ALLEN INSTITUTE
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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.PoissonSpikeGenerator 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.bionet.pyfunction_cache)
(in module bmtk.simulator.pointnet.pyfunction_cache)
add_cell_processor() (in module bmtk.simulator.bionet.pyfunction_cache)
(in module bmtk.simulator.filternet.pyfunction_cache)
(in module bmtk.simulator.pointnet.pyfunction_cache)
add_component() (bmtk.simulator.core.graph.SimGraph method)
(bmtk.simulator.core.simulator_network.SimNetwork method)
add_edges() (bmtk.builder.network.Network method)
(bmtk.simulator.core.graph.SimGraph method)
(bmtk.simulator.core.simulator_network.SimNetwork method)
add_gap_junctions() (bmtk.builder.network.Network method)
add_gids() (bmtk.simulator.pointnet.gids.GidPool method)
(bmtk.utils.sonata.population.NodePopulation method)
add_hdf5_attrs() (in module bmtk.builder.networks.dm_network)
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_nestids() (bmtk.simulator.pointnet.gids.GidPool method)
add_node_set() (bmtk.simulator.core.simulator_network.SimNetwork method)
add_nodes() (bmtk.builder.network.Network 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_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_step_currents() (bmtk.simulator.pointnet.pointsimulator.PointSimulator method)
add_synapse_model() (in module bmtk.simulator.bionet.pyfunction_cache)
(in module bmtk.simulator.pointnet.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.bionet.pyfunction_cache)
(in module bmtk.simulator.pointnet.pyfunction_cache)
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)
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)
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)
attach_current() (bmtk.simulator.bionet.iclamp.FileIClamp method)
(bmtk.simulator.bionet.iclamp.IClamp method)
(bmtk.simulator.bionet.seclamp.SEClamp method)
attach_current_clamp() (bmtk.simulator.bionet.biosimulator.BioSimulator method)
attach_file_current_clamp() (bmtk.simulator.bionet.biosimulator.BioSimulator method)
attach_se_voltage_clamp() (bmtk.simulator.bionet.biosimulator.BioSimulator method)
attributes() (bmtk.utils.sonata.column_property.ColumnProperty property)
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)
B
barrier() (bmtk.simulator.bionet.io_tools.NEURONIOUtils method)
(bmtk.simulator.core.io_tools.IOUtils method)
(bmtk.simulator.pointnet.io_tools.NestIOUtils method)
(bmtk.utils.io.ioutils.BMTKWorldComm method)
(in module bmtk.utils.reports.compartment.compartment_writer)
base_dir() (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)
BioCell (class in bmtk.simulator.bionet.biocell)
BioEdge (class in bmtk.simulator.bionet.sonata_adaptors)
BioEdgeAdaptor (class in bmtk.simulator.bionet.sonata_adaptors)
BioNetEnvBuilder (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)
(in module bmtk.tests.simulator.bionet.set_cell_params)
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
module
bmtk.analyzer
module
bmtk.analyzer.cell_vars
module
bmtk.analyzer.compartment
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.connection_map
module
bmtk.builder.connector
module
bmtk.builder.edge
module
bmtk.builder.functor_cache
module
bmtk.builder.id_generator
module
bmtk.builder.iterator
module
bmtk.builder.network
module
bmtk.builder.networks
module
bmtk.builder.networks.dm_network
module
bmtk.builder.networks.input_network
module
bmtk.builder.networks.mpi_network
module
bmtk.builder.networks.nxnetwork
module
bmtk.builder.networks.sparse_network
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.ecp
module
bmtk.simulator.bionet.modules.record_cellvars
module
bmtk.simulator.bionet.modules.record_clamp
module
bmtk.simulator.bionet.modules.record_netcons
module
bmtk.simulator.bionet.modules.record_spikes
module
bmtk.simulator.bionet.modules.save_synapses
module
bmtk.simulator.bionet.modules.sim_module
module
bmtk.simulator.bionet.modules.xstim
module
bmtk.simulator.bionet.modules.xstim_waveforms
module
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.network_reader
module
bmtk.simulator.core.node_population
module
bmtk.simulator.core.node_sets
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.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.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.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.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.multimeter_reporter
module
bmtk.simulator.pointnet.modules.record_spikes
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.tests
module
bmtk.tests.simulator
module
bmtk.tests.simulator.bionet
module
bmtk.tests.simulator.bionet.bionet_virtual_files
module
bmtk.tests.simulator.bionet.conftest
module
bmtk.tests.simulator.bionet.set_cell_params
module
bmtk.tests.simulator.bionet.set_syn_params
module
bmtk.tests.simulator.bionet.set_weights
module
bmtk.tests.simulator.bionet.test_biograph
module
bmtk.tests.simulator.bionet.test_gids
module
bmtk.tests.simulator.bionet.test_nrn
module
bmtk.tests.simulator.pointnet
module
bmtk.tests.simulator.pointnet.conftest
module
bmtk.tests.simulator.pointnet.pointnet_virtual_files
module
bmtk.tests.simulator.pointnet.test_glif_utils
module
bmtk.tests.simulator.pointnet.test_pointgraph
module
bmtk.tests.simulator.popnet
module
bmtk.tests.simulator.popnet.popnet_virtual_files
module
bmtk.tests.simulator.popnet.test_popgraph
module
bmtk.utils
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.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.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.sim_setup.BioNetEnvBuilder property)
(bmtk.utils.sim_setup.EnvBuilder property)
(bmtk.utils.sim_setup.FilterNetEnvBuilder property)
(bmtk.utils.sim_setup.PointNetEnvBuilder property)
BMTKWorldComm (class in bmtk.utils.io.ioutils)
build() (bmtk.builder.network.Network 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.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.pointnet.property_map.EdgePropertyMap class method)
(bmtk.simulator.pointnet.property_map.NodePropertyMap class 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_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_seg_coords() (bmtk.simulator.bionet.biocell.BioCell method)
(bmtk.simulator.bionet.bionetwork.BioNetwork method)
(bmtk.simulator.bionet.morphology.Morphology method)
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)
Cell (class in bmtk.simulator.bionet.cell)
(class in bmtk.simulator.filternet.cell)
cell_model() (in module bmtk.simulator.bionet.pyfunction_cache)
(in module bmtk.simulator.pointnet.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)
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)
choose_sections() (bmtk.builder.bionet.swc_reader.SWCReader 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.Network 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.sim_setup.BioNetEnvBuilder method)
ComplexWaveform (class in bmtk.simulator.bionet.modules.xstim_waveforms)
components_dir() (bmtk.utils.sim_setup.EnvBuilder property)
compute_FFT_OneCycle() (in module bmtk.simulator.filternet.lgnmodel.util_fns)
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_config() (in module bmtk.utils.sonata.config.sonata_config)
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_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_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_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_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)
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
data() (bmtk.simulator.filternet.lgnmodel.movie.FullFieldMovie property)
(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)
delays() (bmtk.simulator.filternet.sonata_adaptors.FilterNode property)
delays_non_dom() (bmtk.simulator.filternet.sonata_adaptors.FilterNode property)
DenseNetwork (class in bmtk.builder.networks.dm_network)
DenseNetwork.EdgeTable (class in bmtk.builder.networks.dm_network)
DenseNetwork.PropertyTable (class in bmtk.builder.networks.dm_network)
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)
distance_connector() (in module bmtk.builder.auxi.edge_connectors)
drift() (bmtk.simulator.bionet.modules.ecp.RecXElectrode method)
dt() (bmtk.simulator.bionet.biosimulator.BioSimulator property)
(bmtk.simulator.pointnet.pointsimulator.PointSimulator property)
(bmtk.utils.io.cell_vars.CellVarRecorder property)
(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
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_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_properties() (bmtk.builder.connection_map.ConnectionMap property)
(bmtk.builder.edge.Edge 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)
EdgeRow (class in bmtk.tests.simulator.bionet.bionet_virtual_files)
(class in bmtk.tests.simulator.pointnet.pointnet_virtual_files)
(class in bmtk.tests.simulator.popnet.popnet_virtual_files)
edges() (bmtk.builder.network.Network method)
(bmtk.utils.sonata.file.File property)
edges_built() (bmtk.builder.network.Network property)
edges_iter() (bmtk.builder.network.Network method)
(bmtk.builder.networks.dm_network.DenseNetwork method)
(bmtk.builder.networks.mpi_network.MPINetwork method)
edges_itr() (bmtk.tests.simulator.bionet.bionet_virtual_files.EdgesFile method)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.EdgesFile method)
(bmtk.tests.simulator.popnet.popnet_virtual_files.EdgesFile method)
edges_table() (bmtk.builder.networks.dm_network.DenseNetwork method)
EdgeSet (class in bmtk.utils.sonata.edge)
EdgesFile (class in bmtk.tests.simulator.bionet.bionet_virtual_files)
(class in bmtk.tests.simulator.pointnet.pointnet_virtual_files)
(class in bmtk.tests.simulator.popnet.popnet_virtual_files)
EdgesReader (class in bmtk.simulator.core.network_reader)
EdgesRoot (class in bmtk.utils.sonata.file_root)
EdgeTypesTable (class in bmtk.utils.sonata.types_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.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)
examples_dir() (bmtk.utils.sim_setup.BioNetEnvBuilder property)
(bmtk.utils.sim_setup.EnvBuilder property)
(bmtk.utils.sim_setup.FilterNetEnvBuilder property)
(bmtk.utils.sim_setup.PointNetEnvBuilder 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)
(in module bmtk.tests.simulator.bionet.set_syn_params)
expsyn() (in module bmtk.simulator.bionet.default_setters.synapse_models)
external_edge_populations() (bmtk.simulator.core.graph.SimGraph method)
F
f_rate_to_spike_train() (in module bmtk.simulator.filternet.modules.create_spikes)
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)
FilterCursor (class in bmtk.simulator.filternet.lgnmodel.cursor)
FilterNetEnvBuilder (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.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)
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_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() (in module bmtk.tests.simulator.bionet.set_cell_params)
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)
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)
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
gaussianLL() (in module bmtk.simulator.bionet.default_setters.synaptic_weights)
(in module bmtk.tests.simulator.bionet.set_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_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.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_coord() (bmtk.builder.bionet.swc_reader.SWCReader method)
get_cursor() (bmtk.simulator.filternet.lgnmodel.lnunit.LNUnit method)
(bmtk.simulator.filternet.lgnmodel.lnunit.MultiLNUnit method)
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_dist() (bmtk.builder.bionet.swc_reader.SWCReader 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_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_im() (bmtk.simulator.bionet.biocell.BioCell method)
get_kernel() (bmtk.simulator.filternet.lgnmodel.spatialfilter.ArrayFilter method)
(bmtk.simulator.filternet.lgnmodel.spatialfilter.GaussianSpatialFilter method)
(bmtk.simulator.filternet.lgnmodel.temporalfilter.TemporalFilter 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)
(bmtk.tests.simulator.bionet.bionet_virtual_files.NodesFile method)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.NodesFile method)
(bmtk.tests.simulator.popnet.popnet_virtual_files.NodesFile 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() (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_nseg() (bmtk.simulator.bionet.morphology.Morphology 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_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.simulator.bionet.biocell.BioCell method)
get_sections() (bmtk.simulator.bionet.biocell.BioCell method)
get_sections_id() (bmtk.simulator.bionet.biocell.BioCell method)
get_seg_coords() (bmtk.simulator.bionet.biocell.BioCell method)
get_segments() (bmtk.simulator.bionet.biocell.BioCell method)
get_soma_pos() (bmtk.simulator.bionet.morphology.Morphology method)
get_source() (bmtk.simulator.core.sonata_reader.network_reader.SonataEdges method)
(bmtk.utils.sonata.population.EdgePopulation 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_spike_generator_params() (bmtk.simulator.pointnet.pointsimulator.PointSimulator 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_target() (bmtk.simulator.core.sonata_reader.network_reader.SonataEdges method)
(bmtk.utils.sonata.population.EdgePopulation method)
get_target_population() (bmtk.utils.sonata.population.EdgePopulation static method)
get_target_segments() (bmtk.simulator.bionet.morphology.Morphology 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_transfer_resistance() (bmtk.simulator.bionet.modules.ecp.RecXElectrode method)
get_translation_matrix() (in module bmtk.simulator.filternet.lgnmodel.utilities)
get_type() (bmtk.builder.bionet.swc_reader.SWCReader method)
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.utils.sonata.utils)
get_vext() (bmtk.simulator.bionet.modules.xstim.StimXElectrode method)
get_virtual_cells() (bmtk.simulator.bionet.bionetwork.BioNetwork method)
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)
(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.core.node_sets.NodeSet method)
(bmtk.simulator.pointnet.gids.GidPool property)
(bmtk.simulator.pointnet.sonata_adaptors.PointNode property)
(bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property)
(bmtk.tests.simulator.bionet.bionet_virtual_files.NodesFile property)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.NodesFile property)
(bmtk.tests.simulator.popnet.popnet_virtual_files.NodesFile 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)
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.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.networks.dm_network.DenseNetwork.EdgeTable method)
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)
IDGenerator (class in bmtk.builder.id_generator)
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.Network method)
(bmtk.builder.networks.dm_network.DenseNetwork 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.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)
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.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.record_spikes.SpikesMod method)
(bmtk.simulator.bionet.modules.save_synapses.SaveSynapses 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.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.pointnet.modules.multimeter_reporter.MultimeterMod method)
(bmtk.simulator.pointnet.modules.record_spikes.SpikesMod 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)
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)
(in module bmtk.tests.simulator.bionet.set_cell_params)
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)
iterator() (bmtk.builder.connection_map.ConnectionMap property)
IteratorCache (class in bmtk.builder.iterator)
itr_vals() (bmtk.builder.networks.dm_network.DenseNetwork.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)
KernelCursor (class in bmtk.simulator.filternet.lgnmodel.cursor)
KeyDefaultDict (class in bmtk.simulator.popnet.utils)
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)
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)
listify() (in module bmtk.analyzer.utils)
(in module bmtk.utils.sonata.utils)
LNUnit (class in bmtk.simulator.filternet.lgnmodel.lnunit)
LNUnitCursor (class in bmtk.simulator.filternet.lgnmodel.cursor)
load() (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.tests.simulator.bionet.bionet_virtual_files.EdgesFile method)
(bmtk.tests.simulator.bionet.bionet_virtual_files.NodesFile method)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.EdgesFile method)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.NodesFile method)
(bmtk.tests.simulator.popnet.popnet_virtual_files.EdgesFile method)
(bmtk.tests.simulator.popnet.popnet_virtual_files.NodesFile 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_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.bionet.pyfunction_cache)
(in module bmtk.simulator.filternet.pyfunction_cache)
(in module bmtk.simulator.pointnet.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)
local_gids() (bmtk.simulator.bionet.bionetwork.BioNetwork property)
(bmtk.simulator.bionet.biosimulator.BioSimulator property)
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_morphologies() (bmtk.simulator.bionet.bionetwork.BioNetwork method)
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)
max_connections() (bmtk.builder.connection_map.ConnectionMap method)
max_spikes_per_node (bmtk.utils.reports.spike_trains.spike_trains.PoissonSpikeGenerator attribute)
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_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.NodeAdaptor method)
(bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
model_template() (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property)
(bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method)
(bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
model_type() (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method)
(bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
(bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property)
(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.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.connection_map
bmtk.builder.connector
bmtk.builder.edge
bmtk.builder.functor_cache
bmtk.builder.id_generator
bmtk.builder.iterator
bmtk.builder.network
bmtk.builder.networks
bmtk.builder.networks.dm_network
bmtk.builder.networks.input_network
bmtk.builder.networks.mpi_network
bmtk.builder.networks.nxnetwork
bmtk.builder.networks.sparse_network
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.ecp
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.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.network_reader
bmtk.simulator.core.node_population
bmtk.simulator.core.node_sets
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.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.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.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.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.multimeter_reporter
bmtk.simulator.pointnet.modules.record_spikes
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.tests
bmtk.tests.simulator
bmtk.tests.simulator.bionet
bmtk.tests.simulator.bionet.bionet_virtual_files
bmtk.tests.simulator.bionet.conftest
bmtk.tests.simulator.bionet.set_cell_params
bmtk.tests.simulator.bionet.set_syn_params
bmtk.tests.simulator.bionet.set_weights
bmtk.tests.simulator.bionet.test_biograph
bmtk.tests.simulator.bionet.test_gids
bmtk.tests.simulator.bionet.test_nrn
bmtk.tests.simulator.pointnet
bmtk.tests.simulator.pointnet.conftest
bmtk.tests.simulator.pointnet.pointnet_virtual_files
bmtk.tests.simulator.pointnet.test_glif_utils
bmtk.tests.simulator.pointnet.test_pointgraph
bmtk.tests.simulator.popnet
bmtk.tests.simulator.popnet.popnet_virtual_files
bmtk.tests.simulator.popnet.test_popgraph
bmtk.utils
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.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.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 (class in bmtk.simulator.bionet.morphology)
morphology() (bmtk.simulator.bionet.biocell.BioCell property)
morphology_file() (bmtk.simulator.bionet.biocell.BioCell property)
(bmtk.simulator.bionet.sonata_adaptors.BioNode property)
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)
MPINetwork (class in bmtk.builder.networks.mpi_network)
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_elements() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method)
(bmtk.utils.reports.compartment.core.CompartmentReaderABC method)
n_nodes() (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes method)
(bmtk.simulator.pointnet.sonata_adaptors.PointNode property)
(bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched 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)
(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)
name() (bmtk.builder.network.Network 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.tests.simulator.bionet.bionet_virtual_files.NodesFile property)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.NodesFile property)
(bmtk.tests.simulator.popnet.popnet_virtual_files.NodesFile property)
(bmtk.utils.sonata.column_property.ColumnProperty property)
(bmtk.utils.sonata.population.Population property)
names() (bmtk.builder.connection_map.ConnectionMap.ParamsRules property)
nedges() (bmtk.builder.network.Network property)
(bmtk.builder.networks.dm_network.DenseNetwork property)
(bmtk.builder.networks.nxnetwork.NxNetwork 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)
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 (class in bmtk.builder.network)
network() (bmtk.builder.node_pool.NodePool property)
(bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
network_dict_to_target_adjacency_dict() (in module bmtk.simulator.popnet.utils)
network_dir() (bmtk.utils.sim_setup.EnvBuilder property)
network_name() (bmtk.builder.node_pool.NodePool property)
(bmtk.simulator.bionet.cell.Cell property)
NEURONIOUtils (class in bmtk.simulator.bionet.io_tools)
next() (bmtk.builder.id_generator.IDGenerator method)
(bmtk.tests.simulator.bionet.bionet_virtual_files.NodesFile method)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.NodesFile method)
(bmtk.tests.simulator.popnet.popnet_virtual_files.NodesFile 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.Network property)
(bmtk.builder.networks.dm_network.DenseNetwork property)
(bmtk.builder.networks.nxnetwork.NxNetwork property)
no_nsyns() (in module bmtk.simulator.core.sonata_reader.edge_adaptor)
no_syns() (in module bmtk.simulator.pointnet.property_map)
Node (class in bmtk.builder.node)
(class in bmtk.utils.sonata.node)
node() (bmtk.simulator.bionet.cell.Cell property)
node_id (bmtk.simulator.bionet.gids.PopulationID attribute)
(bmtk.simulator.pointnet.gids.PopulationID attribute)
node_id() (bmtk.builder.node.Node property)
(bmtk.simulator.bionet.cell.Cell property)
(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.NodeAdaptor method)
(bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
(bmtk.utils.sonata.node.Node property)
(in module bmtk.simulator.pointnet.property_map)
node_ids() (bmtk.simulator.pointnet.sonata_adaptors.PointNode property)
(bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property)
(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)
(bmtk.utils.sonata.group.NodeGroup property)
(bmtk.utils.sonata.node.NodeSet property)
(bmtk.utils.sonata.population.NodePopulation property)
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.tests.simulator.bionet.bionet_virtual_files.NodesFile property)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.NodesFile property)
(bmtk.tests.simulator.popnet.popnet_virtual_files.NodesFile property)
(bmtk.utils.sonata.file_root.NodesRoot property)
(bmtk.utils.sonata.population.NodePopulation property)
(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)
NodeRow (class in bmtk.tests.simulator.bionet.bionet_virtual_files)
(class in bmtk.tests.simulator.pointnet.pointnet_virtual_files)
(class in bmtk.tests.simulator.popnet.popnet_virtual_files)
nodes() (bmtk.builder.network.Network method)
(bmtk.simulator.core.node_sets.NodeSet method)
(bmtk.utils.sonata.file.File property)
nodes_built() (bmtk.builder.network.Network property)
nodes_df() (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes method)
nodes_iter() (bmtk.builder.network.Network method)
(bmtk.builder.networks.dm_network.DenseNetwork 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)
NodesFile (class in bmtk.tests.simulator.bionet.bionet_virtual_files)
(class in bmtk.tests.simulator.pointnet.pointnet_virtual_files)
(class in bmtk.tests.simulator.popnet.popnet_virtual_files)
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)
(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)
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)
nsteps_block() (bmtk.simulator.bionet.biosimulator.BioSimulator property)
nsyn_table() (bmtk.builder.networks.dm_network.DenseNetwork.EdgeTable property)
nsyns() (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property)
(in module bmtk.simulator.core.sonata_reader.edge_adaptor)
(in module bmtk.simulator.pointnet.property_map)
NWBSTReader (class in bmtk.utils.reports.spike_trains.spike_train_readers)
NxNetwork (class in bmtk.builder.networks.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)
output_dir() (bmtk.utils.sim_setup.EnvBuilder property)
P
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)
patch_adaptor() (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)
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_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)
PointEdge (class in bmtk.simulator.pointnet.sonata_adaptors)
PointEdgeAdaptor (class in bmtk.simulator.pointnet.sonata_adaptors)
PointEdgeBatched (class in bmtk.simulator.pointnet.sonata_adaptors)
PointNetEnvBuilder (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)
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)
PopNetEdge (class in bmtk.simulator.popnet.sonata_adaptors)
population (bmtk.simulator.bionet.gids.PopulationID attribute)
(bmtk.simulator.pointnet.gids.PopulationID attribute)
Population (class in bmtk.utils.sonata.population)
population() (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
(bmtk.simulator.filternet.cell.Cell property)
population_list_to_csv() (in module bmtk.simulator.popnet.utils)
population_list_to_dataframe() (in module bmtk.simulator.popnet.utils)
population_names() (bmtk.simulator.core.node_sets.NodeSet method)
(bmtk.utils.sonata.file_root.FileRoot property)
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.core.node_sets.NodeSet method)
(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)
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)
(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_cuboid() (in module bmtk.builder.auxi.node_params)
positions_default() (in module bmtk.simulator.bionet.sonata_adaptors)
positions_list() (in module bmtk.builder.auxi.node_params)
post_fadvance() (bmtk.simulator.bionet.biosimulator.BioSimulator method)
predefined_jitter() (bmtk.simulator.filternet.sonata_adaptors.FilterNode property)
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)
properties_keys() (bmtk.builder.connection_map.ConnectionMap method)
property_names() (bmtk.builder.connection_map.ConnectionMap property)
py_function_caches() (bmtk.simulator.bionet.bionetwork.BioNetwork property)
(bmtk.simulator.core.simulator_network.SimNetwork property)
(bmtk.simulator.pointnet.pointnetwork.PointNetwork property)
Q
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
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_electrode_mesh() (bmtk.simulator.bionet.modules.xstim.StimXElectrode method)
read_LGN_activity() (in module bmtk.simulator.pointnet.utils)
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_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)
Resistivity (class in bmtk.simulator.bionet.nml_reader)
ret_none_function() (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.simulator.bionet.utils)
rotations() (bmtk.simulator.bionet.sonata_adaptors.BioNode property)
(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)
save() (bmtk.builder.network.Network 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.Network method)
save_nodes() (bmtk.builder.network.Network method)
(bmtk.builder.networks.mpi_network.MPINetwork 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)
scripts_root() (bmtk.utils.sim_setup.EnvBuilder property)
SEClamp (class in bmtk.simulator.bionet.seclamp)
SEClampReport (class in bmtk.simulator.utils.simulation_reports)
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_morphology() (bmtk.simulator.bionet.biocell.BioCell method)
set_nseg() (bmtk.simulator.bionet.biocell.BioCell 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)
(in module bmtk.tests.simulator.bionet.set_cell_params)
set_ptr2e_extracellular() (bmtk.simulator.bionet.biocell.BioCell method)
set_sec_array() (bmtk.simulator.bionet.biocell.BioCell method)
set_seg_props() (bmtk.simulator.bionet.bionetwork.BioNetwork 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_recording() (bmtk.simulator.bionet.biosimulator.BioSimulator method)
set_stim() (bmtk.simulator.bionet.virtualcell.VirtualCell method)
set_syn_connection() (bmtk.simulator.bionet.biocell.BioCell method)
(bmtk.simulator.bionet.pointprocesscell.PointProcessCell 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.lnunit.LNUnit method)
(bmtk.simulator.filternet.lgnmodel.lnunit.MultiLNUnit method)
show_temporal_filter() (bmtk.simulator.filternet.lgnmodel.linearfilter.SpatioTemporalFilter method)
(bmtk.simulator.filternet.lgnmodel.lnunit.LNUnit method)
(bmtk.simulator.filternet.lgnmodel.lnunit.MultiLNUnit method)
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)
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)
soma_position() (bmtk.simulator.bionet.cell.Cell 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_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.networks.dm_network.DenseNetwork.EdgeTable property)
source_network() (bmtk.tests.simulator.bionet.bionet_virtual_files.EdgesFile property)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.EdgesFile property)
(bmtk.tests.simulator.popnet.popnet_virtual_files.EdgesFile 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_population() (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property)
(bmtk.utils.sonata.edge.Edge property)
(bmtk.utils.sonata.population.EdgePopulation property)
SparseNetwork (class in bmtk.builder.networks.sparse_network)
SpatioTemporalFilter (class in bmtk.simulator.filternet.lgnmodel.linearfilter)
SpecificCapacitance (class in bmtk.simulator.bionet.nml_reader)
spike_files_equal() (in module bmtk.analyzer.spikes_analyzer)
spike_statistics() (in module bmtk.analyzer.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_table() (bmtk.simulator.bionet.biosimulator.BioSimulator property)
(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)
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.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.sim_module.SimulatorMod method)
(bmtk.simulator.bionet.modules.xstim.XStimMod 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)
store_segments() (bmtk.simulator.bionet.biocell.BioCell method)
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)
SWCReader (class in bmtk.builder.bionet.swc_reader)
syn_weight() (bmtk.simulator.bionet.biocell.ConnectionStruct property)
(bmtk.simulator.bionet.pointprocesscell.ConnectionStruct property)
(bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge method)
(bmtk.simulator.popnet.sonata_adaptors.PopNetEdge property)
(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.bionet.pyfunction_cache)
(in module bmtk.simulator.pointnet.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.bionet.pyfunction_cache)
(in module bmtk.simulator.pointnet.pyfunction_cache)
synpatic_params() (bmtk.simulator.pointnet.property_map.EdgePropertyMap method)
T
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)
target_distance() (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property)
target_gid() (bmtk.builder.edge.Edge property)
target_ids() (bmtk.builder.networks.dm_network.DenseNetwork.EdgeTable property)
target_network() (bmtk.tests.simulator.bionet.bionet_virtual_files.EdgesFile property)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.EdgesFile property)
(bmtk.tests.simulator.popnet.popnet_virtual_files.EdgesFile 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_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.sim_setup.BioNetEnvBuilder property)
(bmtk.utils.sim_setup.EnvBuilder property)
(bmtk.utils.sim_setup.FilterNetEnvBuilder property)
(bmtk.utils.sim_setup.PointNetEnvBuilder 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_add_edges() (in module bmtk.tests.simulator.bionet.test_biograph)
(in module bmtk.tests.simulator.pointnet.test_pointgraph)
test_add_nodes() (in module bmtk.tests.simulator.bionet.test_biograph)
(in module bmtk.tests.simulator.pointnet.test_pointgraph)
(in module bmtk.tests.simulator.popnet.test_popgraph)
test_cell_model() (in module bmtk.tests.simulator.bionet.test_nrn)
test_cell_model_decorator() (in module bmtk.tests.simulator.bionet.test_nrn)
test_converter_psc() (in module bmtk.tests.simulator.pointnet.test_glif_utils)
test_gid_pool() (in module bmtk.tests.simulator.bionet.test_gids)
test_load_py_modules() (in module bmtk.tests.simulator.bionet.test_nrn)
test_synapse_model() (in module bmtk.tests.simulator.bionet.test_nrn)
test_synapse_model_decorator() (in module bmtk.tests.simulator.bionet.test_nrn)
test_weight() (in module bmtk.tests.simulator.bionet.test_nrn)
test_weight_decorator() (in module bmtk.tests.simulator.bionet.test_nrn)
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.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)
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.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.linearfilter.SpatioTemporalFilter 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)
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_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.networks.dm_network.DenseNetwork.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)
(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)
(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_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)
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)
unknown (bmtk.simulator.core.network_reader.EdgesReader attribute)
(bmtk.utils.reports.spike_trains.core.SortOrder attribute)
usr_vars() (bmtk.utils.sonata.config.sonata_config.ConfigParser 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)
(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.tests.simulator.bionet.bionet_virtual_files.NodesFile property)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.NodesFile property)
(bmtk.tests.simulator.popnet.popnet_virtual_files.NodesFile property)
(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)
weight_function() (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property)
(in module bmtk.simulator.core.sonata_reader.edge_adaptor)
(in module bmtk.simulator.pointnet.property_map)
weights() (bmtk.simulator.filternet.sonata_adaptors.FilterNode property)
(in module bmtk.simulator.filternet.sonata_adaptors)
weights_non_dom() (bmtk.simulator.filternet.sonata_adaptors.FilterNode property)
with_dynamics_params() (bmtk.tests.simulator.bionet.bionet_virtual_files.EdgeRow property)
(bmtk.tests.simulator.bionet.bionet_virtual_files.NodeRow property)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.EdgeRow property)
(bmtk.tests.simulator.pointnet.pointnet_virtual_files.NodeRow property)
(bmtk.tests.simulator.popnet.popnet_virtual_files.EdgeRow property)
(bmtk.tests.simulator.popnet.popnet_virtual_files.NodeRow property)
wmax() (in module bmtk.simulator.bionet.default_setters.synaptic_weights)
(in module bmtk.tests.simulator.bionet.set_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_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
xiter_random() (in module bmtk.builder.auxi.node_params)
XStimMod (class in bmtk.simulator.bionet.modules.xstim)
Contents
Installation Guide
Building Networks
Simulation Engines
BioNet
PointNet
PopNet
FilterNet
Analyzing the Results
Tutorials
Builder: Using the Network Builder
BioNet: Single cell with current injection
BioNet: Single with with synaptic input
BioNet: Multiple Nodes with single cell-type
BioNet: Heterogeneous network
PointNet: Point-neuron modeling
PopNet: Population-based firing rate models
FilterNet: Full-field flashing movie
Example Networks
Github Profile
Contributors
Source Documentation
bmtk.analyzer package
bmtk.builder package
bmtk.simulator package
bmtk.tests package
bmtk.utils package
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