bmtk.utils.io.spike_trains.SpikeTrainWriter method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsReadOnlyAPI method)

add_spike_trains() (bmtk.simulator.bionet.bionetwork.BioNetwork method) (bmtk.simulator.pointnet.pointnetwork.PointNetwork method) add_spikes() (bmtk.utils.io.spike_trains.SpikeTrainWriter method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsReadOnlyAPI method) add_spikes_file() (bmtk.utils.io.spike_trains.SpikeTrainWriter method) add_spikes_generator() (in module bmtk.simulator.core.pyfunction_cache) add_synapse_model() (in module bmtk.simulator.core.pyfunction_cache) add_table() (bmtk.utils.sonata.types_table.TypesTable method) add_variables() (bmtk.simulator.utils.simulation_reports.MembraneReport method) add_weight_function() (bmtk.simulator.pointnet.pointnetwork.PointNetwork method) (in module bmtk.simulator.core.pyfunction_cache) aff_sec_id() (in module bmtk.simulator.bionet.sonata_adaptors) aff_sec_id_old() (in module bmtk.simulator.bionet.sonata_adaptors) aff_sec_pos() (in module bmtk.simulator.bionet.sonata_adaptors) aff_sec_pos_old() (in module bmtk.simulator.bionet.sonata_adaptors) afferent_section_id (bmtk.simulator.bionet.sonata_adaptors.BioEdge property) afferent_section_pos (bmtk.simulator.bionet.sonata_adaptors.BioEdge property) aibs_allactive() (in module bmtk.simulator.bionet.default_setters.cell_models) aibs_allactive_directed() (in module bmtk.simulator.bionet.default_setters.cell_models) aibs_perisomatic() (in module bmtk.simulator.bionet.default_setters.cell_models) aibs_perisomatic_directed() (in module bmtk.simulator.bionet.default_setters.cell_models) all_columns (bmtk.utils.sonata.group.Group property) all_null() (in module bmtk.simulator.pointnet.sonata_adaptors) all_to_one_iterator() (in module bmtk.builder.iterator) all_to_one_list_iterator() (in module bmtk.builder.iterator) amplitude (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) AmpsReader (class in bmtk.simulator.core.modules.iclamp) AmpsReaderNRN (class in bmtk.simulator.bionet.modules.iclamp) apply_dot_product() (bmtk.simulator.filternet.lgnmodel.cursor.KernelCursor method) apply_threshold() (bmtk.simulator.filternet.lgnmodel.kernel.Kernel2D method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel3D method) apply_transformation_matrix() (in module bmtk.simulator.filternet.lgnmodel.utilities) area (bmtk.builder.bionet.swc_reader.SegmentProps attribute) ArrayFilter (class in bmtk.simulator.filternet.lgnmodel.spatialfilter) ArrayTemporalFilter (class in bmtk.simulator.filternet.lgnmodel.temporalfilter) assert_model_known() (in module bmtk.simulator.popnet.utils) assign_groups() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) attach_current() (bmtk.simulator.bionet.iclamp.FileIClamp method) (bmtk.simulator.bionet.iclamp.IClamp method) (bmtk.simulator.bionet.seclamp.SEClamp method) attach_se_voltage_clamp() (bmtk.simulator.bionet.biosimulator.BioSimulator method) attributes (bmtk.utils.sonata.column_property.ColumnProperty property) AuditoryInput (class in bmtk.simulator.filternet.auditory_processing) avail_modules() (bmtk.simulator.utils.simulation_reports.ClampReport static method) (bmtk.simulator.utils.simulation_reports.ECPReport static method) (bmtk.simulator.utils.simulation_reports.MembraneReport static method) (bmtk.simulator.utils.simulation_reports.MultimeterReport static method) (bmtk.simulator.utils.simulation_reports.NetconReport static method) (bmtk.simulator.utils.simulation_reports.SaveSynapses static method) (bmtk.simulator.utils.simulation_reports.SEClampReport static method) (bmtk.simulator.utils.simulation_reports.SimReport static method) (bmtk.simulator.utils.simulation_reports.SpikesReport static method) (bmtk.simulator.utils.simulation_reports.WeightRecorder static method)

B

b_t (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) barrier() (bmtk.simulator.bionet.io_tools.NEURONIOUtils method) (bmtk.simulator.core.io_tools.IOUtils method) (bmtk.simulator.filternet.io_tools.FilterNetIOUtils method) (bmtk.simulator.pointnet.io_tools.NestIOUtils method) (bmtk.utils.io.ioutils.BMTKWorldComm method) (in module bmtk.builder.builder_utils) (in module bmtk.builder.network_adaptors.dm_network_orig) (in module bmtk.simulator.core.modules.ecephys_module) (in module bmtk.utils.reports.compartment.compartment_writer) base_dir (bmtk.utils.create_environment.env_builder.EnvBuilder property) (bmtk.utils.sim_setup.EnvBuilder property) BaseWaveform (class in bmtk.simulator.bionet.modules.xstim_waveforms) BaseWaveformType (class in bmtk.simulator.bionet.modules.xstim_waveforms) batch_process (bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor property) (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor property) (bmtk.simulator.pointnet.sonata_adaptors.PointEdgeAdaptor property) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeAdaptor property) bcast() (in module bmtk.simulator.core.modules.ecephys_module) BioCell (class in bmtk.simulator.bionet.biocell) BioCellSpontSyn (class in bmtk.simulator.bionet.biocell) BioECEphysUnitsModule (class in bmtk.simulator.bionet.modules.ecephys_module) BioEdge (class in bmtk.simulator.bionet.sonata_adaptors) BioEdgeAdaptor (class in bmtk.simulator.bionet.sonata_adaptors) BioNetBuilder (class in bmtk.builder.network_builder) BioNetEnvBuilder (class in bmtk.utils.create_environment.env_builder) (class in bmtk.utils.sim_setup) BioNetwork (class in bmtk.simulator.bionet.bionetwork) BioNode (class in bmtk.simulator.bionet.sonata_adaptors) BioNodeAdaptor (class in bmtk.simulator.bionet.sonata_adaptors) Biophys1() (in module bmtk.simulator.bionet.default_setters.cell_models) Biophys1_dict() (in module bmtk.simulator.bionet.default_setters.cell_models) Biophys1_nml() (in module bmtk.simulator.bionet.default_setters.cell_models) biophysical_gids (bmtk.simulator.bionet.biosimulator.BioSimulator property) BioSimulator (class in bmtk.simulator.bionet.biosimulator) block() (bmtk.simulator.bionet.modules.ecp.EcpMod method) (bmtk.simulator.bionet.modules.record_cellvars.MembraneReport method) (bmtk.simulator.bionet.modules.record_clamp.ClampReport method) (bmtk.simulator.bionet.modules.record_netcons.NetconReport method) (bmtk.simulator.bionet.modules.record_spikes.SpikesMod method) (bmtk.simulator.bionet.modules.sim_module.SimulatorMod method) (bmtk.simulator.core.modules.simulator_module.SimulatorMod method) (bmtk.simulator.pointnet.modules.sim_module.SimulatorMod method) bmtk module bmtk.analyzer module bmtk.analyzer.cell_vars module bmtk.analyzer.compartment module bmtk.analyzer.ecp module bmtk.analyzer.edges module bmtk.analyzer.firing_rates module bmtk.analyzer.io_tools module bmtk.analyzer.spike_trains module bmtk.analyzer.spikes_analyzer module bmtk.analyzer.spikes_loader module bmtk.analyzer.utils module bmtk.builder module bmtk.builder.auxi module bmtk.builder.auxi.edge_connectors module bmtk.builder.auxi.node_params module bmtk.builder.bionet module bmtk.builder.bionet.swc_reader module bmtk.builder.builder_utils module bmtk.builder.connection_map module bmtk.builder.connector module bmtk.builder.edge module bmtk.builder.edges_sorter module bmtk.builder.edges_sorter.memory_sorter module bmtk.builder.edges_sorter.merge_sorter module bmtk.builder.functor_cache module bmtk.builder.id_generator module bmtk.builder.index_builders module bmtk.builder.iterator module bmtk.builder.network_adaptors module bmtk.builder.network_adaptors.dm_network module bmtk.builder.network_adaptors.dm_network_orig module bmtk.builder.network_adaptors.edge_props_table module bmtk.builder.network_adaptors.edges_collator module bmtk.builder.network_adaptors.network module bmtk.builder.network_adaptors.nxnetwork module bmtk.builder.network_builder module bmtk.builder.networks module bmtk.builder.node module bmtk.builder.node_pool module bmtk.builder.node_set module bmtk.simulator module bmtk.simulator.bionet module bmtk.simulator.bionet.biocell module bmtk.simulator.bionet.bionetwork module bmtk.simulator.bionet.biosimulator module bmtk.simulator.bionet.cell module bmtk.simulator.bionet.config module bmtk.simulator.bionet.default_setters module bmtk.simulator.bionet.default_setters.cell_models module bmtk.simulator.bionet.default_setters.synapse_models module bmtk.simulator.bionet.default_setters.synaptic_weights module bmtk.simulator.bionet.gids module bmtk.simulator.bionet.iclamp module bmtk.simulator.bionet.io_tools module bmtk.simulator.bionet.modules module 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.seclamp module bmtk.simulator.bionet.modules.sim_module module bmtk.simulator.bionet.modules.xstim module bmtk.simulator.bionet.modules.xstim_waveforms module bmtk.simulator.bionet.morphology module 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 bmtk.simulator.bionet.utils module bmtk.simulator.bionet.virtualcell module bmtk.simulator.core module bmtk.simulator.core.edge_population module bmtk.simulator.core.graph module bmtk.simulator.core.io_tools module bmtk.simulator.core.modules module bmtk.simulator.core.modules.ecephys_module module bmtk.simulator.core.modules.iclamp module bmtk.simulator.core.modules.simulator_module 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 bmtk.simulator.core.sonata_reader module bmtk.simulator.core.sonata_reader.edge_adaptor module bmtk.simulator.core.sonata_reader.network_reader module bmtk.simulator.core.sonata_reader.node_adaptor module bmtk.simulator.filternet module bmtk.simulator.filternet.auditory_processing module bmtk.simulator.filternet.cell module bmtk.simulator.filternet.cell_models module bmtk.simulator.filternet.config module bmtk.simulator.filternet.default_setters module bmtk.simulator.filternet.default_setters.cell_loaders 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.lgnmodel module 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 bmtk.simulator.filternet.lgnmodel.waveletfilter module bmtk.simulator.filternet.modules module bmtk.simulator.filternet.modules.base module bmtk.simulator.filternet.modules.create_spikes module bmtk.simulator.filternet.modules.record_rates module bmtk.simulator.filternet.pyfunction_cache module bmtk.simulator.filternet.sonata_adaptors module bmtk.simulator.filternet.transfer_functions module bmtk.simulator.filternet.utils module bmtk.simulator.pointnet module bmtk.simulator.pointnet.config module bmtk.simulator.pointnet.default_setters module bmtk.simulator.pointnet.default_setters.cell_models module bmtk.simulator.pointnet.default_setters.synapse_models module bmtk.simulator.pointnet.default_setters.synaptic_weights module bmtk.simulator.pointnet.gids module bmtk.simulator.pointnet.glif_utils module bmtk.simulator.pointnet.io_tools module bmtk.simulator.pointnet.modules module 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 bmtk.simulator.pointnet.modules.sim_module module bmtk.simulator.pointnet.modules.spikes_inputs module bmtk.simulator.pointnet.modules.weight_recorder module bmtk.simulator.pointnet.nest_utils module bmtk.simulator.pointnet.pointnetwork module bmtk.simulator.pointnet.pointsimulator module bmtk.simulator.pointnet.property_map module bmtk.simulator.pointnet.pyfunction_cache module bmtk.simulator.pointnet.sonata_adaptors module bmtk.simulator.pointnet.utils module bmtk.simulator.popnet.sonata_adaptors module bmtk.simulator.popnet.utils module bmtk.simulator.utils module bmtk.simulator.utils.simulation_inputs module bmtk.simulator.utils.simulation_reports module bmtk.utils module bmtk.utils.cell_types_db module bmtk.utils.compile_mechanisms module bmtk.utils.compile_mechanisms.compile_mechanisms module bmtk.utils.create_environment module bmtk.utils.create_environment.create_environment module bmtk.utils.create_environment.env_builder module bmtk.utils.hdf5_helper module bmtk.utils.io module bmtk.utils.io.cell_vars module bmtk.utils.io.firing_rates module bmtk.utils.io.ioutils module bmtk.utils.io.spike_trains module bmtk.utils.lazy_property module bmtk.utils.reports module bmtk.utils.reports.compartment module bmtk.utils.reports.compartment.compartment_reader module bmtk.utils.reports.compartment.compartment_report module bmtk.utils.reports.compartment.compartment_writer module bmtk.utils.reports.compartment.core module bmtk.utils.reports.compartment.plotting module bmtk.utils.reports.current_writer module bmtk.utils.reports.spike_trains module bmtk.utils.reports.spike_trains.core module bmtk.utils.reports.spike_trains.plotting module bmtk.utils.reports.spike_trains.spike_train_buffer module bmtk.utils.reports.spike_trains.spike_train_readers module bmtk.utils.reports.spike_trains.spike_trains module bmtk.utils.reports.spike_trains.spike_trains_api module bmtk.utils.reports.spike_trains.spikes_file_writers module bmtk.utils.reports.spike_trains.stats module bmtk.utils.sim_setup module bmtk.utils.sonata module bmtk.utils.sonata.column_property module bmtk.utils.sonata.config module bmtk.utils.sonata.config.sonata_config module bmtk.utils.sonata.edge module bmtk.utils.sonata.edge_stats module bmtk.utils.sonata.file module bmtk.utils.sonata.file_root module bmtk.utils.sonata.group module bmtk.utils.sonata.node module bmtk.utils.sonata.population module bmtk.utils.sonata.types_table module bmtk.utils.sonata.utils module bmtk_simulator (bmtk.utils.create_environment.env_builder.BioNetEnvBuilder property) (bmtk.utils.create_environment.env_builder.EnvBuilder property) (bmtk.utils.create_environment.env_builder.FilterNetEnvBuilder property) (bmtk.utils.create_environment.env_builder.PointNetEnvBuilder property) (bmtk.utils.create_environment.env_builder.PopNetEnvBuilder property) (bmtk.utils.sim_setup.BioNetEnvBuilder property) (bmtk.utils.sim_setup.EnvBuilder property) (bmtk.utils.sim_setup.FilterNetEnvBuilder property) (bmtk.utils.sim_setup.PointNetEnvBuilder property) (bmtk.utils.sim_setup.PopNetEnvBuilder property) BMTKWorldComm (class in bmtk.utils.io.ioutils) build() (bmtk.builder.network_adaptors.network.Network method) (bmtk.builder.network_builder.NetworkBuilder method) (bmtk.builder.node_set.NodeSet method) (bmtk.simulator.core.simulator_network.SimNetwork method) (bmtk.simulator.filternet.cell.Cell method) (bmtk.simulator.filternet.filternetwork.FilterNetwork method) (bmtk.simulator.pointnet.sonata_adaptors.PointNode method) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched method) (bmtk.simulator.utils.simulation_inputs.SimInput class method) (bmtk.simulator.utils.simulation_reports.ECPReport class method) (bmtk.simulator.utils.simulation_reports.MembraneReport class method) (bmtk.simulator.utils.simulation_reports.SimReport class method) (bmtk.simulator.utils.simulation_reports.SpikesReport class method) (bmtk.utils.create_environment.env_builder.EnvBuilder method) (bmtk.utils.sim_setup.EnvBuilder method) build_env() (bmtk.simulator.bionet.config.Config method) (bmtk.simulator.core.simulation_config.SimulationConfig method) build_env_bionet() (in module bmtk.utils.sim_setup) build_env_filternet() (in module bmtk.utils.sim_setup) build_env_pointnet() (in module bmtk.utils.sim_setup) build_env_popnet() (in module bmtk.utils.sim_setup) build_indicies() (bmtk.utils.sonata.group.EdgeGroup method) (bmtk.utils.sonata.group.Group method) (bmtk.utils.sonata.group.NodeGroup method) (bmtk.utils.sonata.population.EdgePopulation method) build_map() (bmtk.simulator.core.modules.ecephys_module.MappingStrategy method) (bmtk.simulator.core.modules.ecephys_module.SamplingStrategy method) (bmtk.simulator.core.modules.ecephys_module.UnitIdMapStrategy method) (bmtk.simulator.pointnet.property_map.EdgePropertyMap class method) (bmtk.simulator.pointnet.property_map.NodePropertyMap class method) build_morphology() (bmtk.simulator.bionet.biocell.BioCell method) build_nodes() (bmtk.simulator.bionet.bionetwork.BioNetwork method) (bmtk.simulator.core.graph.SimGraph method) (bmtk.simulator.core.simulator_network.SimNetwork method) (bmtk.simulator.filternet.filternetwork.FilterNetwork method) (bmtk.simulator.pointnet.pointnetwork.PointNetwork method) build_recurrent_edges() (bmtk.simulator.bionet.bionetwork.BioNetwork method) (bmtk.simulator.core.graph.SimGraph method) (bmtk.simulator.core.simulator_network.SimNetwork method) (bmtk.simulator.pointnet.pointnetwork.PointNetwork method) build_replay_inputs() (bmtk.simulator.bionet.bionetwork.BioNetwork method) build_time_uuid() (in module bmtk.builder.builder_utils) build_virtual_connections() (bmtk.simulator.core.simulator_network.SimNetwork method) by_id (bmtk.utils.reports.spike_trains.core.SortOrder attribute) by_time (bmtk.utils.reports.spike_trains.core.SortOrder attribute)

C

calc_transfer_resistance() (bmtk.simulator.bionet.modules.ecp.RecXElectrode method) calculate() (bmtk.simulator.bionet.modules.xstim_waveforms.BaseWaveform method) (bmtk.simulator.bionet.modules.xstim_waveforms.ComplexWaveform method) (bmtk.simulator.bionet.modules.xstim_waveforms.WaveformCustom method) (bmtk.simulator.bionet.modules.xstim_waveforms.WaveformTypeDC method) (bmtk.simulator.bionet.modules.xstim_waveforms.WaveformTypeSin method) calculate_waveforms() (bmtk.simulator.bionet.modules.xstim.StimXElectrode method) can_combine() (bmtk.simulator.utils.simulation_reports.MembraneReport method) CCF_orientation (bmtk.builder.auxi.node_params.CellLocations property) Cell (class in bmtk.simulator.bionet.cell) (class in bmtk.simulator.filternet.cell) cell_model() (in module bmtk.simulator.core.pyfunction_cache) cell_processor() (in module bmtk.simulator.filternet.pyfunction_cache) cell_type_maps() (bmtk.simulator.bionet.bionetwork.BioNetwork method) cell_var_output (bmtk.simulator.bionet.biosimulator.BioSimulator property) cell_variables (bmtk.simulator.bionet.biosimulator.BioSimulator property) CellLocations (class in bmtk.builder.auxi.node_params) cells() (bmtk.simulator.filternet.filternetwork.FilterNetwork method) CellVarRecorder (class in bmtk.utils.io.cell_vars) CellVarRecorder.DataTable (class in bmtk.utils.io.cell_vars) CellVarRecorderParallel (class in bmtk.utils.io.cell_vars) celsius (bmtk.simulator.bionet.biosimulator.BioSimulator property) ChannelDensity (class in bmtk.simulator.bionet.nml_reader) ChannelDensityNernst (class in bmtk.simulator.bionet.nml_reader) check_format() (bmtk.utils.sonata.file_root.FileRoot method) (bmtk.utils.sonata.group.Group method) check_magic() (in module bmtk.utils.sonata.utils) check_optim_results_against_bounds() (in module bmtk.simulator.filternet.lgnmodel.util_fns) check_properties_across_ranks() (in module bmtk.builder.builder_utils) chisquare() (in module bmtk.utils.sonata.edge_stats) choose_sections() (bmtk.builder.bionet.swc_reader.SWCReader method) (bmtk.simulator.bionet.morphology.Morphology method) chunks() (in module bmtk.simulator.filternet.lgnmodel.util_fns) ClampReport (class in bmtk.simulator.bionet.modules.record_clamp) (class in bmtk.simulator.utils.simulation_reports) clean_ends() (bmtk.simulator.bionet.modules.save_synapses.ConnectionWriter.H5Index method) clear() (bmtk.builder.network_adaptors.network.Network method) (bmtk.builder.network_builder.NetworkBuilder method) clear_gids() (in module bmtk.simulator.bionet.nrn) close() (bmtk.simulator.bionet.modules.save_synapses.ConnectionWriter method) (bmtk.utils.io.cell_vars.CellVarRecorder method) (bmtk.utils.io.spike_trains.SpikeTrainWriter method) (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsReadOnlyAPI method) close_h5() (bmtk.simulator.bionet.modules.save_synapses.ConnectionWriter.H5Index method) close_tmp_file() (bmtk.utils.io.spike_trains.SpikeTrainWriter method) COL_DYNAMICS_PARAM (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor attribute) COL_GID (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor attribute) COL_MODEL_PROCESSING (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor attribute) COL_MODEL_TEMPLATE (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor attribute) COL_MODEL_TYPE (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor attribute) col_range (bmtk.simulator.filternet.lgnmodel.cursor.KernelCursor property) column() (bmtk.utils.sonata.group.Group method) (bmtk.utils.sonata.types_table.TypesTable method) ColumnProperty (class in bmtk.utils.sonata.column_property) columns (bmtk.utils.sonata.group.Group property) (bmtk.utils.sonata.types_table.TypesTable property) comm (bmtk.utils.io.ioutils.BMTKWorldComm property) common_name() (bmtk.simulator.bionet.nml_reader.NMLTree static method) CompartmentReaderABC (class in bmtk.utils.reports.compartment.core) CompartmentReaderVer01 (class in bmtk.utils.reports.compartment.compartment_reader) CompartmentReport (class in bmtk.utils.reports.compartment.compartment_report) CompartmentWriterABC (class in bmtk.utils.reports.compartment.core) CompartmentWriterv01 (class in bmtk.utils.reports.compartment.compartment_writer) compile_mechanisms() (bmtk.utils.create_environment.env_builder.BioNetEnvBuilder method) (bmtk.utils.create_environment.env_builder.EnvBuilder method) (bmtk.utils.sim_setup.BioNetEnvBuilder method) (in module bmtk.utils.compile_mechanisms.compile_mechanisms)

ComplexWaveform (class in bmtk.simulator.bionet.modules.xstim_waveforms) components_dir (bmtk.utils.create_environment.env_builder.EnvBuilder property) (bmtk.utils.sim_setup.EnvBuilder property) compute_FFT_OneCycle() (in module bmtk.simulator.filternet.lgnmodel.util_fns) ComsolMod (class in bmtk.simulator.bionet.modules.comsol) ConcentrationModel (class in bmtk.simulator.bionet.nml_reader) Config (class in bmtk.simulator.bionet.config) (class in bmtk.simulator.filternet.config) (class in bmtk.simulator.pointnet.config) ConfigParser (class in bmtk.utils.sonata.config.sonata_config) connect_random() (in module bmtk.builder.auxi.edge_connectors) connection_itr() (bmtk.builder.connection_map.ConnectionMap method) ConnectionMap (class in bmtk.builder.connection_map) ConnectionMap.ParamsRules (class in bmtk.builder.connection_map) connections() (bmtk.simulator.bionet.biocell.BioCell method) (bmtk.simulator.bionet.pointprocesscell.PointProcessCell method) ConnectionStruct (class in bmtk.simulator.bionet.biocell) (class in bmtk.simulator.bionet.pointprocesscell) ConnectionWriter (class in bmtk.simulator.bionet.modules.save_synapses) ConnectionWriter.H5Index (class in bmtk.simulator.bionet.modules.save_synapses) connector (bmtk.builder.connection_map.ConnectionMap property) connector_params (bmtk.builder.connection_map.ConnectionMap property) convert_aibs2nest() (in module bmtk.simulator.pointnet.glif_utils) convert_rates() (in module bmtk.analyzer.firing_rates) convert_tmin_tmax_framerate_to_trange() (in module bmtk.simulator.filternet.lgnmodel.utilities) converter_builtin() (in module bmtk.simulator.pointnet.glif_utils) converter_modules() (in module bmtk.simulator.pointnet.glif_utils) copy() (bmtk.simulator.filternet.lgnmodel.kernel.Kernel2D class method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel3D class method) copy_attributes() (in module bmtk.builder.edges_sorter.memory_sorter) copy_config() (in module bmtk.utils.sonata.config.sonata_config) copy_modfiles() (in module bmtk.utils.compile_mechanisms.compile_mechanisms) copy_to_output() (bmtk.simulator.core.simulation_config.SimulationConfig method) create() (bmtk.builder.functor_cache.FunctorCache method) (bmtk.builder.iterator.IteratorCache method) (in module bmtk.builder.connector) (in module bmtk.builder.iterator) create_adaptor() (bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor class method) (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor class method) create_clamp() (bmtk.simulator.bionet.modules.seclamp.SEClamp method) create_clamps() (bmtk.simulator.bionet.modules.iclamp.AmpsReaderNRN method) (bmtk.simulator.bionet.modules.iclamp.CSVAmpReaderNRN method) (bmtk.simulator.bionet.modules.iclamp.NWBReaderNRN method) create_environment() (in module bmtk.utils.create_environment.create_environment) create_ff_mov() (in module bmtk.simulator.filternet.lgnmodel.util_fns) create_firing_rate_server() (in module bmtk.simulator.popnet.utils) create_grating_movie_list() (in module bmtk.simulator.filternet.lgnmodel.util_fns) create_index_in_memory() (in module bmtk.builder.index_builders) create_index_on_disk() (in module bmtk.builder.index_builders) create_instance() (in module bmtk.simulator.popnet.utils) create_movie() (bmtk.simulator.filternet.lgnmodel.movie.FullFieldMovie method) (bmtk.simulator.filternet.lgnmodel.movie.GratingMovie method) (bmtk.simulator.filternet.lgnmodel.movie.LoomingMovie method) create_multimeter() (in module bmtk.simulator.pointnet.modules.multimeter_reporter) create_multimeter_nest2() (in module bmtk.simulator.pointnet.modules.multimeter_reporter) create_multimeter_nest3() (in module bmtk.simulator.pointnet.modules.multimeter_reporter) create_nwb_server_file_path() (in module bmtk.simulator.popnet.utils) create_output_dir() (bmtk.simulator.bionet.config.Config method) create_pool() (bmtk.simulator.pointnet.gids.GidPool method) create_population_list() (in module bmtk.simulator.popnet.utils) create_property() (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory method) create_spike_detector() (in module bmtk.simulator.pointnet.modules.record_spikes) create_spike_detector_nest2() (in module bmtk.simulator.pointnet.modules.record_spikes) create_spike_detector_nest3() (in module bmtk.simulator.pointnet.modules.record_spikes) create_two_sub_cell() (in module bmtk.simulator.filternet.default_setters.cell_loaders) createOneUnitOfTwoSubunitFilter() (in module bmtk.simulator.filternet.default_setters.cell_loaders) cross_from_above() (in module bmtk.simulator.filternet.lgnmodel.util_fns) CSVAmpReader (class in bmtk.simulator.core.modules.iclamp) CSVAmpReaderNRN (class in bmtk.simulator.bionet.modules.iclamp) CSVSTReader (class in bmtk.utils.reports.spike_trains.spike_train_readers) CurrentWriterv01 (class in bmtk.utils.reports.current_writer) CurrentWriterv01.DataTable (class in bmtk.utils.reports.current_writer) custom_columns() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method)

D

DandiFileWrapper (class in bmtk.simulator.core.modules.ecephys_module) data (bmtk.simulator.filternet.lgnmodel.movie.FullFieldMovie property) data() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) default_cell_loader() (in module bmtk.simulator.filternet.default_setters.cell_loaders) default_dir (bmtk.simulator.utils.simulation_reports.SimReport attribute) default_jitter (bmtk.simulator.filternet.cell.Cell property) default_population (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 property) default_weight_fnc() (in module bmtk.simulator.bionet.default_setters.synaptic_weights) (in module bmtk.simulator.pointnet.default_setters.synaptic_weights) delay (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) delays (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) delays_non_dom (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) delete_axon() (bmtk.builder.bionet.swc_reader.SWCReader method) DenseNetwork (class in bmtk.builder.network_adaptors.dm_network) DenseNetworkOrig (class in bmtk.builder.network_adaptors.dm_network_orig) DenseNetworkOrig.EdgeTable (class in bmtk.builder.network_adaptors.dm_network_orig) DenseNetworkOrig.PropertyTable (class in bmtk.builder.network_adaptors.dm_network_orig) df_to_csv() (in module bmtk.simulator.popnet.utils) DFIndexedGIDs (class in bmtk.utils.io.spike_trains) DictIndexedGIDs (class in bmtk.utils.io.spike_trains) dimension (bmtk.utils.sonata.column_property.ColumnProperty property)

direction (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) dist (bmtk.builder.bionet.swc_reader.SegmentProps attribute) dist0 (bmtk.builder.bionet.swc_reader.SegmentProps attribute) dist1 (bmtk.builder.bionet.swc_reader.SegmentProps attribute) distance_connector() (in module bmtk.builder.auxi.edge_connectors) dmin (bmtk.builder.auxi.node_params.CellLocations property) download_ephys_data() (in module bmtk.utils.cell_types_db) download_model() (in module bmtk.utils.cell_types_db) drift() (bmtk.simulator.bionet.modules.ecp.RecXElectrode method) dt (bmtk.simulator.bionet.biosimulator.BioSimulator property) (bmtk.simulator.filternet.filtersimulator.FilterSimulator property) (bmtk.simulator.pointnet.pointsimulator.PointSimulator property) (bmtk.utils.io.cell_vars.CellVarRecorder property) dt() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) dtype (bmtk.utils.sonata.column_property.ColumnProperty property) dtypes (bmtk.builder.connection_map.ConnectionMap.ParamsRules property) dynamics_params (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property) (bmtk.utils.sonata.edge.Edge property) (bmtk.utils.sonata.node.Node property)

E

ECEphysUnitsModule (class in bmtk.simulator.core.modules.ecephys_module) EcpMod (class in bmtk.simulator.bionet.modules.ecp) ECPReport (class in bmtk.simulator.utils.simulation_reports) Edge (class in bmtk.builder.edge) (class in bmtk.utils.sonata.edge) edge_converter_csv() (in module bmtk.simulator.bionet.utils) edge_props_distribution() (in module bmtk.utils.sonata.edge_stats) edge_stats_table() (in module bmtk.utils.sonata.edge_stats) edge_type_id (bmtk.builder.connection_map.ConnectionMap property) (bmtk.builder.edge.Edge property) (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) (bmtk.utils.sonata.edge.Edge property) edge_type_ids (bmtk.utils.sonata.group.EdgeGroup property) (bmtk.utils.sonata.types_table.EdgeTypesTable property) edge_type_node_ids (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory property) edge_type_properties (bmtk.builder.connection_map.ConnectionMap property) (bmtk.builder.edge.Edge property) (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory property) edge_types_table (bmtk.utils.sonata.file_root.EdgesRoot property) (bmtk.utils.sonata.population.EdgePopulation property) EdgeAdaptor (class in bmtk.simulator.core.sonata_reader.edge_adaptor) EdgeGroup (class in bmtk.utils.sonata.group) EdgePopulation (class in bmtk.simulator.core.edge_population) (class in bmtk.utils.sonata.population) EdgePropertyMap (class in bmtk.simulator.pointnet.property_map) edges (bmtk.utils.sonata.file.File property) edges() (bmtk.builder.network_adaptors.network.Network method) (bmtk.builder.network_builder.NetworkBuilder method) edges_built (bmtk.builder.network_adaptors.network.Network property) (bmtk.builder.network_builder.NetworkBuilder property) edges_iter() (bmtk.builder.network_adaptors.dm_network.DenseNetwork method) (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig method) (bmtk.builder.network_adaptors.network.Network method) edges_table() (bmtk.builder.network_adaptors.dm_network.DenseNetwork method) (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig method) EdgesCollator (class in bmtk.builder.network_adaptors.edges_collator) EdgesCollatorMPI (class in bmtk.builder.network_adaptors.edges_collator) EdgesCollatorSingular (class in bmtk.builder.network_adaptors.edges_collator) EdgeSet (class in bmtk.utils.sonata.edge) EdgesReader (class in bmtk.simulator.core.network_reader) EdgesRoot (class in bmtk.utils.sonata.file_root) EdgeTypesTable (class in bmtk.builder.network_adaptors.edge_props_table) (class in bmtk.utils.sonata.types_table) EdgeTypesTableIFace (class in bmtk.builder.network_adaptors.edge_props_table)

EdgeTypesTableMemory (class in bmtk.builder.network_adaptors.edge_props_table) EdgeTypesTableMPI (class in bmtk.builder.network_adaptors.edge_props_table) element_ids() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) element_pos() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) element_registry (bmtk.simulator.bionet.nml_reader.NMLTree attribute) element_tag() (bmtk.simulator.bionet.nml_reader.ChannelDensity static method) (bmtk.simulator.bionet.nml_reader.ChannelDensityNernst static method) (bmtk.simulator.bionet.nml_reader.ConcentrationModel static method) (bmtk.simulator.bionet.nml_reader.NMLElement static method) (bmtk.simulator.bionet.nml_reader.Resistivity static method) (bmtk.simulator.bionet.nml_reader.SpecificCapacitance static method) empty_list() (in module bmtk.simulator.core.sonata_reader.node_adaptor) EmptySonataReader (class in bmtk.utils.reports.spike_trains.spike_train_readers) EnvBuilder (class in bmtk.utils.create_environment.env_builder) (class in bmtk.utils.sim_setup) evaluate() (bmtk.simulator.filternet.lgnmodel.cursor.KernelCursor method) (bmtk.simulator.filternet.lgnmodel.cursor.MultiLNUnitCursor method) (bmtk.simulator.filternet.lgnmodel.cursor.SeparableKernelCursor method) (bmtk.simulator.filternet.lgnmodel.cursor.SeparableLNUnitCursor method) (bmtk.simulator.filternet.lgnmodel.cursor.SeparableMultiLNUnitCursor method) (bmtk.simulator.filternet.lgnmodel.lgnmodel1.LGNModel method) (bmtk.simulator.filternet.lgnmodel.lnunit.LNUnit method) (bmtk.simulator.filternet.lgnmodel.lnunit.MultiLNUnit method) evaluate_cell_and_plot() (in module bmtk.simulator.filternet.lgnmodel.make_cell_list) evolve() (bmtk.simulator.core.simulation_config_validator.SimulationConfigValidator method) examples_dir (bmtk.utils.create_environment.env_builder.BioNetEnvBuilder property) (bmtk.utils.create_environment.env_builder.EnvBuilder property) (bmtk.utils.create_environment.env_builder.FilterNetEnvBuilder property) (bmtk.utils.create_environment.env_builder.PointNetEnvBuilder property) (bmtk.utils.create_environment.env_builder.PopNetEnvBuilder property) (bmtk.utils.sim_setup.BioNetEnvBuilder property) (bmtk.utils.sim_setup.EnvBuilder property) (bmtk.utils.sim_setup.FilterNetEnvBuilder property) (bmtk.utils.sim_setup.PointNetEnvBuilder property) (bmtk.utils.sim_setup.PopNetEnvBuilder property) exp1isyn() (in module bmtk.simulator.bionet.default_setters.synapse_models) exp1syn() (in module bmtk.simulator.bionet.default_setters.synapse_models) Exp2Syn() (in module bmtk.simulator.bionet.default_setters.synapse_models) exp2syn() (in module bmtk.simulator.bionet.default_setters.synapse_models) expsyn() (in module bmtk.simulator.bionet.default_setters.synapse_models) external_edge_populations() (bmtk.simulator.core.graph.SimGraph method) external_merge_sort() (in module bmtk.builder.edges_sorter.merge_sorter)

F

f_rate_to_spike_train() (in module bmtk.simulator.filternet.modules.create_spikes) fetch_nodes() (bmtk.simulator.core.node_sets.NodeSet method) ff() (in module bmtk.simulator.filternet.lgnmodel.fitfuns) File (class in bmtk.utils.sonata.file) FileIClamp (class in bmtk.simulator.bionet.iclamp) FileRoot (class in bmtk.utils.sonata.file_root) filter() (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes method) (bmtk.utils.sonata.group.EdgeGroup method) (bmtk.utils.sonata.group.NodeGroup method) (bmtk.utils.sonata.population.EdgePopulation method) (bmtk.utils.sonata.population.NodePopulation method) filter_str (bmtk.builder.node_pool.NodePool property) filter_table() (in module bmtk.simulator.core.modules.ecephys_module) FilterCursor (class in bmtk.simulator.filternet.lgnmodel.cursor) FilterNetEnvBuilder (class in bmtk.utils.create_environment.env_builder) (class in bmtk.utils.sim_setup) FilterNetIOUtils (class in bmtk.simulator.filternet.io_tools) FilterNetwork (class in bmtk.simulator.filternet.filternetwork) FilterNode (class in bmtk.simulator.filternet.sonata_adaptors) FilterNodeAdaptor (class in bmtk.simulator.filternet.sonata_adaptors) FilterSimulator (class in bmtk.simulator.filternet.filtersimulator) finalize() (bmtk.simulator.bionet.modules.ecp.EcpMod method) (bmtk.simulator.bionet.modules.record_cellvars.MembraneReport method) (bmtk.simulator.bionet.modules.record_clamp.ClampReport method) (bmtk.simulator.bionet.modules.record_netcons.NetconReport method) (bmtk.simulator.bionet.modules.record_spikes.SpikesMod method) (bmtk.simulator.bionet.modules.sim_module.SimulatorMod method) (bmtk.simulator.core.modules.simulator_module.SimulatorMod method) (bmtk.simulator.filternet.modules.base.SimModule method) (bmtk.simulator.filternet.modules.create_spikes.SpikesGenerator method) (bmtk.simulator.filternet.modules.record_rates.RecordRates method) (bmtk.simulator.pointnet.modules.multimeter_reporter.MultimeterMod method) (bmtk.simulator.pointnet.modules.record_spikes.SpikesMod method) (bmtk.simulator.pointnet.modules.sim_module.SimulatorMod method) (bmtk.simulator.pointnet.modules.weight_recorder.WeightRecorder method) find() (bmtk.utils.sonata.types_table.TypesTable method) find_conversion() (in module bmtk.utils.reports.spike_trains.core) find_delays_params() (in module bmtk.simulator.filternet.sonata_adaptors) find_edges() (bmtk.simulator.bionet.bionetwork.BioNetwork method) (bmtk.simulator.pointnet.pointnetwork.PointNetwork method) find_file_type() (in module bmtk.utils.reports.spike_trains.core) find_kpeaks_params() (in module bmtk.simulator.filternet.sonata_adaptors) find_l_r_in_t_range() (in module bmtk.simulator.filternet.lgnmodel.kernel) find_nondom_delays_params() (in module bmtk.simulator.filternet.sonata_adaptors) find_nondom_kpeaks_params() (in module bmtk.simulator.filternet.sonata_adaptors) find_nondom_weight_params() (in module bmtk.simulator.filternet.sonata_adaptors) find_params() (bmtk.simulator.filternet.filtersimulator.FilterSimulator static method) find_sections() (bmtk.builder.bionet.swc_reader.SWCReader method) (bmtk.simulator.bionet.morphology.Morphology method) find_spectrotemporal_params() (in module bmtk.simulator.filternet.sonata_adaptors) find_weight_params() (in module bmtk.simulator.filternet.sonata_adaptors) firing_rates_equal() (in module bmtk.analyzer.firing_rates) first_element() (in module bmtk.simulator.bionet.modules.record_cellvars) fix_axon() (bmtk.builder.bionet.swc_reader.SWCReader method)

fix_axon_allactive() (in module bmtk.simulator.bionet.default_setters.cell_models) fix_axon_allactive_directed() (in module bmtk.simulator.bionet.default_setters.cell_models) fix_axon_peri() (in module bmtk.simulator.bionet.default_setters.cell_models) fix_axon_perisomatic_directed() (in module bmtk.simulator.bionet.default_setters.cell_models) flush() (bmtk.utils.io.cell_vars.CellVarRecorder method) (bmtk.utils.io.spike_trains.SpikeTrainWriter method) (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsReadOnlyAPI method) format_checker (bmtk.simulator.core.simulation_config_validator.SimulationConfigValidator attribute) fr_corr() (in module bmtk.utils.reports.spike_trains.spike_trains) fr_mean() (in module bmtk.utils.reports.spike_trains.stats) frame_rate (bmtk.simulator.filternet.lgnmodel.cursor.KernelCursor property) (bmtk.simulator.filternet.lgnmodel.movie.FullFieldMovie property) free_data() (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory method) from_builder() (bmtk.simulator.core.simulator_network.SimNetwork class method) from_config() (bmtk.simulator.bionet.biosimulator.BioSimulator class method) (bmtk.simulator.core.graph.SimGraph class method) (bmtk.simulator.core.simulator_network.SimNetwork class method) (bmtk.simulator.filternet.filtersimulator.FilterSimulator class method) (bmtk.simulator.pointnet.pointsimulator.PointSimulator class method) (in module bmtk.simulator.utils.simulation_inputs) (in module bmtk.simulator.utils.simulation_reports) from_csv() (bmtk.utils.reports.spike_trains.spike_trains.SpikeTrains class method) (bmtk.utils.sonata.column_property.ColumnProperty class method) from_dense() (bmtk.simulator.filternet.lgnmodel.kernel.Kernel2D class method) from_dict() (bmtk.utils.sonata.config.sonata_config.SonataConfig class method) (in module bmtk.simulator.core.simulation_config) (in module bmtk.simulator.pointnet.config) (in module bmtk.utils.sonata.config.sonata_config) from_filter() (bmtk.builder.node_pool.NodePool class method) from_h5() (bmtk.utils.sonata.column_property.ColumnProperty class method) from_json() (bmtk.utils.sonata.config.sonata_config.SonataConfig class method) (in module bmtk.simulator.core.simulation_config) (in module bmtk.simulator.pointnet.config) (in module bmtk.utils.sonata.config.sonata_config) from_manifest() (bmtk.simulator.core.simulator_network.SimNetwork class method) from_nwb() (bmtk.utils.reports.spike_trains.spike_trains.SpikeTrains class method) from_output_dict() (bmtk.simulator.utils.simulation_reports.SpikesReport class method) from_sonata() (bmtk.utils.reports.spike_trains.spike_trains.SpikeTrains class method) from_yaml() (bmtk.utils.sonata.config.sonata_config.SonataConfig class method) (in module bmtk.utils.sonata.config.sonata_config) full() (bmtk.simulator.filternet.lgnmodel.kernel.Kernel1D method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel2D method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel3D method) (bmtk.simulator.filternet.lgnmodel.movie.FullFieldMovie method) FullFieldFlashMovie (class in bmtk.simulator.filternet.lgnmodel.movie) FullFieldMovie (class in bmtk.simulator.filternet.lgnmodel.movie) FunctorCache (class in bmtk.builder.functor_cache)

G

GaborFilter (class in bmtk.simulator.filternet.lgnmodel.gaborfilter) GammaSpikeGenerator (class in bmtk.utils.reports.spike_trains.spike_trains) gaussianLL() (in module bmtk.simulator.bionet.default_setters.synaptic_weights) GaussianSpatialFilter (class in bmtk.simulator.filternet.lgnmodel.spatialfilter) gen_recurrent_csv() (in module bmtk.simulator.pointnet.utils) gen_recurrent_h5() (in module bmtk.simulator.pointnet.utils) generate_gids() (bmtk.utils.sonata.file_root.NodesRoot method) generate_inhomogenous_poisson() (in module bmtk.simulator.filternet.lgnmodel.poissongeneration) generate_poisson_process() (in module bmtk.simulator.filternet.lgnmodel.poissongeneration) generate_poisson_rescaling() (in module bmtk.simulator.filternet.lgnmodel.poissongeneration) generate_poisson_rescaling_function() (in module bmtk.simulator.filternet.lgnmodel.poissongeneration) generate_renewal_process() (in module bmtk.simulator.filternet.lgnmodel.poissongeneration) get() (bmtk.builder.node.Node method) (bmtk.simulator.filternet.cell.Cell method) get_attribute_h5() (in module bmtk.utils.hdf5_helper) (in module bmtk.utils.sonata.utils) get_axon_direction() (in module bmtk.simulator.bionet.default_setters.cell_models) get_batches() (bmtk.simulator.pointnet.sonata_adaptors.PointEdgeAdaptor method) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeAdaptor method) get_cell_gid() (bmtk.simulator.bionet.bionetwork.BioNetwork method) get_cell_node_id() (bmtk.simulator.bionet.bionetwork.BioNetwork method) get_cochleagram() (bmtk.simulator.filternet.auditory_processing.AuditoryInput method) get_column() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) get_component() (bmtk.simulator.core.graph.SimGraph method) (bmtk.simulator.core.simulator_network.SimNetwork method) get_connection_info() (bmtk.simulator.bionet.biocell.BioCell method) (bmtk.simulator.bionet.cell.Cell method) (bmtk.simulator.bionet.pointprocesscell.PointProcessCell method) get_connections() (bmtk.builder.network_adaptors.network.Network method) get_contour() (in module bmtk.simulator.filternet.lgnmodel.kernel) get_convolution() (in module bmtk.simulator.filternet.lgnmodel.utilities) get_convolution_ind() (in module bmtk.simulator.filternet.lgnmodel.utilities) get_coords() (bmtk.builder.bionet.swc_reader.SWCReader method) (bmtk.simulator.bionet.morphology.Morphology method) get_cursor() (bmtk.simulator.filternet.lgnmodel.lnunit.LNUnit method) (bmtk.simulator.filternet.lgnmodel.lnunit.MultiLNUnit method) get_dandiset() (in module bmtk.simulator.core.modules.ecephys_module) get_data_metrics_for_each_subclass() (in module bmtk.simulator.filternet.lgnmodel.cellmetrics) get_dataset() (bmtk.utils.sonata.group.Group method) get_default_t_grid() (bmtk.simulator.filternet.lgnmodel.temporalfilter.ArrayTemporalFilter method) (bmtk.simulator.filternet.lgnmodel.temporalfilter.TemporalFilter method) (bmtk.simulator.filternet.lgnmodel.temporalfilter.TemporalFilterCosineBump method) get_disconnected_cell() (bmtk.simulator.bionet.bionetwork.BioNetwork method) get_edge() (bmtk.simulator.bionet.sonata_adaptors.BioEdgeAdaptor method) (bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor method) (bmtk.simulator.pointnet.sonata_adaptors.PointEdgeAdaptor method) (bmtk.simulator.popnet.sonata_adaptors.PopEdgeAdaptor method) get_edge_adaptor() (bmtk.simulator.core.simulator_network.SimNetwork method) get_edge_group_ids() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) get_edge_group_indices() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) get_edge_type_ids() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) get_edges() (bmtk.simulator.core.sonata_reader.network_reader.SonataEdges method) get_firing_rate_from_nwb() (in module bmtk.simulator.popnet.utils) get_firing_rates() (in module bmtk.simulator.popnet.utils) get_gid() (bmtk.simulator.bionet.gids.GidPool method) (bmtk.simulator.pointnet.gids.GidPool method) (bmtk.utils.sonata.population.NodePopulation method) get_gids() (bmtk.simulator.pointnet.gids.GidPool method) get_gj_id() (bmtk.simulator.bionet.bionetwork.BioNetwork method) get_group() (bmtk.utils.sonata.population.Population method) get_group_data() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) get_group_metadata() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) get_group_property() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) get_ids() (bmtk.builder.id_generator.IDGenerator method) get_im() (bmtk.simulator.bionet.biocell.BioCell method) get_kernel() (bmtk.simulator.filternet.lgnmodel.gaborfilter.GaborFilter method) (bmtk.simulator.filternet.lgnmodel.spatialfilter.ArrayFilter method) (bmtk.simulator.filternet.lgnmodel.spatialfilter.GaussianSpatialFilter method) (bmtk.simulator.filternet.lgnmodel.temporalfilter.TemporalFilter method) (bmtk.simulator.filternet.lgnmodel.waveletfilter.WaveletFilter method) get_local_cells() (bmtk.simulator.bionet.bionetwork.BioNetwork method) get_mean_firing_rates() (in module bmtk.analyzer.spikes_analyzer) get_mesoscale_connectivity_dict() (in module bmtk.simulator.popnet.utils) get_metrics() (bmtk.simulator.filternet.lgnmodel.cellmetrics.SubclassMetricsCache method) get_nestids() (bmtk.simulator.pointnet.gids.GidPool method) get_node() (bmtk.simulator.bionet.sonata_adaptors.BioNodeAdaptor method) (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes method) (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method) (bmtk.simulator.filternet.sonata_adaptors.FilterNodeAdaptor method) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeAdaptor method) get_node_adaptor() (bmtk.simulator.core.simulator_network.SimNetwork method) get_node_description() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) get_node_groups() (bmtk.simulator.core.simulator_network.SimNetwork method) get_node_id() (bmtk.simulator.bionet.bionetwork.BioNetwork method) (bmtk.simulator.pointnet.pointnetwork.PointNetwork method) (bmtk.utils.sonata.population.NodePopulation method) get_node_ids() (bmtk.simulator.pointnet.gids.GidPool method) (in module bmtk.utils.sonata.utils) get_node_population() (bmtk.simulator.core.graph.SimGraph method) (bmtk.simulator.core.simulator_network.SimNetwork method) get_node_populations() (bmtk.simulator.core.graph.SimGraph method) (bmtk.simulator.core.simulator_network.SimNetwork method) get_node_set() (bmtk.simulator.core.graph.SimGraph method) (bmtk.simulator.core.simulator_network.SimNetwork method) get_node_sets() (bmtk.simulator.core.simulator_network.SimNetwork method) get_nodes() (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes method) get_nodes_df() (bmtk.simulator.pointnet.pointnetwork.PointNetwork method) get_pool_id() (bmtk.simulator.bionet.gids.GidPool method) (bmtk.simulator.pointnet.gids.GidPool method) get_population() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) (bmtk.utils.sonata.file_root.FileRoot method) get_populations() (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVMPIBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMPIBuffer method) (bmtk.utils.sonata.file_root.EdgesRoot method) get_prop_dtype() (bmtk.builder.connection_map.ConnectionMap.ParamsRules method) get_properties() (bmtk.utils.sonata.node.NodeSet method) get_property_metatadata() (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory method)

get_property_value() (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory method) get_rate() (bmtk.utils.io.firing_rates.RatesInput method) get_report_description() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) get_rotation_matrix() (in module bmtk.simulator.filternet.lgnmodel.utilities) get_row() (bmtk.utils.sonata.population.EdgePopulation method) (bmtk.utils.sonata.population.NodePopulation method) get_rows() (bmtk.utils.sonata.population.NodePopulation method) get_scale_matrix() (in module bmtk.simulator.filternet.lgnmodel.utilities) get_section() (bmtk.builder.bionet.swc_reader.SWCReader method) (bmtk.simulator.bionet.biocell.BioCell method) (bmtk.simulator.bionet.cell.Cell method) (bmtk.simulator.bionet.morphology.Morphology method) get_sections() (bmtk.simulator.bionet.biocell.BioCell method) get_sections_id() (bmtk.simulator.bionet.biocell.BioCell method) get_sigma() (in module bmtk.simulator.filternet.default_setters.cell_loaders) get_source() (bmtk.simulator.core.sonata_reader.network_reader.SonataEdges method) (bmtk.utils.sonata.population.EdgePopulation method) get_source_node_ids() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) get_source_population() (bmtk.utils.sonata.population.EdgePopulation static method) get_sources() (bmtk.utils.sonata.population.EdgePopulation method) get_spatiotemporal_kernel() (bmtk.simulator.filternet.lgnmodel.linearfilter.SpatioTemporalFilter method) (bmtk.simulator.filternet.lgnmodel.lnunit.LNUnit method) (bmtk.simulator.filternet.lgnmodel.lnunit.MultiLNUnit method) get_spectrotemporal_kernel() (bmtk.simulator.filternet.lgnmodel.linearfilter.SpectroTemporalFilter method) (bmtk.simulator.filternet.lgnmodel.lnunit.LNUnit method) get_spike_generator_params() (bmtk.simulator.pointnet.pointsimulator.PointSimulator method) get_spike_trains() (bmtk.simulator.core.modules.ecephys_module.MappingStrategy method) get_spikes() (bmtk.utils.io.spike_trains.DFIndexedGIDs method) (bmtk.utils.io.spike_trains.DictIndexedGIDs method) (bmtk.utils.io.spike_trains.SONATAIndexer method) (bmtk.utils.io.spike_trains.SpikesInput method) (bmtk.utils.io.spike_trains.SpikesInputCSV method) (bmtk.utils.io.spike_trains.SpikesInputH5 method) (bmtk.utils.io.spike_trains.SpikesInputNWBv1 method) get_swc() (in module bmtk.builder.bionet.swc_reader) get_swc_id() (bmtk.builder.bionet.swc_reader.SWCReader method) (bmtk.simulator.bionet.morphology.Morphology method) get_target() (bmtk.simulator.core.sonata_reader.network_reader.SonataEdges method) (bmtk.utils.sonata.population.EdgePopulation method) get_target_node_ids() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) get_target_population() (bmtk.utils.sonata.population.EdgePopulation static method) get_targets() (bmtk.utils.sonata.population.EdgePopulation method) get_tcross_from_temporal_kernel() (in module bmtk.simulator.filternet.lgnmodel.util_fns) get_tf_params() (in module bmtk.simulator.filternet.default_setters.cell_loaders) get_times() (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVMPIBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMPIBuffer method) (bmtk.utils.reports.spike_trains.spike_train_readers.CSVSTReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.EmptySonataReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.NWBSTReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataOldReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) get_tmp_table_path() (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMPI static method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI static method) get_transfer_resistance() (bmtk.simulator.bionet.modules.ecp.RecXElectrode method) get_translation_matrix() (in module bmtk.simulator.filternet.lgnmodel.utilities) get_values() (bmtk.utils.sonata.group.EdgeGroup method) (bmtk.utils.sonata.group.Group method) (bmtk.utils.sonata.group.NodeGroup method) get_vanhateren() (in module bmtk.simulator.filternet.lgnmodel.utilities) get_version() (in module bmtk.simulator.pointnet.nest_utils) (in module bmtk.utils.sonata.utils) get_vext() (bmtk.simulator.bionet.modules.xstim.StimXElectrode method) get_virtual_cells() (bmtk.simulator.bionet.bionetwork.BioNetwork method) get_wavelet_params() (in module bmtk.simulator.filternet.default_setters.cell_loaders) get_weight_function() (bmtk.simulator.pointnet.pointnetwork.PointNetwork method) gid (bmtk.simulator.bionet.cell.Cell property) (bmtk.simulator.core.edge_population.SimEdge property) (bmtk.simulator.core.node_population.SimNode property) (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property) (bmtk.simulator.filternet.cell.Cell property) (bmtk.utils.sonata.node.Node property) gid() (in module bmtk.simulator.pointnet.property_map) gid_map (bmtk.simulator.pointnet.pointnetwork.PointNetwork property) (bmtk.simulator.pointnet.pointsimulator.PointSimulator property) gid_pool (bmtk.simulator.bionet.bionetwork.BioNetwork property) (bmtk.simulator.pointnet.pointnetwork.PointNetwork property) GidPool (class in bmtk.simulator.bionet.gids) (class in bmtk.simulator.pointnet.gids) gids (bmtk.simulator.pointnet.gids.GidPool property) (bmtk.simulator.pointnet.sonata_adaptors.PointNode property) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property) (bmtk.utils.io.spike_trains.SpikesInputH5 property) (bmtk.utils.sonata.group.NodeGroup property) (bmtk.utils.sonata.node.NodeSet property) (bmtk.utils.sonata.population.NodePopulation property) gids() (bmtk.simulator.core.node_sets.NodeSet method) GratingMovie (class in bmtk.simulator.filternet.lgnmodel.movie) Group (class in bmtk.utils.sonata.group) group_columns (bmtk.utils.sonata.group.Group property) group_dynamics_params() (in module bmtk.simulator.core.sonata_reader.edge_adaptor) (in module bmtk.simulator.core.sonata_reader.node_adaptor) (in module bmtk.simulator.pointnet.property_map) group_id (bmtk.simulator.bionet.cell.Cell property) (bmtk.utils.sonata.edge.Edge property) (bmtk.utils.sonata.group.Group property) (bmtk.utils.sonata.node.Node property) group_id_column (bmtk.utils.sonata.population.EdgePopulation property) (bmtk.utils.sonata.population.NodePopulation property) (bmtk.utils.sonata.population.Population property) group_id_ds (bmtk.utils.sonata.population.Population property) group_ids (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI property) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular property) (bmtk.utils.sonata.population.Population property) group_index_column (bmtk.utils.sonata.population.EdgePopulation property) (bmtk.utils.sonata.population.NodePopulation property) (bmtk.utils.sonata.population.Population property) group_index_ds (bmtk.utils.sonata.population.Population property) group_indicies() (bmtk.utils.sonata.population.EdgePopulation method) (bmtk.utils.sonata.population.Population method) group_props (bmtk.utils.sonata.node.Node property) groups (bmtk.utils.sonata.population.Population property)

H

h (bmtk.simulator.bionet.biosimulator.BioSimulator property) h5_base (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 property) H5Merger (class in bmtk.simulator.bionet.modules.save_synapses) has_component() (bmtk.simulator.core.simulator_network.SimNetwork method) has_dynamics_params (bmtk.utils.sonata.group.Group property) has_edges (bmtk.utils.sonata.file.File property) has_gids (bmtk.utils.sonata.file_root.NodesRoot property) (bmtk.utils.sonata.group.Group property) (bmtk.utils.sonata.population.NodePopulation property)

has_nodes (bmtk.utils.sonata.file.File property) has_target() (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig.EdgeTable method) hash_key (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory property) hcp() (in module bmtk.builder.auxi.node_params) HDF5IndexedGIDs (class in bmtk.utils.io.spike_trains) heat_plot() (in module bmtk.simulator.filternet.lgnmodel.lgnmodel1) hobj (bmtk.simulator.bionet.cell.Cell property) (bmtk.simulator.bionet.virtualcell.VirtualCell property)

I

IClamp (class in bmtk.simulator.bionet.iclamp) iclamp_waveform_factory() (in module bmtk.simulator.bionet.modules.xstim_waveforms) IClampMod (class in bmtk.simulator.bionet.modules.iclamp) (class in bmtk.simulator.core.modules.iclamp) (class in bmtk.simulator.pointnet.modules.iclamp) IDGenerator (class in bmtk.builder.id_generator) ids2list() (in module bmtk.simulator.pointnet.gids) ids2list_nest2() (in module bmtk.simulator.pointnet.gids) ids2list_nest3() (in module bmtk.simulator.pointnet.gids) igids() (bmtk.utils.sonata.population.NodePopulation method) igroup_ids() (bmtk.utils.sonata.population.Population method) igroup_indicies() (bmtk.utils.sonata.population.Population method) import_nodes() (bmtk.builder.network_adaptors.dm_network.DenseNetwork method) (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig method) (bmtk.builder.network_adaptors.network.Network method) (bmtk.builder.network_builder.NetworkBuilder method) import_spikes() (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsReadOnlyAPI method) imshow() (bmtk.simulator.filternet.lgnmodel.gaborfilter.GaborFilter method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel1D method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel2D method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel3D method) (bmtk.simulator.filternet.lgnmodel.movie.Movie method) (bmtk.simulator.filternet.lgnmodel.spatialfilter.ArrayFilter method) (bmtk.simulator.filternet.lgnmodel.spatialfilter.GaussianSpatialFilter method) (bmtk.simulator.filternet.lgnmodel.temporalfilter.TemporalFilter method) (bmtk.simulator.filternet.lgnmodel.transferfunction.ScalarTransferFunction method) (bmtk.simulator.filternet.lgnmodel.waveletfilter.WaveletFilter method) imshow_summary() (bmtk.simulator.filternet.lgnmodel.movie.Movie method) index() (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) index_column_name (bmtk.utils.sonata.population.NodePopulation property) (bmtk.utils.sonata.types_table.EdgeTypesTable property) (bmtk.utils.sonata.types_table.NodeTypesTable property) (bmtk.utils.sonata.types_table.TypesTable property) init_connections() (bmtk.simulator.bionet.biocell.BioCell method) (bmtk.simulator.bionet.cell.Cell method) initialize() (bmtk.simulator.bionet.modules.comsol.ComsolMod method) (bmtk.simulator.bionet.modules.ecephys_module.BioECEphysUnitsModule method) (bmtk.simulator.bionet.modules.ecp.EcpMod method) (bmtk.simulator.bionet.modules.iclamp.IClampMod method) (bmtk.simulator.bionet.modules.record_cellvars.MembraneReport method) (bmtk.simulator.bionet.modules.record_cellvars.SomaReport method) (bmtk.simulator.bionet.modules.record_clamp.ClampReport method) (bmtk.simulator.bionet.modules.record_netcons.NetconReport method) (bmtk.simulator.bionet.modules.record_spikes.SpikesMod method) (bmtk.simulator.bionet.modules.save_synapses.SaveSynapses method) (bmtk.simulator.bionet.modules.seclamp.SEClamp method) (bmtk.simulator.bionet.modules.sim_module.SimulatorMod method) (bmtk.simulator.bionet.modules.xstim.XStimMod method) (bmtk.simulator.core.edge_population.EdgePopulation method) (bmtk.simulator.core.modules.ecephys_module.ECEphysUnitsModule method) (bmtk.simulator.core.modules.simulator_module.SimulatorMod method) (bmtk.simulator.core.network_reader.EdgesReader method) (bmtk.simulator.core.network_reader.NodesReader method) (bmtk.simulator.core.node_population.NodePopulation method) (bmtk.simulator.core.sonata_reader.network_reader.SonataEdges method) (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes method) (bmtk.simulator.filternet.modules.base.SimModule method) (bmtk.simulator.filternet.modules.record_rates.RecordRates method) (bmtk.simulator.pointnet.modules.ecephys_module.PointECEphysUnitsModule method) (bmtk.simulator.pointnet.modules.iclamp.IClampMod method) (bmtk.simulator.pointnet.modules.multimeter_reporter.MultimeterMod method) (bmtk.simulator.pointnet.modules.record_spikes.SpikesMod method) (bmtk.simulator.pointnet.modules.sim_module.SimulatorMod method) (bmtk.simulator.pointnet.modules.spikes_inputs.SpikesInputsMod method) (bmtk.utils.io.cell_vars.CellVarRecorder method) (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method)

inode_ids() (bmtk.utils.sonata.population.NodePopulation method) inode_type_ids() (bmtk.utils.sonata.population.NodePopulation method) input2reader_map (bmtk.simulator.bionet.modules.iclamp.IClampMod property) (bmtk.simulator.core.modules.iclamp.IClampMod property) internal_nodes_only (bmtk.simulator.core.network_reader.NodesReader property) (bmtk.simulator.core.node_population.NodePopulation property) IntFire1() (in module bmtk.simulator.bionet.default_setters.cell_models) invnl() (in module bmtk.simulator.filternet.lgnmodel.fitfuns) io (bmtk.simulator.core.graph.SimGraph property) (bmtk.simulator.core.simulation_config.SimulationConfig property) (bmtk.simulator.core.simulator_network.SimNetwork property) (bmtk.simulator.filternet.config.Config property) (bmtk.simulator.filternet.filtersimulator.FilterSimulator property) (bmtk.simulator.pointnet.config.Config property) IOUtils (class in bmtk.simulator.core.io_tools) is_active() (bmtk.simulator.bionet.modules.xstim_waveforms.BaseWaveformType method) is_equal() (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) is_gap_junc (bmtk.simulator.bionet.biocell.ConnectionStruct property) is_gap_junction (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) is_initialized (bmtk.utils.io.cell_vars.CellVarRecorder property) is_subset() (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) is_type() (bmtk.simulator.core.simulation_config_validator.SimulationConfigValidator method) is_virtual (bmtk.simulator.bionet.biocell.ConnectionStruct property) (bmtk.simulator.bionet.pointprocesscell.ConnectionStruct property) iter_edges() (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory method) iterator (bmtk.builder.connection_map.ConnectionMap property) IteratorCache (class in bmtk.builder.iterator) itr_chunks() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) itr_vals() (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig.PropertyTable method)

J

jitter (bmtk.simulator.filternet.config.Config property) (bmtk.simulator.filternet.filternetwork.FilterNetwork property) (bmtk.simulator.filternet.sonata_adaptors.FilterNode property)

K

Kernel1D (class in bmtk.simulator.filternet.lgnmodel.kernel) Kernel2D (class in bmtk.simulator.filternet.lgnmodel.kernel) Kernel3D (class in bmtk.simulator.filternet.lgnmodel.kernel) kernel_dot_product() (in module bmtk.simulator.filternet.lgnmodel.cursor)

KernelCursor (class in bmtk.simulator.filternet.lgnmodel.cursor) KeyDefaultDict (class in bmtk.simulator.popnet.utils) kolmogorov_smirnov() (in module bmtk.utils.sonata.edge_stats) kpeaks (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) kpeaks_non_dom (bmtk.simulator.filternet.sonata_adaptors.FilterNode property)

L

lambda_iterator() (in module bmtk.builder.iterator) lazy_property() (in module bmtk.utils.lazy_property) length (bmtk.builder.bionet.swc_reader.SegmentProps attribute) lgn_cell_obj (bmtk.simulator.filternet.cell.Cell property) LGNModel (class in bmtk.simulator.filternet.lgnmodel.lgnmodel1) LGNOnOffCell (class in bmtk.simulator.filternet.lgnmodel.cellmodel) lif_aibs_converter() (in module bmtk.simulator.pointnet.glif_utils) lif_asc_aibs_converter() (in module bmtk.simulator.pointnet.glif_utils) lif_asc_psc_aibs_converter() (in module bmtk.simulator.pointnet.glif_utils) lif_psc_aibs_converter() (in module bmtk.simulator.pointnet.glif_utils) lif_r_aibs_converter() (in module bmtk.simulator.pointnet.glif_utils) lif_r_asc_a_aibs_converter() (in module bmtk.simulator.pointnet.glif_utils) lif_r_asc_a_psc_aibs_converter() (in module bmtk.simulator.pointnet.glif_utils) lif_r_asc_aibs_converter() (in module bmtk.simulator.pointnet.glif_utils) lif_r_asc_psc_aibs_converter() (in module bmtk.simulator.pointnet.glif_utils) lif_r_psc_aibs_converter() (in module bmtk.simulator.pointnet.glif_utils) line_plot() (in module bmtk.simulator.filternet.lgnmodel.lgnmodel1) list_of_dicts_to_dict_of_lists() (in module bmtk.simulator.popnet.utils) list_to_hash() (in module bmtk.builder.builder_utils) listify() (in module bmtk.analyzer.utils) (in module bmtk.utils.sonata.utils) ListIterator (class in bmtk.builder.connection_map) LNUnit (class in bmtk.simulator.filternet.lgnmodel.lnunit) LNUnitCursor (class in bmtk.simulator.filternet.lgnmodel.cursor) load() (bmtk.simulator.bionet.morphology.Morphology class method) (bmtk.simulator.core.network_reader.NodesReader class method) (bmtk.simulator.core.node_population.NodePopulation class method) (bmtk.simulator.core.sonata_reader.network_reader.SonataEdges class method) (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes class method) (bmtk.utils.io.spike_trains.SpikesInput static method) (bmtk.utils.reports.compartment.compartment_report.CompartmentReport static method) (bmtk.utils.reports.spike_trains.spike_trains.SpikeTrains class method) (bmtk.utils.sonata.config.sonata_config.SonataConfig class method) load_cell() (bmtk.simulator.bionet.sonata_adaptors.BioNode method) (bmtk.simulator.pointnet.property_map.NodePropertyMap method) load_comsol() (bmtk.simulator.bionet.modules.comsol.ComsolMod method)

load_config() (in module bmtk.analyzer.io_tools) load_conns() (in module bmtk.simulator.pointnet.utils) load_csv() (in module bmtk.utils.sonata.utils) load_dir() (bmtk.simulator.filternet.lgnmodel.cellmetrics.SubclassMetricsCache class method) load_edges() (in module bmtk.simulator.core.sonata_reader.network_reader) load_gap_junc_files() (bmtk.simulator.core.simulator_network.SimNetwork method) load_h5() (in module bmtk.utils.sonata.utils) load_neuron_modules() (in module bmtk.simulator.bionet.nrn) load_nodes() (in module bmtk.simulator.core.sonata_reader.network_reader) load_nrn_modules() (bmtk.simulator.bionet.config.Config method) load_params() (in module bmtk.simulator.pointnet.utils) load_py_modules() (in module bmtk.simulator.core.pyfunction_cache) (in module bmtk.simulator.filternet.pyfunction_cache) load_sonata_file() (in module bmtk.utils.reports.spike_trains.spike_train_readers) load_spikes() (in module bmtk.analyzer.spikes_loader) load_spikes_from_h5() (in module bmtk.analyzer.spikes_loader) load_spikes_from_nwb() (in module bmtk.analyzer.spikes_loader) load_spikes_from_txt() (in module bmtk.analyzer.spikes_loader) load_synapses() (bmtk.simulator.bionet.sonata_adaptors.BioEdge method) load_templates() (in module bmtk.simulator.bionet.nrn) loadHOC() (in module bmtk.simulator.bionet.default_setters.cell_models) loadNESTModel() (in module bmtk.simulator.pointnet.default_setters.cell_models) local_cells() (bmtk.simulator.filternet.filtersimulator.FilterSimulator method) local_gids (bmtk.simulator.bionet.bionetwork.BioNetwork property) (bmtk.simulator.bionet.biosimulator.BioSimulator property) log_debug() (bmtk.simulator.core.io_tools.IOUtils method) (bmtk.simulator.filternet.io_tools.FilterNetIOUtils method) log_error() (bmtk.simulator.core.io_tools.IOUtils method) log_exception() (bmtk.simulator.core.io_tools.IOUtils method) log_info() (bmtk.simulator.core.io_tools.IOUtils method) (bmtk.simulator.filternet.io_tools.FilterNetIOUtils method) log_to_console (bmtk.simulator.core.io_tools.IOUtils property) log_warning() (bmtk.simulator.core.io_tools.IOUtils method) (in module bmtk.utils.io) logger (bmtk.simulator.core.io_tools.IOUtils property) LoomingMovie (class in bmtk.simulator.filternet.lgnmodel.movie)

M

make_lattice_unit() (in module bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor) make_on_off_cell_list() (in module bmtk.simulator.filternet.lgnmodel.make_cell_list) make_overlapping_onoff_cell_list() (in module bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor) make_separate_onoff_cell_list() (in module bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor) make_single_unit_cell_list() (in module bmtk.simulator.filternet.lgnmodel.make_cell_list) make_sOFF_cell_list() (in module bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor) make_sON_cell_list() (in module bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor) make_tOFF_cell_list() (in module bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor) make_tON_cell_list() (in module bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor) makeBasis_StimKernel() (in module bmtk.simulator.filternet.lgnmodel.fitfuns) makeBasis_StimKernel_exp() (in module bmtk.simulator.filternet.lgnmodel.fitfuns) makeFitStruct_GLM() (in module bmtk.simulator.filternet.lgnmodel.fitfuns) MappingStrategy (class in bmtk.simulator.core.modules.ecephys_module) max_connections() (bmtk.builder.connection_map.ConnectionMap method) MembraneReport (class in bmtk.simulator.bionet.modules.record_cellvars) (class in bmtk.simulator.utils.simulation_reports) merge() (bmtk.simulator.bionet.modules.record_clamp.ClampReport method) (bmtk.utils.io.cell_vars.CellVarRecorder method) (bmtk.utils.io.cell_vars.CellVarRecorderParallel method) (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) merge_spatial_temporal() (in module bmtk.simulator.filternet.lgnmodel.kernel) mixed (bmtk.simulator.core.network_reader.EdgesReader attribute) mixed_connections (bmtk.simulator.core.network_reader.EdgesReader property) mixed_nodes (bmtk.simulator.core.network_reader.NodesReader property) (bmtk.simulator.core.node_population.NodePopulation property) model_name (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property) model_params() (in module bmtk.simulator.pointnet.property_map) model_params_batched() (in module bmtk.simulator.pointnet.property_map) model_processing (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property) model_processing() (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method) (in module bmtk.simulator.core.pyfunction_cache) model_schema (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property) model_template (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property) model_template() (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method) model_type (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property) model_type() (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method) (in module bmtk.simulator.pointnet.property_map) model_type_batched() (in module bmtk.simulator.pointnet.property_map) model_type_col (bmtk.simulator.bionet.bionetwork.BioNetwork attribute) (bmtk.simulator.core.graph.SimGraph attribute) module bmtk bmtk.analyzer bmtk.analyzer.cell_vars bmtk.analyzer.compartment bmtk.analyzer.ecp bmtk.analyzer.edges bmtk.analyzer.firing_rates bmtk.analyzer.io_tools bmtk.analyzer.spike_trains bmtk.analyzer.spikes_analyzer bmtk.analyzer.spikes_loader bmtk.analyzer.utils bmtk.builder bmtk.builder.auxi bmtk.builder.auxi.edge_connectors bmtk.builder.auxi.node_params bmtk.builder.bionet bmtk.builder.bionet.swc_reader bmtk.builder.builder_utils bmtk.builder.connection_map bmtk.builder.connector bmtk.builder.edge bmtk.builder.edges_sorter bmtk.builder.edges_sorter.memory_sorter bmtk.builder.edges_sorter.merge_sorter bmtk.builder.functor_cache bmtk.builder.id_generator bmtk.builder.index_builders bmtk.builder.iterator bmtk.builder.network_adaptors bmtk.builder.network_adaptors.dm_network bmtk.builder.network_adaptors.dm_network_orig bmtk.builder.network_adaptors.edge_props_table bmtk.builder.network_adaptors.edges_collator bmtk.builder.network_adaptors.network bmtk.builder.network_adaptors.nxnetwork bmtk.builder.network_builder bmtk.builder.networks bmtk.builder.node bmtk.builder.node_pool bmtk.builder.node_set bmtk.simulator bmtk.simulator.bionet bmtk.simulator.bionet.biocell bmtk.simulator.bionet.bionetwork bmtk.simulator.bionet.biosimulator bmtk.simulator.bionet.cell bmtk.simulator.bionet.config bmtk.simulator.bionet.default_setters bmtk.simulator.bionet.default_setters.cell_models bmtk.simulator.bionet.default_setters.synapse_models bmtk.simulator.bionet.default_setters.synaptic_weights bmtk.simulator.bionet.gids bmtk.simulator.bionet.iclamp bmtk.simulator.bionet.io_tools bmtk.simulator.bionet.modules bmtk.simulator.bionet.modules.comsol bmtk.simulator.bionet.modules.ecephys_module bmtk.simulator.bionet.modules.ecp bmtk.simulator.bionet.modules.iclamp bmtk.simulator.bionet.modules.record_cellvars bmtk.simulator.bionet.modules.record_clamp bmtk.simulator.bionet.modules.record_netcons bmtk.simulator.bionet.modules.record_spikes bmtk.simulator.bionet.modules.save_synapses bmtk.simulator.bionet.modules.seclamp bmtk.simulator.bionet.modules.sim_module bmtk.simulator.bionet.modules.xstim bmtk.simulator.bionet.modules.xstim_waveforms bmtk.simulator.bionet.morphology bmtk.simulator.bionet.nml_reader bmtk.simulator.bionet.nrn bmtk.simulator.bionet.pointprocesscell bmtk.simulator.bionet.pointsomacell bmtk.simulator.bionet.pyfunction_cache bmtk.simulator.bionet.seclamp bmtk.simulator.bionet.sonata_adaptors bmtk.simulator.bionet.utils bmtk.simulator.bionet.virtualcell bmtk.simulator.core bmtk.simulator.core.edge_population bmtk.simulator.core.graph bmtk.simulator.core.io_tools bmtk.simulator.core.modules bmtk.simulator.core.modules.ecephys_module bmtk.simulator.core.modules.iclamp bmtk.simulator.core.modules.simulator_module bmtk.simulator.core.network_reader bmtk.simulator.core.node_population bmtk.simulator.core.node_sets bmtk.simulator.core.pyfunction_cache bmtk.simulator.core.simulation_config bmtk.simulator.core.simulation_config_validator bmtk.simulator.core.simulator bmtk.simulator.core.simulator_network bmtk.simulator.core.sonata_reader bmtk.simulator.core.sonata_reader.edge_adaptor bmtk.simulator.core.sonata_reader.network_reader bmtk.simulator.core.sonata_reader.node_adaptor bmtk.simulator.filternet bmtk.simulator.filternet.auditory_processing bmtk.simulator.filternet.cell bmtk.simulator.filternet.cell_models bmtk.simulator.filternet.config bmtk.simulator.filternet.default_setters bmtk.simulator.filternet.default_setters.cell_loaders bmtk.simulator.filternet.filternetwork bmtk.simulator.filternet.filters bmtk.simulator.filternet.filtersimulator bmtk.simulator.filternet.io_tools bmtk.simulator.filternet.lgnmodel bmtk.simulator.filternet.lgnmodel.cellmetrics bmtk.simulator.filternet.lgnmodel.cellmodel bmtk.simulator.filternet.lgnmodel.cursor bmtk.simulator.filternet.lgnmodel.fitfuns bmtk.simulator.filternet.lgnmodel.gaborfilter bmtk.simulator.filternet.lgnmodel.kernel bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor bmtk.simulator.filternet.lgnmodel.lgnmodel1 bmtk.simulator.filternet.lgnmodel.linearfilter bmtk.simulator.filternet.lgnmodel.lnunit bmtk.simulator.filternet.lgnmodel.make_cell_list bmtk.simulator.filternet.lgnmodel.movie bmtk.simulator.filternet.lgnmodel.poissongeneration bmtk.simulator.filternet.lgnmodel.singleunitcell bmtk.simulator.filternet.lgnmodel.spatialfilter bmtk.simulator.filternet.lgnmodel.temporalfilter bmtk.simulator.filternet.lgnmodel.transferfunction bmtk.simulator.filternet.lgnmodel.util_fns bmtk.simulator.filternet.lgnmodel.utilities bmtk.simulator.filternet.lgnmodel.waveletfilter bmtk.simulator.filternet.modules bmtk.simulator.filternet.modules.base bmtk.simulator.filternet.modules.create_spikes bmtk.simulator.filternet.modules.record_rates bmtk.simulator.filternet.pyfunction_cache bmtk.simulator.filternet.sonata_adaptors bmtk.simulator.filternet.transfer_functions bmtk.simulator.filternet.utils bmtk.simulator.pointnet bmtk.simulator.pointnet.config bmtk.simulator.pointnet.default_setters bmtk.simulator.pointnet.default_setters.cell_models bmtk.simulator.pointnet.default_setters.synapse_models bmtk.simulator.pointnet.default_setters.synaptic_weights bmtk.simulator.pointnet.gids bmtk.simulator.pointnet.glif_utils bmtk.simulator.pointnet.io_tools bmtk.simulator.pointnet.modules bmtk.simulator.pointnet.modules.ecephys_module bmtk.simulator.pointnet.modules.iclamp bmtk.simulator.pointnet.modules.multimeter_reporter bmtk.simulator.pointnet.modules.record_spikes bmtk.simulator.pointnet.modules.sim_module bmtk.simulator.pointnet.modules.spikes_inputs bmtk.simulator.pointnet.modules.weight_recorder bmtk.simulator.pointnet.nest_utils bmtk.simulator.pointnet.pointnetwork bmtk.simulator.pointnet.pointsimulator bmtk.simulator.pointnet.property_map bmtk.simulator.pointnet.pyfunction_cache bmtk.simulator.pointnet.sonata_adaptors bmtk.simulator.pointnet.utils bmtk.simulator.popnet.sonata_adaptors bmtk.simulator.popnet.utils bmtk.simulator.utils bmtk.simulator.utils.simulation_inputs bmtk.simulator.utils.simulation_reports bmtk.utils bmtk.utils.cell_types_db bmtk.utils.compile_mechanisms bmtk.utils.compile_mechanisms.compile_mechanisms bmtk.utils.create_environment bmtk.utils.create_environment.create_environment bmtk.utils.create_environment.env_builder bmtk.utils.hdf5_helper bmtk.utils.io bmtk.utils.io.cell_vars bmtk.utils.io.firing_rates bmtk.utils.io.ioutils bmtk.utils.io.spike_trains bmtk.utils.lazy_property bmtk.utils.reports bmtk.utils.reports.compartment bmtk.utils.reports.compartment.compartment_reader bmtk.utils.reports.compartment.compartment_report bmtk.utils.reports.compartment.compartment_writer bmtk.utils.reports.compartment.core bmtk.utils.reports.compartment.plotting bmtk.utils.reports.current_writer bmtk.utils.reports.spike_trains bmtk.utils.reports.spike_trains.core bmtk.utils.reports.spike_trains.plotting bmtk.utils.reports.spike_trains.spike_train_buffer bmtk.utils.reports.spike_trains.spike_train_readers bmtk.utils.reports.spike_trains.spike_trains bmtk.utils.reports.spike_trains.spike_trains_api bmtk.utils.reports.spike_trains.spikes_file_writers bmtk.utils.reports.spike_trains.stats bmtk.utils.sim_setup bmtk.utils.sonata bmtk.utils.sonata.column_property bmtk.utils.sonata.config bmtk.utils.sonata.config.sonata_config bmtk.utils.sonata.edge bmtk.utils.sonata.edge_stats bmtk.utils.sonata.file bmtk.utils.sonata.file_root bmtk.utils.sonata.group bmtk.utils.sonata.node bmtk.utils.sonata.population bmtk.utils.sonata.types_table bmtk.utils.sonata.utils

morphology (bmtk.simulator.bionet.biocell.BioCell property) Morphology (class in bmtk.simulator.bionet.morphology) morphology_file (bmtk.simulator.bionet.biocell.BioCell property) (bmtk.simulator.bionet.sonata_adaptors.BioNode property) move_and_rotate() (bmtk.builder.bionet.swc_reader.SWCReader method) (bmtk.simulator.bionet.morphology.Morphology method) Movie (class in bmtk.simulator.filternet.lgnmodel.movie) moving_average() (in module bmtk.utils.reports.spike_trains.plotting) MPI_rank (bmtk.utils.io.ioutils.BMTKWorldComm property) MPI_size (bmtk.utils.io.ioutils.BMTKWorldComm property) multi_cell_random_generator() (in module bmtk.simulator.filternet.lgnmodel.make_cell_list) MultiLNUnit (class in bmtk.simulator.filternet.lgnmodel.lnunit) MultiLNUnitCursor (class in bmtk.simulator.filternet.lgnmodel.cursor) MultiLNUnitMultiMovieCursor (class in bmtk.simulator.filternet.lgnmodel.cursor) MultimeterMod (class in bmtk.simulator.pointnet.modules.multimeter_reporter) MultimeterReport (class in bmtk.simulator.utils.simulation_reports) MultiTransferFunction (class in bmtk.simulator.filternet.lgnmodel.transferfunction)

N

N (bmtk.builder.node_set.NodeSet property) n_edges (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableIFace property) (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory property) n_elements() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) n_nodes (bmtk.simulator.pointnet.sonata_adaptors.PointNode property) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property) n_nodes() (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes method) n_sections (bmtk.builder.bionet.swc_reader.SWCReader property) (bmtk.simulator.bionet.morphology.Morphology property) n_spikes() (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVMPIBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMPIBuffer method) (bmtk.utils.reports.spike_trains.spike_train_readers.CSVSTReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.EmptySonataReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.NWBSTReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataOldReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) n_steps (bmtk.simulator.bionet.biosimulator.BioSimulator property) (bmtk.simulator.pointnet.pointsimulator.PointSimulator property) n_steps() (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) n_syns (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableIFace property) (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory property) name (bmtk.builder.network_adaptors.network.Network property) (bmtk.builder.network_builder.NetworkBuilder property) (bmtk.simulator.core.network_reader.NodesReader property) (bmtk.simulator.core.node_population.NodePopulation property) (bmtk.simulator.core.sonata_reader.network_reader.SonataEdges property) (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes property) (bmtk.utils.sonata.column_property.ColumnProperty property) (bmtk.utils.sonata.population.Population property) names (bmtk.builder.connection_map.ConnectionMap.ParamsRules property) nconnections_distributions() (in module bmtk.utils.sonata.edge_stats) nedges (bmtk.builder.network_adaptors.dm_network.DenseNetwork property) (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig property) (bmtk.builder.network_adaptors.network.Network property) (bmtk.builder.network_adaptors.nxnetwork.NxNetwork property) (bmtk.builder.network_builder.NetworkBuilder property) nest_ids (bmtk.simulator.pointnet.sonata_adaptors.PointNode property) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property) nest_model (bmtk.simulator.pointnet.sonata_adaptors.PointNode property) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property) nest_params (bmtk.simulator.pointnet.sonata_adaptors.PointEdge property) (bmtk.simulator.pointnet.sonata_adaptors.PointEdgeBatched property) (bmtk.simulator.pointnet.sonata_adaptors.PointNode property) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property) nestid2nodeid_df (bmtk.simulator.pointnet.gids.GidPool property) NestIOUtils (class in bmtk.simulator.pointnet.io_tools) net (bmtk.simulator.pointnet.pointsimulator.PointSimulator property) NetconReport (class in bmtk.simulator.bionet.modules.record_netcons) (class in bmtk.simulator.utils.simulation_reports) netcons (bmtk.simulator.bionet.cell.Cell property) network (bmtk.builder.node_pool.NodePool property) (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property) Network (class in bmtk.builder.network_adaptors.network) network_dict_to_target_adjacency_dict() (in module bmtk.simulator.popnet.utils) network_dir (bmtk.utils.create_environment.env_builder.EnvBuilder property) (bmtk.utils.sim_setup.EnvBuilder property) network_name (bmtk.builder.node_pool.NodePool property) (bmtk.simulator.bionet.cell.Cell property) NetworkBuilder (class in bmtk.builder.network_builder) NEURONIOUtils (class in bmtk.simulator.bionet.io_tools) next() (bmtk.builder.id_generator.IDGenerator method) (bmtk.utils.sonata.edge.EdgeSet method) (bmtk.utils.sonata.group.EdgeGroup method) (bmtk.utils.sonata.node.NodeSet method) (bmtk.utils.sonata.population.EdgePopulation method) (bmtk.utils.sonata.population.NodePopulation method) (bmtk.utils.sonata.types_table.TypesTable method) nlin() (in module bmtk.simulator.filternet.lgnmodel.fitfuns) nml_ns (bmtk.simulator.bionet.nml_reader.NMLTree attribute) NMLElement (class in bmtk.simulator.bionet.nml_reader) NMLLoad() (in module bmtk.simulator.bionet.default_setters.cell_models) NMLTree (class in bmtk.simulator.bionet.nml_reader) nnodes (bmtk.builder.network_adaptors.dm_network.DenseNetwork property) (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig property) (bmtk.builder.network_adaptors.network.Network property) (bmtk.builder.network_adaptors.nxnetwork.NxNetwork property) (bmtk.builder.network_builder.NetworkBuilder property) no_nsyns() (in module bmtk.simulator.core.sonata_reader.edge_adaptor) no_syns() (in module bmtk.simulator.pointnet.property_map) node (bmtk.simulator.bionet.cell.Cell property) Node (class in bmtk.builder.node) (class in bmtk.utils.sonata.node) node_id (bmtk.builder.node.Node property) (bmtk.simulator.bionet.cell.Cell property) (bmtk.simulator.bionet.gids.PopulationID attribute) (bmtk.simulator.bionet.virtualcell.VirtualCell property) (bmtk.simulator.core.edge_population.SimEdge property) (bmtk.simulator.core.node_population.SimNode property) (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property) (bmtk.simulator.pointnet.gids.PopulationID attribute) (bmtk.utils.sonata.node.Node property)

node_id() (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method) (in module bmtk.simulator.pointnet.property_map) node_ids (bmtk.simulator.core.node_sets.NodeSet property) (bmtk.simulator.pointnet.sonata_adaptors.PointNode property) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property) (bmtk.utils.sonata.group.NodeGroup property) (bmtk.utils.sonata.node.NodeSet property) (bmtk.utils.sonata.population.NodePopulation property) node_ids() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVMPIBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMPIBuffer method) (bmtk.utils.reports.spike_trains.spike_train_readers.CSVSTReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.EmptySonataReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.NWBSTReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataOldReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) node_populations (bmtk.simulator.core.graph.SimGraph property) (bmtk.simulator.core.simulator_network.SimNetwork property) node_properties() (bmtk.simulator.core.simulator_network.SimNetwork method) node_set (bmtk.simulator.utils.simulation_inputs.SimInput property) (bmtk.simulator.utils.simulation_reports.ClampReport property) (bmtk.simulator.utils.simulation_reports.SimReport property) node_sets_file (bmtk.utils.sim_setup.EnvBuilder property) node_type_id (bmtk.builder.node.Node property) (bmtk.builder.node_set.NodeSet property) (bmtk.utils.sonata.node.Node property) node_type_ids (bmtk.utils.sonata.group.NodeGroup property) (bmtk.utils.sonata.node.NodeSet property) (bmtk.utils.sonata.types_table.NodeTypesTable property) node_type_properties (bmtk.builder.node.Node property) (bmtk.utils.sonata.node.Node property) node_types_table (bmtk.utils.sonata.file_root.NodesRoot property) (bmtk.utils.sonata.population.NodePopulation property) node_types_table() (in module bmtk.analyzer) NodeAdaptor (class in bmtk.simulator.core.sonata_reader.node_adaptor) NodeGroup (class in bmtk.utils.sonata.group) NodePool (class in bmtk.builder.node_pool) NodePopulation (class in bmtk.simulator.core.node_population) (class in bmtk.utils.sonata.population) NodePropertyMap (class in bmtk.simulator.pointnet.property_map) nodes (bmtk.utils.sonata.file.File property) nodes() (bmtk.builder.network_adaptors.network.Network method) (bmtk.builder.network_builder.NetworkBuilder method) (bmtk.simulator.core.node_sets.NodeSet method) nodes_built (bmtk.builder.network_adaptors.network.Network property) (bmtk.builder.network_builder.NetworkBuilder property) nodes_df() (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes method) nodes_iter() (bmtk.builder.network_adaptors.dm_network.DenseNetwork method) (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig method) (bmtk.builder.network_adaptors.network.Network method) nodes_table() (in module bmtk.analyzer) NodeSet (class in bmtk.builder.node_set) (class in bmtk.simulator.core.node_sets) (class in bmtk.utils.sonata.node) NodeSetAll (class in bmtk.simulator.core.node_sets) NodesReader (class in bmtk.simulator.core.network_reader) NodesRoot (class in bmtk.utils.sonata.file_root) NodeTypesTable (class in bmtk.utils.sonata.types_table) non_dom_params (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) non_dom_params() (in module bmtk.simulator.filternet.sonata_adaptors) none (bmtk.utils.reports.spike_trains.core.SortOrder attribute) none_function() (in module bmtk.simulator.core.sonata_reader.node_adaptor) normalize() (bmtk.simulator.filternet.lgnmodel.kernel.Kernel1D method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel2D method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel3D method) normalize2() (bmtk.simulator.filternet.lgnmodel.kernel.Kernel2D method) normalize_matrix() (bmtk.simulator.filternet.lgnmodel.movie.Movie static method) normalizecols() (in module bmtk.simulator.filternet.lgnmodel.fitfuns) nrows (bmtk.utils.sonata.column_property.ColumnProperty property) ns_name() (bmtk.simulator.bionet.nml_reader.NMLTree class method) nseg (bmtk.builder.bionet.swc_reader.SWCReader property) (bmtk.simulator.bionet.morphology.Morphology property) nsteps_block (bmtk.simulator.bionet.biosimulator.BioSimulator property) nsyn_table (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig.EdgeTable property) nsyns (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) nsyns() (in module bmtk.simulator.core.sonata_reader.edge_adaptor) (in module bmtk.simulator.pointnet.property_map) nsyns_distribution() (in module bmtk.utils.sonata.edge_stats) nwb_files (bmtk.simulator.core.modules.ecephys_module.MappingStrategy property) NWBFileWrapper (class in bmtk.simulator.core.modules.ecephys_module) NWBReader (class in bmtk.simulator.core.modules.iclamp) NWBReaderNRN (class in bmtk.simulator.bionet.modules.iclamp) NWBSTReader (class in bmtk.utils.reports.spike_trains.spike_train_readers) NxNetwork (class in bmtk.builder.network_adaptors.nxnetwork)

O

OffUnit (class in bmtk.simulator.filternet.lgnmodel.cellmodel) one_to_all_iterator() (in module bmtk.builder.iterator) one_to_all_list_iterator() (in module bmtk.builder.iterator) one_to_one_iterator() (in module bmtk.builder.iterator)

one_to_one_list_iterator() (in module bmtk.builder.iterator) OnUnit (class in bmtk.simulator.filternet.lgnmodel.cellmodel) order_t (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) output_dir (bmtk.utils.create_environment.env_builder.EnvBuilder property) (bmtk.utils.sim_setup.EnvBuilder property)

P

p0 (bmtk.builder.bionet.swc_reader.SegmentCoords attribute) p05 (bmtk.builder.bionet.swc_reader.SegmentCoords attribute) p1 (bmtk.builder.bionet.swc_reader.SegmentCoords attribute) params (bmtk.builder.connection_map.ConnectionMap property) (bmtk.builder.node.Node property) params_hash (bmtk.builder.node.Node property) (bmtk.builder.node_set.NodeSet property) params_keys (bmtk.builder.node_set.NodeSet property) parent (bmtk.utils.sonata.group.Group property) parse() (bmtk.utils.sonata.config.sonata_config.ConfigParser method) parse_value() (bmtk.simulator.bionet.nml_reader.NMLTree static method) partition_locations() (in module bmtk.builder.auxi.node_params) patch_adaptor() (bmtk.simulator.bionet.sonata_adaptors.BioEdgeAdaptor class method) (bmtk.simulator.bionet.sonata_adaptors.BioNodeAdaptor class method) (bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor static method) (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor class method) (bmtk.simulator.filternet.sonata_adaptors.FilterNodeAdaptor class method) (bmtk.simulator.pointnet.sonata_adaptors.PointEdgeAdaptor static method) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeAdaptor static method) pearson_r() (in module bmtk.utils.sonata.edge_stats) place_the_electrodes() (bmtk.simulator.bionet.modules.xstim.StimXElectrode method) play() (bmtk.simulator.filternet.lgnmodel.movie.Movie method) plot_calcium() (in module bmtk.analyzer) plot_calcium_hdf5() (in module bmtk.analyzer) plot_correlation() (in module bmtk.utils.sonata.edge_stats) plot_distribution() (in module bmtk.utils.sonata.edge_stats) plot_ecp() (in module bmtk.analyzer.ecp) plot_locs() (bmtk.builder.auxi.node_params.CellLocations method) plot_positions() (in module bmtk.builder.auxi.node_params) plot_potential() (in module bmtk.analyzer) plot_potential_hdf5() (in module bmtk.analyzer) plot_raster() (in module bmtk.analyzer.spike_trains) (in module bmtk.utils.reports.spike_trains.plotting) plot_rates() (in module bmtk.analyzer.spike_trains) (in module bmtk.utils.reports.spike_trains.plotting) plot_rates_boxplot() (in module bmtk.analyzer.spike_trains) (in module bmtk.utils.reports.spike_trains.plotting) plot_rates_popnet() (in module bmtk.analyzer.firing_rates) plot_single_contour() (in module bmtk.simulator.filternet.lgnmodel.kernel) plot_traces() (in module bmtk.analyzer.compartment) (in module bmtk.utils.reports.compartment.plotting) plot_traces_averaged() (in module bmtk.utils.reports.compartment.plotting) plot_traces_individual() (in module bmtk.utils.reports.compartment.plotting) point_syn_weight() (in module bmtk.simulator.pointnet.sonata_adaptors) PointECEphysUnitsModule (class in bmtk.simulator.pointnet.modules.ecephys_module) PointEdge (class in bmtk.simulator.pointnet.sonata_adaptors) PointEdgeAdaptor (class in bmtk.simulator.pointnet.sonata_adaptors) PointEdgeBatched (class in bmtk.simulator.pointnet.sonata_adaptors) PointNetBuilder (class in bmtk.builder.network_builder) PointNetEnvBuilder (class in bmtk.utils.create_environment.env_builder) (class in bmtk.utils.sim_setup) PointNetwork (class in bmtk.simulator.pointnet.pointnetwork) PointNode (class in bmtk.simulator.pointnet.sonata_adaptors) PointNodeAdaptor (class in bmtk.simulator.pointnet.sonata_adaptors) PointNodeBatched (class in bmtk.simulator.pointnet.sonata_adaptors) PointProcessCell (class in bmtk.simulator.bionet.pointprocesscell) PointProcessCellSpontSyns (class in bmtk.simulator.bionet.pointprocesscell) PointSimulator (class in bmtk.simulator.pointnet.pointsimulator) PointSomaCell (class in bmtk.simulator.bionet.pointsomacell) PoissonSpikeGenerator (class in bmtk.utils.reports.spike_trains.spike_trains) PoissonSpikesGenerator (class in bmtk.utils.io.spike_trains) PopEdgeAdaptor (class in bmtk.simulator.popnet.sonata_adaptors) PopNetBuilder (class in bmtk.builder.network_builder) PopNetEdge (class in bmtk.simulator.popnet.sonata_adaptors) PopNetEnvBuilder (class in bmtk.utils.create_environment.env_builder) (class in bmtk.utils.sim_setup) population (bmtk.simulator.bionet.gids.PopulationID attribute) (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property) (bmtk.simulator.filternet.cell.Cell property) (bmtk.simulator.pointnet.gids.PopulationID attribute)

Population (class in bmtk.utils.sonata.population) population_list_to_csv() (in module bmtk.simulator.popnet.utils) population_list_to_dataframe() (in module bmtk.simulator.popnet.utils) population_name (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property) (bmtk.utils.sonata.node.Node property) population_names (bmtk.utils.sonata.file_root.FileRoot property) population_names() (bmtk.simulator.core.node_sets.NodeSet method) population_to_dict_for_dataframe() (in module bmtk.simulator.popnet.utils) PopulationID (class in bmtk.simulator.bionet.gids) (class in bmtk.simulator.pointnet.gids) populations (bmtk.simulator.pointnet.gids.GidPool property) (bmtk.utils.io.firing_rates.RatesInput property) (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 property) (bmtk.utils.reports.compartment.core.CompartmentReaderABC property) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer property) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVMPIBuffer property) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer property) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMPIBuffer property) (bmtk.utils.reports.spike_trains.spike_train_readers.CSVSTReader property) (bmtk.utils.reports.spike_trains.spike_train_readers.EmptySonataReader property) (bmtk.utils.reports.spike_trains.spike_train_readers.NWBSTReader property) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader property) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI property) (bmtk.utils.sonata.file_root.FileRoot property) populations() (bmtk.simulator.core.node_sets.NodeSet method) PopulationWriterv01 (class in bmtk.utils.reports.compartment.compartment_writer) PopulationWriterv01.DataTable (class in bmtk.utils.reports.compartment.compartment_writer) position (bmtk.simulator.bionet.sonata_adaptors.BioNode property) position() (in module bmtk.simulator.bionet.sonata_adaptors) position_x() (in module bmtk.simulator.bionet.sonata_adaptors) position_xy() (in module bmtk.simulator.bionet.sonata_adaptors) position_xyz() (in module bmtk.simulator.bionet.sonata_adaptors) positions() (in module bmtk.simulator.bionet.sonata_adaptors) positions_columinar() (in module bmtk.builder.auxi.node_params) positions_columnar() (in module bmtk.builder.auxi.node_params) positions_cuboid() (in module bmtk.builder.auxi.node_params) positions_default() (in module bmtk.simulator.bionet.sonata_adaptors) positions_density_matrix() (in module bmtk.builder.auxi.node_params) positions_dmin_lattice() (in module bmtk.builder.auxi.node_params) positions_dmin_prog() (in module bmtk.builder.auxi.node_params) positions_ellipsoid() (in module bmtk.builder.auxi.node_params) positions_list() (in module bmtk.builder.auxi.node_params) positions_nrrd() (in module bmtk.builder.auxi.node_params) positions_rect_prism() (in module bmtk.builder.auxi.node_params) post_fadvance() (bmtk.simulator.bionet.biosimulator.BioSimulator method) predefined_jitter (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) preload() (bmtk.simulator.core.modules.simulator_module.SimulatorMod method) (bmtk.simulator.pointnet.modules.sim_module.SimulatorMod method) (bmtk.simulator.pointnet.modules.weight_recorder.WeightRecorder method) preprocess_edge_types() (bmtk.simulator.core.sonata_reader.edge_adaptor.EdgeAdaptor static method) (bmtk.simulator.pointnet.sonata_adaptors.PointEdgeAdaptor static method) preprocess_node_types() (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor static method) (bmtk.simulator.filternet.sonata_adaptors.FilterNodeAdaptor static method) (bmtk.simulator.pointnet.sonata_adaptors.PointNodeAdaptor static method) preselected_targets (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) print_synapses() (bmtk.simulator.bionet.biocell.BioCell method) (bmtk.simulator.bionet.pointprocesscell.PointProcessCell method) process() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) ProgressFile (class in bmtk.builder.edges_sorter.merge_sorter) properties_keys() (bmtk.builder.connection_map.ConnectionMap method) property_names (bmtk.builder.connection_map.ConnectionMap property) psi (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) py_function_caches (bmtk.simulator.bionet.bionetwork.BioNetwork property) (bmtk.simulator.core.simulator_network.SimNetwork property) (bmtk.simulator.pointnet.pointnetwork.PointNetwork property)

Q

quicksort_edges() (in module bmtk.builder.edges_sorter.memory_sorter) quiet_simulator() (bmtk.simulator.core.io_tools.IOUtils method) (bmtk.simulator.pointnet.io_tools.NestIOUtils method)

quit_execution() (in module bmtk.simulator.bionet.nrn)

R

rand_syn_locations() (in module bmtk.builder.bionet) ranges (bmtk.simulator.filternet.lgnmodel.movie.Movie property) RatesInput (class in bmtk.utils.io.firing_rates) RatesWriter (class in bmtk.utils.io.firing_rates) read_conns() (in module bmtk.simulator.pointnet.utils) read_dat() (in module bmtk.simulator.pointnet.modules.multimeter_reporter) read_dat_nest2() (in module bmtk.simulator.pointnet.modules.multimeter_reporter) read_dat_nest3() (in module bmtk.simulator.pointnet.modules.multimeter_reporter) read_electrode_mesh() (bmtk.simulator.bionet.modules.xstim.StimXElectrode method) read_LGN_activity() (in module bmtk.simulator.pointnet.utils) read_spikes_file() (in module bmtk.simulator.pointnet.modules.record_spikes) read_spikes_file_nest2() (in module bmtk.simulator.pointnet.modules.record_spikes) read_spikes_file_nest3() (in module bmtk.simulator.pointnet.modules.record_spikes) record_cell() (bmtk.utils.io.cell_vars.CellVarRecorder method) (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) record_cell_block() (bmtk.utils.io.cell_vars.CellVarRecorder method) (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) record_clamps() (bmtk.utils.reports.current_writer.CurrentWriterv01 method) RecordRates (class in bmtk.simulator.filternet.modules.record_rates) recurrent (bmtk.simulator.core.network_reader.EdgesReader attribute) recurrent_connections (bmtk.simulator.core.network_reader.EdgesReader property) recurrent_edges (bmtk.simulator.core.simulator_network.SimNetwork property) RecXElectrode (class in bmtk.simulator.bionet.modules.ecp) register() (bmtk.builder.functor_cache.FunctorCache method) (bmtk.builder.iterator.IteratorCache method) (in module bmtk.builder.connector) (in module bmtk.builder.iterator) register_module() (bmtk.simulator.bionet.nml_reader.NMLTree class method) (bmtk.simulator.utils.simulation_inputs.SimInput class method) (bmtk.simulator.utils.simulation_reports.SimReport class method) registry (bmtk.simulator.utils.simulation_inputs.SimInput attribute) (bmtk.simulator.utils.simulation_reports.SimReport attribute)

remove_id() (bmtk.builder.id_generator.IDGenerator method) remove_index() (in module bmtk.builder.index_builders) remove_nans() (in module bmtk.utils.sonata.types_table) reorder_columns_in_frame() (in module bmtk.simulator.popnet.utils) report_group (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 property) report_load_balance() (bmtk.simulator.bionet.biosimulator.BioSimulator method) rescale() (bmtk.simulator.filternet.lgnmodel.kernel.Kernel1D method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel2D method) (bmtk.simulator.filternet.lgnmodel.kernel.Kernel3D method) reset() (in module bmtk.simulator.bionet.nrn) Resistivity (class in bmtk.simulator.bionet.nml_reader) ret_none_function() (in module bmtk.simulator.bionet.sonata_adaptors) (in module bmtk.simulator.core.sonata_reader.edge_adaptor) return_none() (in module bmtk.simulator.filternet.sonata_adaptors) root_name (bmtk.utils.sonata.file_root.FileRoot property) rotate_the_electrodes() (bmtk.simulator.bionet.modules.xstim.StimXElectrode method) rotation_angle_default() (in module bmtk.simulator.bionet.sonata_adaptors) rotation_angle_x() (in module bmtk.simulator.bionet.sonata_adaptors) rotation_angle_xaxis (bmtk.simulator.bionet.sonata_adaptors.BioNode property) rotation_angle_y() (in module bmtk.simulator.bionet.sonata_adaptors) rotation_angle_yaxis (bmtk.simulator.bionet.sonata_adaptors.BioNode property) rotation_angle_z() (in module bmtk.simulator.bionet.sonata_adaptors) rotation_angle_zaxis (bmtk.simulator.bionet.sonata_adaptors.BioNode property) rotation_matrix() (in module bmtk.builder.bionet.swc_reader) (in module bmtk.simulator.bionet.morphology) (in module bmtk.simulator.bionet.utils) rotations (bmtk.simulator.bionet.sonata_adaptors.BioNode property) rotations() (in module bmtk.simulator.bionet.sonata_adaptors) rotations_quaternion (bmtk.simulator.bionet.sonata_adaptors.BioNode property) row_range (bmtk.simulator.filternet.lgnmodel.cursor.KernelCursor property) rule (bmtk.builder.connection_map.ConnectionMap.ParamsRules property) run() (bmtk.simulator.bionet.biosimulator.BioSimulator method) (bmtk.simulator.core.simulator.Simulator method) (bmtk.simulator.filternet.filtersimulator.FilterSimulator method) (bmtk.simulator.pointnet.pointsimulator.PointSimulator method)

S

sameconv() (in module bmtk.simulator.filternet.lgnmodel.fitfuns) SamplingStrategy (class in bmtk.simulator.core.modules.ecephys_module) save() (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory method) (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMPI method) (bmtk.builder.network_adaptors.network.Network method) (bmtk.builder.network_builder.NetworkBuilder method) (bmtk.simulator.filternet.modules.base.SimModule method) (bmtk.simulator.filternet.modules.create_spikes.SpikesGenerator method) (bmtk.simulator.filternet.modules.record_rates.RecordRates method) save_edges() (bmtk.builder.network_adaptors.network.Network method) (bmtk.builder.network_builder.NetworkBuilder method) save_nodes() (bmtk.builder.network_adaptors.network.Network method) (bmtk.builder.network_builder.NetworkBuilder method) saved_metrics_dir (bmtk.simulator.filternet.lgnmodel.cellmetrics.SubclassMetricsCache property) SaveSynapses (class in bmtk.simulator.bionet.modules.save_synapses) (class in bmtk.simulator.utils.simulation_reports) ScalarTransferFunction (class in bmtk.simulator.filternet.lgnmodel.transferfunction) scale_weights() (bmtk.simulator.bionet.cell.Cell method) schema (bmtk.simulator.core.simulation_config_validator.SimulationConfigValidator attribute) scripts_root (bmtk.utils.create_environment.env_builder.EnvBuilder property) (bmtk.utils.sim_setup.EnvBuilder property) sec_id (bmtk.builder.bionet.swc_reader.SegmentProps attribute) sec_type_swc (bmtk.builder.bionet.swc_reader.SWCReader attribute) (bmtk.simulator.bionet.morphology.Morphology attribute) SEClamp (class in bmtk.simulator.bionet.modules.seclamp) (class in bmtk.simulator.bionet.seclamp) SEClampReport (class in bmtk.simulator.utils.simulation_reports) sections (bmtk.builder.bionet.swc_reader.SWCReader property) (bmtk.simulator.bionet.morphology.Morphology property) seg_coords (bmtk.builder.bionet.swc_reader.SWCReader property) (bmtk.simulator.bionet.biocell.BioCell property) (bmtk.simulator.bionet.morphology.Morphology property) seg_props (bmtk.builder.bionet.swc_reader.SWCReader property) (bmtk.simulator.bionet.morphology.Morphology property) SegmentCoords (class in bmtk.builder.bionet.swc_reader) SegmentProps (class in bmtk.builder.bionet.swc_reader) segments (bmtk.simulator.bionet.morphology.Morphology property) SeparableKernelCursor (class in bmtk.simulator.filternet.lgnmodel.cursor) SeparableLNUnitCursor (class in bmtk.simulator.filternet.lgnmodel.cursor) SeparableMultiLNUnitCursor (class in bmtk.simulator.filternet.lgnmodel.cursor) SeparableSpatioTemporalFilterCursor (class in bmtk.simulator.filternet.lgnmodel.cursor) set_connection_type() (bmtk.simulator.core.network_reader.EdgesReader method) set_default_processing() (bmtk.simulator.filternet.filternetwork.FilterNetwork method) set_default_weight_function() (bmtk.simulator.pointnet.pointnetwork.PointNetwork method) set_dt() (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) set_e_extracellular() (bmtk.simulator.bionet.biocell.BioCell method) set_extracellular() (in module bmtk.simulator.bionet.default_setters.cell_models) set_gid_table() (bmtk.utils.sonata.file_root.NodesRoot method) set_im_ptr() (bmtk.simulator.bionet.biocell.BioCell method) (bmtk.simulator.bionet.pointprocesscell.PointProcessCell method) set_log_format() (bmtk.simulator.core.io_tools.IOUtils method) set_log_level() (bmtk.simulator.core.io_tools.IOUtils method) set_nsyns() (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory method) set_params_allactive() (in module bmtk.simulator.bionet.default_setters.cell_models) set_params_peri() (in module bmtk.simulator.bionet.default_setters.cell_models) set_property_value() (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory method) set_ptr2e_extracellular() (bmtk.simulator.bionet.biocell.BioCell method) set_sec_array() (bmtk.simulator.bionet.biocell.BioCell method) set_segment_dl() (bmtk.builder.bionet.swc_reader.SWCReader method) (bmtk.simulator.bionet.morphology.Morphology method) set_soma_position() (bmtk.simulator.bionet.cell.Cell method) set_spike_detector() (bmtk.simulator.bionet.biocell.BioCell method) (bmtk.simulator.bionet.pointprocesscell.PointProcessCell method) set_spike_generator_params() (bmtk.simulator.pointnet.pointsimulator.PointSimulator method) set_spikes() (in module bmtk.simulator.pointnet.modules.ecephys_module) (in module bmtk.simulator.pointnet.pointnetwork) set_spikes_nest2() (in module bmtk.simulator.pointnet.modules.ecephys_module) (in module bmtk.simulator.pointnet.pointnetwork) set_spikes_nest3() (in module bmtk.simulator.pointnet.modules.ecephys_module) (in module bmtk.simulator.pointnet.pointnetwork) set_spikes_recording() (bmtk.simulator.bionet.biosimulator.BioSimulator method) set_spont_syn_activity() (bmtk.simulator.bionet.bionetwork.BioNetwork method) set_stim() (bmtk.simulator.bionet.virtualcell.VirtualCell method) set_stim_from_generator() (bmtk.simulator.bionet.virtualcell.VirtualCell method) set_syn_connection() (bmtk.simulator.bionet.biocell.BioCell method) (bmtk.simulator.bionet.pointprocesscell.PointProcessCell method) (bmtk.simulator.bionet.pointprocesscell.PointProcessCellSpontSyns method) set_syn_connections() (bmtk.simulator.bionet.cell.Cell method) set_time_trace() (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) set_transfer_resistance() (bmtk.simulator.bionet.modules.xstim.StimXElectrode method) set_tstart() (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) set_tstop() (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) set_units() (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) set_variable() (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentWriterABC method) set_world_comm() (in module bmtk.utils.io.ioutils) setup_ecp() (bmtk.simulator.bionet.biocell.BioCell method) setup_output_dir() (bmtk.simulator.core.io_tools.IOUtils method) (bmtk.simulator.pointnet.io_tools.NestIOUtils method) setup_xstim() (bmtk.simulator.bionet.biocell.BioCell method) sf_sep (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) show_spatial_filter() (bmtk.simulator.filternet.lgnmodel.linearfilter.SpatioTemporalFilter method) (bmtk.simulator.filternet.lgnmodel.linearfilter.SpectroTemporalFilter method) (bmtk.simulator.filternet.lgnmodel.lnunit.LNUnit method) (bmtk.simulator.filternet.lgnmodel.lnunit.MultiLNUnit method) show_temporal_filter() (bmtk.simulator.filternet.lgnmodel.linearfilter.SpatioTemporalFilter method) (bmtk.simulator.filternet.lgnmodel.linearfilter.SpectroTemporalFilter method) (bmtk.simulator.filternet.lgnmodel.lnunit.LNUnit method) (bmtk.simulator.filternet.lgnmodel.lnunit.MultiLNUnit method) sigma_f (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) SimEdge (class in bmtk.simulator.core.edge_population) SimGraph (class in bmtk.simulator.core.graph) SimInput (class in bmtk.simulator.utils.simulation_inputs) SimModule (class in bmtk.simulator.filternet.modules.base) SimNetwork (class in bmtk.simulator.core.simulator_network) SimNode (class in bmtk.simulator.core.node_population)

SimReport (class in bmtk.simulator.utils.simulation_reports) simulation_time() (bmtk.simulator.bionet.biosimulator.BioSimulator method) (bmtk.simulator.pointnet.pointsimulator.PointSimulator method) SimulationConfig (class in bmtk.simulator.core.simulation_config) SimulationConfigValidator (class in bmtk.simulator.core.simulation_config_validator) Simulator (class in bmtk.simulator.core.simulator) SimulatorMod (class in bmtk.simulator.bionet.modules.sim_module) (class in bmtk.simulator.core.modules.simulator_module) (class in bmtk.simulator.pointnet.modules.sim_module) soma (bmtk.simulator.bionet.biocell.BioCell property) (bmtk.simulator.bionet.morphology.Morphology property) soma_position (bmtk.builder.bionet.swc_reader.SWCReader property) (bmtk.simulator.bionet.cell.Cell property) (bmtk.simulator.bionet.morphology.Morphology property) SomaReport (class in bmtk.simulator.bionet.modules.record_cellvars) SonataBaseEdge (class in bmtk.simulator.core.sonata_reader.edge_adaptor) SonataBaseNode (class in bmtk.simulator.core.sonata_reader.node_adaptor) SonataConfig (class in bmtk.utils.sonata.config.sonata_config) SonataEdges (class in bmtk.simulator.core.sonata_reader.network_reader) SONATAIndexer (class in bmtk.utils.io.spike_trains) SonataNodes (class in bmtk.simulator.core.sonata_reader.network_reader) SonataOldReader (class in bmtk.utils.reports.spike_trains.spike_train_readers) SonataSTReader (class in bmtk.utils.reports.spike_trains.spike_train_readers) sort() (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorMPI method) (bmtk.builder.network_adaptors.edges_collator.EdgesCollatorSingular method) sort_edges() (in module bmtk.builder.edges_sorter) sort_order() (bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) SortOrder (class in bmtk.utils.reports.spike_trains.core) source_gid (bmtk.builder.edge.Edge property) source_ids (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig.EdgeTable property) source_network_name (bmtk.builder.connection_map.ConnectionMap property) source_node (bmtk.simulator.bionet.biocell.ConnectionStruct property) (bmtk.simulator.bionet.pointprocesscell.ConnectionStruct property) source_node_id (bmtk.builder.edge.Edge property) (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) (bmtk.utils.sonata.edge.Edge property) source_node_ids (bmtk.simulator.pointnet.sonata_adaptors.PointEdge property) (bmtk.simulator.pointnet.sonata_adaptors.PointEdgeBatched property) source_nodes (bmtk.builder.connection_map.ConnectionMap property) (bmtk.simulator.core.edge_population.EdgePopulation property) (bmtk.simulator.core.network_reader.EdgesReader property) (bmtk.simulator.core.sonata_reader.network_reader.SonataEdges property) source_nodes_map (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory property) source_population (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) (bmtk.utils.sonata.edge.Edge property) (bmtk.utils.sonata.population.EdgePopulation property) sp_mod_freq (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) SpatioTemporalFilter (class in bmtk.simulator.filternet.lgnmodel.linearfilter) SpecificCapacitance (class in bmtk.simulator.bionet.nml_reader) SpectroTemporalFilter (class in bmtk.simulator.filternet.lgnmodel.linearfilter) spike_files_equal() (in module bmtk.analyzer.spikes_analyzer) spike_statistics() (in module bmtk.analyzer.spike_trains) SpikeGenerator (class in bmtk.utils.reports.spike_trains.spike_trains) spikes() (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVMPIBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMPIBuffer method) (bmtk.utils.reports.spike_trains.spike_train_readers.CSVSTReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.EmptySonataReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.NWBSTReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataOldReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) spikes2dict() (in module bmtk.analyzer.spikes_analyzer) spikes_equal_in_window() (in module bmtk.analyzer.spikes_analyzer) spikes_generator() (in module bmtk.simulator.core.pyfunction_cache) spikes_table (bmtk.simulator.bionet.biosimulator.BioSimulator property) spikes_table() (in module bmtk.analyzer) SpikesGenerator (class in bmtk.simulator.filternet.modules.create_spikes) SpikesInput (class in bmtk.utils.io.spike_trains) SpikesInputCSV (class in bmtk.utils.io.spike_trains) SpikesInputH5 (class in bmtk.utils.io.spike_trains) SpikesInputNWBv1 (class in bmtk.utils.io.spike_trains) SpikesInputsMod (class in bmtk.simulator.pointnet.modules.spikes_inputs) SpikesMod (class in bmtk.simulator.bionet.modules.record_spikes) (class in bmtk.simulator.pointnet.modules.record_spikes) SpikesReport (class in bmtk.simulator.utils.simulation_reports) SpikeTrains (class in bmtk.utils.reports.spike_trains.spike_trains) SpikeTrainsAPI (class in bmtk.utils.reports.spike_trains.spike_trains_api) SpikeTrainsReadOnlyAPI (class in bmtk.utils.reports.spike_trains.spike_trains_api) SpikeTrainWriter (class in bmtk.utils.io.spike_trains) SpikeTrainWriter.TmpFileMetadata (class in bmtk.utils.io.spike_trains) src_node_ids (bmtk.utils.sonata.group.EdgeGroup property) static_synapse() (in module bmtk.simulator.pointnet.default_setters.synapse_models) STCSVBuffer (class in bmtk.utils.reports.spike_trains.spike_train_buffer) STCSVMPIBuffer (class in bmtk.utils.reports.spike_trains.spike_train_buffer) STCSVMPIBufferV2 (class in bmtk.utils.reports.spike_trains.spike_train_buffer) step() (bmtk.simulator.bionet.modules.comsol.ComsolMod method) (bmtk.simulator.bionet.modules.ecp.EcpMod method) (bmtk.simulator.bionet.modules.record_cellvars.MembraneReport method) (bmtk.simulator.bionet.modules.record_cellvars.SomaReport method) (bmtk.simulator.bionet.modules.record_clamp.ClampReport method) (bmtk.simulator.bionet.modules.record_netcons.NetconReport method) (bmtk.simulator.bionet.modules.seclamp.SEClamp method) (bmtk.simulator.bionet.modules.sim_module.SimulatorMod method) (bmtk.simulator.bionet.modules.xstim.XStimMod method) (bmtk.simulator.core.modules.simulator_module.SimulatorMod method) (bmtk.simulator.pointnet.modules.sim_module.SimulatorMod method) stimx_waveform_factory() (in module bmtk.simulator.bionet.modules.xstim_waveforms) StimXElectrode (class in bmtk.simulator.bionet.modules.xstim) STMemoryBuffer (class in bmtk.utils.reports.spike_trains.spike_train_buffer) STMPIBuffer (class in bmtk.utils.reports.spike_trains.spike_train_buffer) stp1syn() (in module bmtk.simulator.bionet.default_setters.synapse_models) stp2syn() (in module bmtk.simulator.bionet.default_setters.synapse_models) stp3syn() (in module bmtk.simulator.bionet.default_setters.synapse_models) stp4syn() (in module bmtk.simulator.bionet.default_setters.synapse_models) stp5isyn() (in module bmtk.simulator.bionet.default_setters.synapse_models) stp5syn() (in module bmtk.simulator.bionet.default_setters.synapse_models) SubclassMetricsCache (class in bmtk.simulator.filternet.lgnmodel.cellmetrics) swc_map (bmtk.builder.bionet.swc_reader.SWCReader property) (bmtk.simulator.bionet.morphology.Morphology property) SWCReader (class in bmtk.builder.bionet.swc_reader) syn_weight (bmtk.simulator.bionet.biocell.ConnectionStruct property) (bmtk.simulator.bionet.pointprocesscell.ConnectionStruct property) (bmtk.simulator.popnet.sonata_adaptors.PopNetEdge property) syn_weight() (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge method) (in module bmtk.simulator.core.sonata_reader.edge_adaptor) (in module bmtk.simulator.pointnet.property_map) syn_weight_function() (in module bmtk.simulator.core.sonata_reader.edge_adaptor) synapse_model() (in module bmtk.simulator.core.pyfunction_cache) synaptic_model() (bmtk.simulator.pointnet.property_map.EdgePropertyMap method) synaptic_params() (bmtk.simulator.pointnet.sonata_adaptors.PointEdgeAdaptor method) synaptic_properties (bmtk.builder.edge.Edge property) synaptic_weight() (in module bmtk.simulator.core.pyfunction_cache) synpatic_params() (bmtk.simulator.pointnet.property_map.EdgePropertyMap method)

T

t_mod_freq (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) t_range (bmtk.simulator.filternet.lgnmodel.cursor.KernelCursor property) t_slice() (bmtk.simulator.filternet.lgnmodel.kernel.Kernel3D method) (bmtk.simulator.filternet.lgnmodel.linearfilter.SpatioTemporalFilter method) (bmtk.simulator.filternet.lgnmodel.linearfilter.SpectroTemporalFilter method) target_distance (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) target_gid (bmtk.builder.edge.Edge property) target_ids (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig.EdgeTable property) target_network_name (bmtk.builder.connection_map.ConnectionMap property) target_node_id (bmtk.builder.edge.Edge property) (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) (bmtk.utils.sonata.edge.Edge property) target_node_ids (bmtk.simulator.pointnet.sonata_adaptors.PointEdge property) (bmtk.simulator.pointnet.sonata_adaptors.PointEdgeBatched property) target_nodes (bmtk.builder.connection_map.ConnectionMap property) (bmtk.simulator.core.edge_population.EdgePopulation property) (bmtk.simulator.core.network_reader.EdgesReader property) (bmtk.simulator.core.sonata_reader.network_reader.SonataEdges property) target_nodes_map (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory property) target_population (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) (bmtk.utils.sonata.edge.Edge property) (bmtk.utils.sonata.population.EdgePopulation property) target_sections (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) target_simulator (bmtk.utils.create_environment.env_builder.BioNetEnvBuilder property) (bmtk.utils.create_environment.env_builder.EnvBuilder property) (bmtk.utils.create_environment.env_builder.FilterNetEnvBuilder property) (bmtk.utils.create_environment.env_builder.PointNetEnvBuilder property) (bmtk.utils.create_environment.env_builder.PopNetEnvBuilder property) (bmtk.utils.sim_setup.BioNetEnvBuilder property) (bmtk.utils.sim_setup.EnvBuilder property) (bmtk.utils.sim_setup.FilterNetEnvBuilder property) (bmtk.utils.sim_setup.PointNetEnvBuilder property) (bmtk.utils.sim_setup.PopNetEnvBuilder property) temp_files (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 property) TemporalFilter (class in bmtk.simulator.filternet.lgnmodel.temporalfilter) TemporalFilterCosineBump (class in bmtk.simulator.filternet.lgnmodel.temporalfilter) test_fn() (in module bmtk.utils.cell_types_db) time_range() (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_readers.EmptySonataReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataOldReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method) (bmtk.utils.reports.spike_trains.spike_trains.GammaSpikeGenerator method) (bmtk.utils.reports.spike_trains.spike_trains.PoissonSpikeGenerator method) time_trace() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) timestamps (bmtk.utils.io.spike_trains.SpikesInputH5 property) TimeWindow (class in bmtk.simulator.core.modules.ecephys_module) tmgsyn() (in module bmtk.simulator.bionet.default_setters.synapse_models) to_csv() (bmtk.utils.io.firing_rates.RatesWriter method) (bmtk.utils.io.spike_trains.SpikeTrainWriter method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) to_dataframe() (bmtk.builder.network_adaptors.edge_props_table.EdgeTypesTableMemory method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVMPIBufferV2 method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMPIBuffer method) (bmtk.utils.reports.spike_trains.spike_train_readers.CSVSTReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.EmptySonataReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.NWBSTReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataOldReader method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) (bmtk.utils.sonata.group.EdgeGroup method) (bmtk.utils.sonata.group.Group method) (bmtk.utils.sonata.group.NodeGroup method) (bmtk.utils.sonata.population.EdgePopulation method) (bmtk.utils.sonata.population.NodePopulation method) (bmtk.utils.sonata.population.Population method) (bmtk.utils.sonata.types_table.TypesTable method) (in module bmtk.analyzer.spike_trains)

to_dict() (bmtk.simulator.filternet.lgnmodel.gaborfilter.GaborFilter method) (bmtk.simulator.filternet.lgnmodel.linearfilter.SpatioTemporalFilter method) (bmtk.simulator.filternet.lgnmodel.linearfilter.SpectroTemporalFilter method) (bmtk.simulator.filternet.lgnmodel.lnunit.LNUnit method) (bmtk.simulator.filternet.lgnmodel.spatialfilter.GaussianSpatialFilter method) (bmtk.simulator.filternet.lgnmodel.temporalfilter.TemporalFilter method) (bmtk.simulator.filternet.lgnmodel.temporalfilter.TemporalFilterCosineBump method) (bmtk.simulator.filternet.lgnmodel.transferfunction.MultiTransferFunction method) (bmtk.simulator.filternet.lgnmodel.transferfunction.ScalarTransferFunction method) (bmtk.simulator.filternet.lgnmodel.waveletfilter.WaveletFilter method) to_edges_dataframe() (in module bmtk.utils.sonata.edge_stats) to_h5() (bmtk.utils.io.firing_rates.RatesWriter method) to_hdf5() (bmtk.utils.io.spike_trains.PoissonSpikesGenerator method) (bmtk.utils.io.spike_trains.SpikeTrainWriter method) to_list() (in module bmtk.simulator.core.node_sets) (in module bmtk.utils.reports.spike_trains.spike_train_readers) to_nodes_dataframe() (in module bmtk.utils.sonata.edge_stats) to_nwb() (bmtk.utils.io.spike_trains.SpikeTrainWriter method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) to_sonata() (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method) trg_itr() (bmtk.builder.network_adaptors.dm_network_orig.DenseNetworkOrig.EdgeTable method) trg_node_ids (bmtk.utils.sonata.group.EdgeGroup property) tstart (bmtk.simulator.pointnet.pointsimulator.PointSimulator property) (bmtk.utils.io.cell_vars.CellVarRecorder property) tstart() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) tstop (bmtk.simulator.bionet.biosimulator.BioSimulator property) (bmtk.simulator.pointnet.pointsimulator.PointSimulator property) (bmtk.utils.io.cell_vars.CellVarRecorder property) tstop() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) tuning_angle (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) tuning_angle_preset() (in module bmtk.simulator.filternet.sonata_adaptors) tuning_angle_rand() (in module bmtk.simulator.filternet.sonata_adaptors) TwoSubfieldLinearCell (class in bmtk.simulator.filternet.lgnmodel.cellmodel) type (bmtk.builder.bionet.swc_reader.SegmentProps attribute) type_ids (bmtk.utils.sonata.population.Population property) (bmtk.utils.sonata.types_table.TypesTable property) type_ids_column (bmtk.utils.sonata.population.EdgePopulation property) (bmtk.utils.sonata.population.NodePopulation property) (bmtk.utils.sonata.population.Population property) types_dynamics_params() (in module bmtk.simulator.core.sonata_reader.edge_adaptor) (in module bmtk.simulator.core.sonata_reader.node_adaptor) (in module bmtk.simulator.pointnet.property_map) types_table (bmtk.utils.sonata.file_root.FileRoot property) (bmtk.utils.sonata.population.Population property) TypesTable (class in bmtk.utils.sonata.types_table)

U

UnindexedGIDs (class in bmtk.utils.io.spike_trains) UnitIdMapStrategy (class in bmtk.simulator.core.modules.ecephys_module) units() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) (bmtk.utils.reports.current_writer.CurrentWriterv01 method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method) (bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method) (bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method) (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method)

units2nodes_map (bmtk.simulator.core.modules.ecephys_module.MappingStrategy property) units_lu (bmtk.simulator.core.modules.ecephys_module.TimeWindow property) units_table (bmtk.simulator.core.modules.ecephys_module.MappingStrategy property) unknown (bmtk.simulator.core.network_reader.EdgesReader attribute) (bmtk.utils.reports.spike_trains.core.SortOrder attribute) update() (bmtk.builder.edges_sorter.merge_sorter.ProgressFile method) usr_vars (bmtk.utils.sonata.config.sonata_config.ConfigParser property) uuid (bmtk.simulator.core.modules.ecephys_module.DandiFileWrapper property) (bmtk.simulator.core.modules.ecephys_module.NWBFileWrapper property)

V

v_init (bmtk.simulator.bionet.biosimulator.BioSimulator property) validate() (bmtk.simulator.core.simulation_config.SimulationConfig method) (bmtk.utils.sonata.config.sonata_config.SonataConfig method) validate_file() (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) validator (bmtk.simulator.core.simulation_config.SimulationConfig property) (bmtk.utils.sonata.config.sonata_config.SonataConfig property) value_none() (in module bmtk.simulator.bionet.sonata_adaptors) variable (bmtk.simulator.bionet.modules.record_clamp.ClampReport property)

variable() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method) (bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method) (bmtk.utils.reports.compartment.core.CompartmentReaderABC method) version (bmtk.utils.sonata.file.File property) virtual (bmtk.simulator.core.network_reader.EdgesReader attribute) virtual_connections (bmtk.simulator.core.network_reader.EdgesReader property) virtual_nodes_only (bmtk.simulator.core.network_reader.NodesReader property) (bmtk.simulator.core.node_population.NodePopulation property) VirtualCell (class in bmtk.simulator.bionet.virtualcell)

W

warning_msg (bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsReadOnlyAPI attribute) WaveformCustom (class in bmtk.simulator.bionet.modules.xstim_waveforms) WaveformTypeDC (class in bmtk.simulator.bionet.modules.xstim_waveforms) WaveformTypeSin (class in bmtk.simulator.bionet.modules.xstim_waveforms) WaveletFilter (class in bmtk.simulator.filternet.lgnmodel.waveletfilter) weight_function (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property) weight_function() (in module bmtk.simulator.core.sonata_reader.edge_adaptor) (in module bmtk.simulator.pointnet.property_map) WeightRecorder (class in bmtk.simulator.pointnet.modules.weight_recorder) (class in bmtk.simulator.utils.simulation_reports)

weights (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) weights() (in module bmtk.simulator.filternet.sonata_adaptors) weights_non_dom (bmtk.simulator.filternet.sonata_adaptors.FilterNode property) wmax() (in module bmtk.simulator.bionet.default_setters.synaptic_weights) write_csv() (in module bmtk.utils.reports.spike_trains.spikes_file_writers) write_csv_itr() (in module bmtk.utils.reports.spike_trains.spikes_file_writers) write_nwb() (in module bmtk.utils.reports.spike_trains.spikes_file_writers) write_sonata() (in module bmtk.utils.reports.spike_trains.spikes_file_writers) write_sonata_itr() (in module bmtk.utils.reports.spike_trains.spikes_file_writers)

X

x (bmtk.builder.bionet.swc_reader.SegmentProps attribute)

xiter_random() (in module bmtk.builder.auxi.node_params) XStimMod (class in bmtk.simulator.bionet.modules.xstim)