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.filternet.io_tools.FilterNetIOUtils 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.ecp
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)
data() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method)
(bmtk.utils.reports.compartment.core.CompartmentReaderABC method)
default_cell_loader() (in module bmtk.simulator.filternet.default_setters.cell_loaders)
default_dir (bmtk.simulator.utils.simulation_reports.SimReport attribute)
default_jitter (bmtk.simulator.filternet.cell.Cell property)
default_population (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 property)
default_weight_fnc() (in module bmtk.simulator.bionet.default_setters.synaptic_weights)
(in module bmtk.simulator.pointnet.default_setters.synaptic_weights)
delay (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property)
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.filternet.filtersimulator.FilterSimulator property)
(bmtk.simulator.pointnet.pointsimulator.PointSimulator property)
(bmtk.utils.io.cell_vars.CellVarRecorder property)
dt() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method)
(bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method)
(bmtk.utils.reports.compartment.core.CompartmentReaderABC method)
(bmtk.utils.reports.current_writer.CurrentWriterv01 method)
dtype (bmtk.utils.sonata.column_property.ColumnProperty property)
dtypes (bmtk.builder.connection_map.ConnectionMap.ParamsRules property)
dynamics_params (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property)
(bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
(bmtk.utils.sonata.edge.Edge property)
(bmtk.utils.sonata.node.Node property)
E
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.utils.sonata.file.File property)
edges() (bmtk.builder.network.Network method)
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)
gid() (in module bmtk.simulator.pointnet.property_map)
gid_map (bmtk.simulator.pointnet.pointnetwork.PointNetwork property)
(bmtk.simulator.pointnet.pointsimulator.PointSimulator property)
gid_pool (bmtk.simulator.bionet.bionetwork.BioNetwork property)
(bmtk.simulator.pointnet.pointnetwork.PointNetwork property)
GidPool (class in bmtk.simulator.bionet.gids)
(class in bmtk.simulator.pointnet.gids)
gids (bmtk.simulator.pointnet.gids.GidPool property)
(bmtk.simulator.pointnet.sonata_adaptors.PointNode property)
(bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property)
(bmtk.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)
gids() (bmtk.simulator.core.node_sets.NodeSet method)
GratingMovie (class in bmtk.simulator.filternet.lgnmodel.movie)
Group (class in bmtk.utils.sonata.group)
group_columns (bmtk.utils.sonata.group.Group property)
group_dynamics_params() (in module bmtk.simulator.core.sonata_reader.edge_adaptor)
(in module bmtk.simulator.core.sonata_reader.node_adaptor)
(in module bmtk.simulator.pointnet.property_map)
group_id (bmtk.simulator.bionet.cell.Cell property)
(bmtk.utils.sonata.edge.Edge property)
(bmtk.utils.sonata.group.Group property)
(bmtk.utils.sonata.node.Node property)
group_id_column (bmtk.utils.sonata.population.EdgePopulation property)
(bmtk.utils.sonata.population.NodePopulation property)
(bmtk.utils.sonata.population.Population property)
group_id_ds (bmtk.utils.sonata.population.Population property)
group_ids (bmtk.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_cells() (bmtk.simulator.filternet.filtersimulator.FilterSimulator method)
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.SonataBaseNode property)
model_processing() (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method)
model_template (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge property)
(bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
model_template() (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method)
model_type (bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
(bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property)
model_type() (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method)
(in module bmtk.simulator.pointnet.property_map)
model_type_batched() (in module bmtk.simulator.pointnet.property_map)
model_type_col (bmtk.simulator.bionet.bionetwork.BioNetwork attribute)
(bmtk.simulator.core.graph.SimGraph attribute)
module
bmtk
bmtk.analyzer
bmtk.analyzer.cell_vars
bmtk.analyzer.compartment
bmtk.analyzer.ecp
bmtk.analyzer.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 (bmtk.simulator.bionet.biocell.BioCell property)
Morphology (class in bmtk.simulator.bionet.morphology)
morphology_file (bmtk.simulator.bionet.biocell.BioCell property)
(bmtk.simulator.bionet.sonata_adaptors.BioNode property)
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.pointnet.sonata_adaptors.PointNode property)
(bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property)
n_nodes() (bmtk.simulator.core.sonata_reader.network_reader.SonataNodes method)
n_spikes() (bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVMPIBuffer method)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STMPIBuffer method)
(bmtk.utils.reports.spike_trains.spike_train_readers.CSVSTReader method)
(bmtk.utils.reports.spike_trains.spike_train_readers.EmptySonataReader method)
(bmtk.utils.reports.spike_trains.spike_train_readers.NWBSTReader method)
(bmtk.utils.reports.spike_trains.spike_train_readers.SonataOldReader method)
(bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method)
(bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method)
n_steps (bmtk.simulator.bionet.biosimulator.BioSimulator property)
(bmtk.simulator.pointnet.pointsimulator.PointSimulator property)
n_steps() (bmtk.utils.reports.compartment.compartment_writer.CompartmentWriterv01 method)
(bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method)
(bmtk.utils.reports.compartment.core.CompartmentReaderABC method)
(bmtk.utils.reports.current_writer.CurrentWriterv01 method)
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 (bmtk.builder.node_pool.NodePool property)
(bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
Network (class in bmtk.builder.network)
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 (bmtk.simulator.bionet.cell.Cell property)
Node (class in bmtk.builder.node)
(class in bmtk.utils.sonata.node)
node_id (bmtk.builder.node.Node property)
(bmtk.simulator.bionet.cell.Cell property)
(bmtk.simulator.bionet.gids.PopulationID attribute)
(bmtk.simulator.bionet.virtualcell.VirtualCell property)
(bmtk.simulator.core.edge_population.SimEdge property)
(bmtk.simulator.core.node_population.SimNode property)
(bmtk.simulator.core.sonata_reader.node_adaptor.SonataBaseNode property)
(bmtk.simulator.pointnet.gids.PopulationID attribute)
(bmtk.utils.sonata.node.Node property)
node_id() (bmtk.simulator.core.sonata_reader.node_adaptor.NodeAdaptor method)
(in module bmtk.simulator.pointnet.property_map)
node_ids (bmtk.simulator.pointnet.sonata_adaptors.PointNode property)
(bmtk.simulator.pointnet.sonata_adaptors.PointNodeBatched property)
(bmtk.utils.sonata.group.NodeGroup property)
(bmtk.utils.sonata.node.NodeSet property)
(bmtk.utils.sonata.population.NodePopulation property)
node_ids() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method)
(bmtk.utils.reports.compartment.core.CompartmentReaderABC method)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer method)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVMPIBuffer method)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer method)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STMPIBuffer method)
(bmtk.utils.reports.spike_trains.spike_train_readers.CSVSTReader method)
(bmtk.utils.reports.spike_trains.spike_train_readers.EmptySonataReader method)
(bmtk.utils.reports.spike_trains.spike_train_readers.NWBSTReader method)
(bmtk.utils.reports.spike_trains.spike_train_readers.SonataOldReader method)
(bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader method)
(bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI method)
node_populations (bmtk.simulator.core.graph.SimGraph property)
(bmtk.simulator.core.simulator_network.SimNetwork property)
node_properties() (bmtk.simulator.core.simulator_network.SimNetwork method)
node_set (bmtk.simulator.utils.simulation_inputs.SimInput property)
(bmtk.simulator.utils.simulation_reports.ClampReport property)
(bmtk.simulator.utils.simulation_reports.SimReport property)
node_sets_file (bmtk.utils.sim_setup.EnvBuilder property)
node_type_id (bmtk.builder.node.Node property)
(bmtk.builder.node_set.NodeSet property)
(bmtk.utils.sonata.node.Node property)
node_type_ids (bmtk.utils.sonata.group.NodeGroup property)
(bmtk.utils.sonata.node.NodeSet property)
(bmtk.utils.sonata.types_table.NodeTypesTable property)
node_type_properties (bmtk.builder.node.Node property)
(bmtk.utils.sonata.node.Node property)
node_types_table (bmtk.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)
node_types_table() (in module bmtk.analyzer)
NodeAdaptor (class in bmtk.simulator.core.sonata_reader.node_adaptor)
NodeGroup (class in bmtk.utils.sonata.group)
NodePool (class in bmtk.builder.node_pool)
NodePopulation (class in bmtk.simulator.core.node_population)
(class in bmtk.utils.sonata.population)
NodePropertyMap (class in bmtk.simulator.pointnet.property_map)
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.utils.sonata.file.File property)
nodes() (bmtk.builder.network.Network method)
(bmtk.simulator.core.node_sets.NodeSet method)
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)
non_dom_params() (in module bmtk.simulator.filternet.sonata_adaptors)
none (bmtk.utils.reports.spike_trains.core.SortOrder attribute)
none_function() (in module bmtk.simulator.core.sonata_reader.node_adaptor)
normalize() (bmtk.simulator.filternet.lgnmodel.kernel.Kernel1D method)
(bmtk.simulator.filternet.lgnmodel.kernel.Kernel2D method)
(bmtk.simulator.filternet.lgnmodel.kernel.Kernel3D method)
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)
nsyns() (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_ecp() (in module bmtk.analyzer.ecp)
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.core.sonata_reader.node_adaptor.SonataBaseNode property)
(bmtk.simulator.filternet.cell.Cell property)
(bmtk.simulator.pointnet.gids.PopulationID attribute)
Population (class in bmtk.utils.sonata.population)
population_list_to_csv() (in module bmtk.simulator.popnet.utils)
population_list_to_dataframe() (in module bmtk.simulator.popnet.utils)
population_names (bmtk.utils.sonata.file_root.FileRoot property)
population_names() (bmtk.simulator.core.node_sets.NodeSet method)
population_to_dict_for_dataframe() (in module bmtk.simulator.popnet.utils)
PopulationID (class in bmtk.simulator.bionet.gids)
(class in bmtk.simulator.pointnet.gids)
populations (bmtk.simulator.pointnet.gids.GidPool property)
(bmtk.utils.io.firing_rates.RatesInput property)
(bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 property)
(bmtk.utils.reports.compartment.core.CompartmentReaderABC property)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVBuffer property)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STCSVMPIBuffer property)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STMemoryBuffer property)
(bmtk.utils.reports.spike_trains.spike_train_buffer.STMPIBuffer property)
(bmtk.utils.reports.spike_trains.spike_train_readers.CSVSTReader property)
(bmtk.utils.reports.spike_trains.spike_train_readers.EmptySonataReader property)
(bmtk.utils.reports.spike_trains.spike_train_readers.NWBSTReader property)
(bmtk.utils.reports.spike_trains.spike_train_readers.SonataSTReader property)
(bmtk.utils.reports.spike_trains.spike_trains_api.SpikeTrainsAPI property)
(bmtk.utils.sonata.file_root.FileRoot property)
populations() (bmtk.simulator.core.node_sets.NodeSet method)
PopulationWriterv01 (class in bmtk.utils.reports.compartment.compartment_writer)
PopulationWriterv01.DataTable (class in bmtk.utils.reports.compartment.compartment_writer)
position (bmtk.simulator.bionet.sonata_adaptors.BioNode property)
position() (in module bmtk.simulator.bionet.sonata_adaptors)
position_x() (in module bmtk.simulator.bionet.sonata_adaptors)
position_xy() (in module bmtk.simulator.bionet.sonata_adaptors)
position_xyz() (in module bmtk.simulator.bionet.sonata_adaptors)
positions() (in module bmtk.simulator.bionet.sonata_adaptors)
positions_columinar() (in module bmtk.builder.auxi.node_params)
positions_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)
reset() (in module bmtk.simulator.bionet.nrn)
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)
rotations() (in module bmtk.simulator.bionet.sonata_adaptors)
rotations_quaternion (bmtk.simulator.bionet.sonata_adaptors.BioNode property)
row_range (bmtk.simulator.filternet.lgnmodel.cursor.KernelCursor property)
rule (bmtk.builder.connection_map.ConnectionMap.ParamsRules property)
run() (bmtk.simulator.bionet.biosimulator.BioSimulator method)
(bmtk.simulator.core.simulator.Simulator method)
(bmtk.simulator.filternet.filtersimulator.FilterSimulator method)
(bmtk.simulator.pointnet.pointsimulator.PointSimulator method)
S
sameconv() (in module bmtk.simulator.filternet.lgnmodel.fitfuns)
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)
spikes_table() (in module bmtk.analyzer)
SpikesGenerator (class in bmtk.simulator.filternet.modules.create_spikes)
SpikesInput (class in bmtk.utils.io.spike_trains)
SpikesInputCSV (class in bmtk.utils.io.spike_trains)
SpikesInputH5 (class in bmtk.utils.io.spike_trains)
SpikesInputNWBv1 (class in bmtk.utils.io.spike_trains)
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.popnet.sonata_adaptors.PopNetEdge property)
syn_weight() (bmtk.simulator.core.sonata_reader.edge_adaptor.SonataBaseEdge method)
(in module bmtk.simulator.core.sonata_reader.edge_adaptor)
(in module bmtk.simulator.pointnet.property_map)
syn_weight_function() (in module bmtk.simulator.core.sonata_reader.edge_adaptor)
synapse_model() (in module bmtk.simulator.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)
tstart() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method)
(bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method)
(bmtk.utils.reports.compartment.core.CompartmentReaderABC method)
(bmtk.utils.reports.current_writer.CurrentWriterv01 method)
tstop (bmtk.simulator.bionet.biosimulator.BioSimulator property)
(bmtk.simulator.pointnet.pointsimulator.PointSimulator property)
(bmtk.utils.io.cell_vars.CellVarRecorder property)
tstop() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method)
(bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method)
(bmtk.utils.reports.compartment.core.CompartmentReaderABC method)
(bmtk.utils.reports.current_writer.CurrentWriterv01 method)
tuning_angle (bmtk.simulator.filternet.sonata_adaptors.FilterNode property)
tuning_angle_preset() (in module bmtk.simulator.filternet.sonata_adaptors)
tuning_angle_rand() (in module bmtk.simulator.filternet.sonata_adaptors)
TwoSubfieldLinearCell (class in bmtk.simulator.filternet.lgnmodel.cellmodel)
type_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)
variable() (bmtk.utils.reports.compartment.compartment_reader.CompartmentReaderVer01 method)
(bmtk.utils.reports.compartment.compartment_writer.PopulationWriterv01 method)
(bmtk.utils.reports.compartment.core.CompartmentReaderABC method)
version (bmtk.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)
weight_function() (in module bmtk.simulator.core.sonata_reader.edge_adaptor)
(in module bmtk.simulator.pointnet.property_map)
weights (bmtk.simulator.filternet.sonata_adaptors.FilterNode property)
weights() (in module bmtk.simulator.filternet.sonata_adaptors)
weights_non_dom (bmtk.simulator.filternet.sonata_adaptors.FilterNode property)
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
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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