Index

_

_BoxRTree (class in bsb.trees)

_ExceptionT_co (class in bsb.services._util)

A

abort() (bsb.services.mpi.MPIService method) ABORTED (bsb.services.pool.JobStatus attribute) accept() (bsb.topology._layout.Layout method) Adapter (bsb.simulation.SimulationBackendPlugin attribute) AdapterError add() (bsb.simulation.results.SimulationResult method) add_listener() (bsb.services.pool.JobPool method) add_locals() (bsb.cli.commands.BaseCommand method) add_notification() (bsb.services.pool.JobPool method) add_parser_arguments() (bsb.cli.commands.BaseCommand method) add_parser_options() (bsb.cli.commands.BaseCommand method) add_shape() (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) add_subparsers() (bsb.cli.commands.BaseCommand method) add_to_parser() (bsb.cli.commands.BaseCommand method) (bsb.cli.commands.BsbCommand method) (bsb.option.BsbOption method) adjacency_dictionary (bsb.morphologies.Morphology property) affinity (bsb.connectivity.detailed.shared.Intersectional attribute) (bsb.connectivity.general.AllToAll attribute) (bsb.connectivity.geometric.morphology_shape_intersection.MorphologyToShapeIntersection attribute) (bsb.connectivity.geometric.shape_morphology_intersection.ShapeToMorphologyIntersection attribute) (bsb.connectivity.geometric.shape_shape_intersection.ShapeToShapeIntersection attribute) after() (in module bsb.config) after_connectivity (bsb.core.Scaffold property) after_placement (bsb.core.Scaffold property) AfterConnectivityHook (class in bsb.postprocessing) AfterPlacementHook (class in bsb.postprocessing) all() (bsb.storage.interfaces.ConnectivityIterator method) (bsb.storage.interfaces.FileStore method) (bsb.storage.interfaces.MorphologyRepository method)

AllenApiError AllenStructure (class in bsb.topology.partition) allgather() (bsb.services.mpi.MPIService method) AllToAll (class in bsb.connectivity.general) analogsignals (bsb.simulation.results.SimulationResult property) anchor (bsb.topology.region.Stack attribute) angle (bsb.placement.arrays.ParallelArrayPlacement attribute) any_() (in module bsb.config.types) apex (bsb.connectivity.geometric.geometric_shapes.Cone attribute) append_additional() (bsb.storage.interfaces.PlacementSet method) append_data() (bsb.storage.interfaces.PlacementSet method) as_arc() (bsb.morphologies.Branch method) as_boxes() (bsb.voxels.VoxelSet method) as_boxtree() (bsb.voxels.VoxelSet method) as_filtered() (bsb.morphologies.Morphology method) as_globals() (bsb.storage.interfaces.ConnectivityIterator method) as_scoped() (bsb.storage.interfaces.ConnectivityIterator method) as_spatial_coords() (bsb.voxels.VoxelSet method) assert_indication() (bsb.placement.indicator.PlacementIndicator method) assert_support() (bsb.storage.Storage method) attach_child() (bsb.morphologies.Branch method) attr (bsb.core.Scaffold attribute) (bsb.storage._files.CodeDependencyNode attribute) attr() (in module bsb.config) AttributeMissingError axis (bsb.simulation.targetting.CylindricalTargetting attribute) (bsb.topology.partition.Layer attribute) (bsb.topology.region.Stack attribute)

B

barrier() (bsb.services.mpi.MPIService method) BaseCommand (class in bsb.cli.commands) bcast() (bsb.services.mpi.MPIService method) before() (in module bsb.config) BidirectionalContact (class in bsb.postprocessing) boot() (bsb.placement.arrays.ParallelArrayPlacement method) BootError bounds (bsb.morphologies.SubTree property) (bsb.voxels.VoxelSet property) box_layout() (in module bsb.topology._layout) BoxTree (class in bsb.trees) BoxTreeInterface (class in bsb.trees) Branch (class in bsb.morphologies) branch_adjacency (bsb.morphologies.SubTree property) branch_cls (bsb.morphologies.parsers.parser.MorphologyParser attribute) branch_iter() (in module bsb.morphologies) branches (bsb.morphologies.SubTree property) BranchLocTargetting (class in bsb.simulation.targetting) bsb module bsb.cell_types module bsb.cli module bsb.cli.commands module bsb.config module bsb.config.parsers module bsb.config.refs module bsb.config.types module bsb.connectivity module bsb.connectivity.detailed module bsb.connectivity.detailed.shared module bsb.connectivity.detailed.voxel_intersection module bsb.connectivity.general module bsb.connectivity.geometric.geometric_shapes module bsb.connectivity.geometric.morphology_shape_intersection module bsb.connectivity.geometric.shape_morphology_intersection module bsb.connectivity.geometric.shape_shape_intersection module bsb.connectivity.strategy module bsb.core module bsb.exceptions module bsb.mixins module bsb.morphologies module bsb.morphologies.parsers module bsb.morphologies.parsers.parser module bsb.morphologies.selector module bsb.option module

bsb.options module bsb.placement module bsb.placement.arrays module bsb.placement.distributor module bsb.placement.indicator module bsb.placement.random module bsb.placement.strategy module bsb.plugins module bsb.postprocessing module bsb.reporting module bsb.services._util module bsb.services.mpi module bsb.services.mpilock module bsb.services.pool module bsb.simulation module bsb.simulation.adapter module bsb.simulation.cell module bsb.simulation.component module bsb.simulation.connection module bsb.simulation.device module bsb.simulation.parameter module bsb.simulation.results module bsb.simulation.simulation module bsb.simulation.targetting module bsb.storage module bsb.storage._files module bsb.storage.interfaces module bsb.topology module bsb.topology._layout module bsb.topology.partition module bsb.topology.region module bsb.trees module bsb.voxels module BsbCommand (class in bsb.cli.commands) BsbOption (class in bsb.option) BsbParser (class in bsb.morphologies.parsers.parser) ByIdTargetting (class in bsb.simulation.targetting) ByLabelTargetting (class in bsb.simulation.targetting)

C

cache (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection attribute) cached_load() (bsb.storage.interfaces.StoredMorphology method) cached_voxelize() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) can_move (bsb.topology.partition.Rhomboid attribute) can_rotate (bsb.topology.partition.Rhomboid attribute) can_scale (bsb.topology.partition.Rhomboid attribute) cancel() (bsb.services.pool.Job method) CANCELLED (bsb.services.pool.JobStatus attribute) candidate_intersection() (bsb.connectivity.detailed.shared.Intersectional method) CastConfigurationError CastError casts (bsb.postprocessing.SpoofDetails attribute) catch_all() (in module bsb.config) cdf() (bsb.config.Distribution method) ceil_arc_point() (bsb.morphologies.Branch method) cell_models (bsb.simulation.simulation.Simulation attribute) (bsb.simulation.targetting.CellModelFilter attribute) (bsb.simulation.targetting.CellModelTargetting attribute) cell_type (bsb.placement.indicator.PlacementIndicator property) (bsb.simulation.cell.CellModel attribute) (bsb.storage.interfaces.PlacementSet property) cell_types (bsb.connectivity.strategy.Hemitype attribute) (bsb.core.Scaffold property) (bsb.placement.strategy.PlacementStrategy attribute) (bsb.postprocessing.Relay attribute) CellModel (class in bsb.simulation.cell) CellModelFilter (class in bsb.simulation.targetting) CellModelTargetting (class in bsb.simulation.targetting) CellTargetting (class in bsb.simulation.targetting) CellType (class in bsb.cell_types) center() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) cfgdict (class in bsb.config._attrs) cfglist (class in bsb.config._attrs) CfgReferenceError change_status() (bsb.services.pool.Job method) (bsb.services.pool.JobPool method) check_inside() (bsb.connectivity.geometric.geometric_shapes.Cone method) (bsb.connectivity.geometric.geometric_shapes.Cuboid method) (bsb.connectivity.geometric.geometric_shapes.Cylinder method) (bsb.connectivity.geometric.geometric_shapes.Ellipsoid method) (bsb.connectivity.geometric.geometric_shapes.GeometricShape method) (bsb.connectivity.geometric.geometric_shapes.Parallelepiped method) (bsb.connectivity.geometric.geometric_shapes.Sphere method) check_mbox() (bsb.connectivity.geometric.geometric_shapes.GeometricShape method) children (bsb.morphologies.Branch property) (bsb.topology._layout.Layout property) (bsb.topology.region.Region attribute) Chunk (class in bsb.storage._chunks) chunk_connect() (bsb.storage.interfaces.ConnectivitySet method) chunk_context() (bsb.storage.interfaces.PlacementSet method) chunk_iter() (bsb.storage.interfaces.ConnectivityIterator method) chunk_to_voxels() (bsb.topology.partition.Partition method) (bsb.topology.partition.Rhomboid method) (bsb.topology.partition.Voxels method) ChunkError chunklist() (in module bsb.storage._chunks) chunks (bsb.services.pool.SubmissionContext property) CircularMorphologyError class_ (class in bsb.config.types) ClassError ClassMapMissingError clear() (bsb.cell_types.CellType method) (bsb.core.Scaffold method) (bsb.storage.interfaces.ConnectivitySet method) (bsb.storage.interfaces.PlacementSet method) clear_connections() (bsb.cell_types.CellType method) clear_connectivity() (bsb.core.Scaffold method) (bsb.storage.interfaces.Engine method) (bsb.storage.Storage method) clear_placement() (bsb.cell_types.CellType method) (bsb.core.Scaffold method) (bsb.storage.interfaces.Engine method) (bsb.storage.Storage method) clear_soft_cache() (bsb.morphologies.MorphologySet method) cli (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) CLIError CLIOptionDescriptor (class in bsb.option) close() (bsb.services.mpilock.MockedWindowController method) close_gaps() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) closed (bsb.services.mpilock.MockedWindowController property) CLOSING (bsb.services.pool.PoolStatus attribute) cls (bsb.morphologies.parsers.parser.MorphologyParser attribute)

CodeDependencyNode (class in bsb.storage._files) CodeImportError collapse() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) collect() (bsb.services.mpilock.Fence method) (bsb.simulation.adapter.SimulatorAdapter method) color (bsb.cell_types.Plotting attribute) comm (bsb.storage.interfaces.Engine property) COMM_WORLD (bsb.services.mpi.MPIModule property) CommandError CompartmentError CompilationError compile() (bsb.core.Scaffold method) compose_nodes() (in module bsb.config) compute_n_points() (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) concatenate() (bsb.voxels.VoxelSet class method) Cone (class in bsb.connectivity.geometric.geometric_shapes) ConfigTemplateNotFoundError configuration (bsb.core.Scaffold property) Configuration (class in bsb.config) ConfigurationAttribute (class in bsb.config) ConfigurationError ConfigurationFormatError ConfigurationParser (class in bsb.config.parsers) ConfigurationSyncError ConfigurationWarning connect() (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection method) (bsb.connectivity.general.AllToAll method) (bsb.connectivity.general.Convergence method) (bsb.connectivity.general.FixedIndegree method) (bsb.connectivity.general.FixedOutdegree method) (bsb.connectivity.geometric.morphology_shape_intersection.MorphologyToShapeIntersection method) (bsb.connectivity.geometric.shape_morphology_intersection.ShapeToMorphologyIntersection method) (bsb.connectivity.geometric.shape_shape_intersection.ShapeToShapeIntersection method) (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.storage.interfaces.ConnectivitySet method) connect_cells() (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.core.Scaffold method) connection_models (bsb.simulation.simulation.Simulation attribute) ConnectionModel (class in bsb.simulation.connection) ConnectionStrategy (class in bsb.connectivity.strategy) ConnectionTargetting (class in bsb.simulation.targetting) connectivity (bsb.core.Scaffold property) ConnectivityError ConnectivityIterator (class in bsb.storage.interfaces) ConnectivityJob (class in bsb.services.pool) ConnectivitySet (class in bsb.storage.interfaces) ConnectivityWarning contacts (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection attribute) contains_labels() (bsb.morphologies.Branch method) context (bsb.services.pool.Job property) (bsb.services.pool.SubmissionContext property) ContinuityError convergence (bsb.connectivity.general.Convergence attribute) Convergence (class in bsb.connectivity.general) coordinates_of() (bsb.voxels.VoxelSet method) copy() (bsb.morphologies.Branch method) (bsb.morphologies.Morphology method) (bsb.storage.interfaces.Engine method) (bsb.storage.Storage method) (bsb.topology._layout.Layout method) (bsb.topology._layout.PartitionData method) (bsb.topology._layout.RhomboidData method) (bsb.voxels.VoxelData method) (bsb.voxels.VoxelSet method) copy_configuration_template() (in module bsb.config) count (bsb.cell_types.PlacementIndications attribute) (bsb.simulation.targetting.FractionFilter attribute) count_morphologies() (bsb.morphologies.MorphologySet method) (bsb.storage.interfaces.PlacementSet method) count_ratio (bsb.cell_types.PlacementIndications attribute) count_unique() (bsb.morphologies.MorphologySet method) create() (bsb.storage.interfaces.ConnectivitySet class method) (bsb.storage.interfaces.Engine method) (bsb.storage.interfaces.PlacementSet class method) (bsb.storage.Storage method) create_engine() (in module bsb.storage) create_entities() (bsb.core.Scaffold method) create_job_pool() (bsb.core.Scaffold method) create_recorder() (bsb.simulation.results.SimulationResult method) create_session() (bsb.storage._files.NeuroMorphoScheme method) (bsb.storage._files.UrlScheme method) create_topology() (in module bsb.topology) crop() (bsb.voxels.VoxelSet method) crop_chunk() (bsb.voxels.VoxelSet method) Cuboid (class in bsb.connectivity.geometric.geometric_shapes) Cylinder (class in bsb.connectivity.geometric.geometric_shapes) CylindricalTargetting (class in bsb.simulation.targetting)

D

data (bsb.topology._layout.Layout property) (bsb.topology.partition.Partition property) (bsb.topology.region.Region property) (bsb.voxels.VoxelSet property) data_keys (bsb.voxels.VoxelSet property) DataNotFoundError DataNotProvidedError DatasetExistsError DatasetNotFoundError default() (bsb.config.Configuration class method) default_vector (bsb.placement.distributor.VolumetricRotations attribute) definition_interval() (bsb.config.Distribution method) deg_to_radian (class in bsb.config.types) delete_point() (bsb.morphologies.Branch method) density (bsb.cell_types.PlacementIndications attribute) density_key (bsb.cell_types.PlacementIndications attribute) density_ratio (bsb.cell_types.PlacementIndications attribute) DependencyError depends_on (bsb.connectivity.strategy.ConnectionStrategy attribute) (bsb.placement.strategy.PlacementStrategy attribute) depth (bsb.topology._layout.RhomboidData property) description (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) (bsb.services.pool.Job property) detach() (bsb.morphologies.Branch method) detach_child() (bsb.morphologies.Branch method) DeviceModel (class in bsb.simulation.device) devices (bsb.simulation.simulation.Simulation attribute) dict() (in module bsb.config) (in module bsb.config.types) dimensions (bsb.topology._layout.RhomboidData property) (bsb.topology.partition.Rhomboid attribute)

discover() (in module bsb.plugins) discover_engines() (in module bsb.storage) discover_options() (in module bsb.options) dispatcher() (in module bsb.services.pool) display_name (bsb.cell_types.Plotting attribute) distribute (bsb.placement.strategy.PlacementStrategy attribute) distribute() (bsb.placement.distributor.Distributor method) (bsb.placement.distributor.ExplicitNoRotations method) (bsb.placement.distributor.ImplicitNoRotations method) (bsb.placement.distributor.MorphologyDistributor method) (bsb.placement.distributor.MorphologyGenerator method) (bsb.placement.distributor.RandomMorphologies method) (bsb.placement.distributor.RandomRotations method) (bsb.placement.distributor.RotationDistributor method) (bsb.placement.distributor.RoundRobinMorphologies method) (bsb.placement.distributor.VolumetricRotations method) distribution (bsb.config.Distribution attribute) Distribution (class in bsb.config) distribution (class in bsb.config.types) DistributionCastError DistributionContext (class in bsb.placement.distributor) Distributor (class in bsb.placement.distributor) DistributorError DistributorsNode (class in bsb.placement.distributor) do_layout() (bsb.topology.region.Region method) draw() (bsb.config.Distribution method) DryrunError duration (bsb.simulation.simulation.Simulation attribute) dynamic() (in module bsb.config) DynamicClassError DynamicClassInheritanceError DynamicObjectNotFoundError

E

Ellipsoid (class in bsb.connectivity.geometric.geometric_shapes) empty() (bsb.morphologies.Morphology class method) (bsb.morphologies.MorphologySet class method) (bsb.voxels.VoxelSet class method) EmptyBranchError EmptySelectionError EmptyVoxelSetError end (bsb.morphologies.Branch property) engine (bsb.storage.interfaces.StorageNode attribute) Engine (class in bsb.storage.interfaces) Entities (class in bsb.placement.strategy) entity (bsb.cell_types.CellType attribute) env (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) EnvOptionDescriptor (class in bsb.option) epsilon (bsb.connectivity.geometric.geometric_shapes.GeometricShape attribute) equilateral (bsb.voxels.VoxelSet property)

error (bsb.services.pool.Job property) ErrorModule (class in bsb.services._util) euclidean_dist (bsb.morphologies.Branch property) evaluation (class in bsb.config.types) execute() (bsb.services.pool.ConnectivityJob static method) (bsb.services.pool.FunctionJob static method) (bsb.services.pool.Job static method) (bsb.services.pool.JobPool method) (bsb.services.pool.PlacementJob static method) execute_checkpoints() (bsb.simulation.adapter.SimulatorAdapter method) execute_handler() (bsb.cli.commands.BaseCommand method) EXECUTING (bsb.services.pool.PoolStatus attribute) exists() (bsb.storage.interfaces.ConnectivitySet static method) (bsb.storage.interfaces.Engine method) (bsb.storage.interfaces.PlacementSet static method) (bsb.storage.Storage method) ExplicitNoRotations (class in bsb.placement.distributor) ExternalSourceError

F

FAILED (bsb.services.pool.JobStatus attribute) favor_cache (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection attribute) Fence (class in bsb.services.mpilock) FencedSignal file (bsb.storage._files.CodeDependencyNode attribute) (bsb.storage._files.FileDependencyNode attribute) file() (in module bsb.config) FileDependency (class in bsb.storage._files) FileDependencyNode (class in bsb.storage._files) FileImportError FileReferenceError files (bsb.core.Scaffold property) (bsb.storage.Storage property) FileScheme (class in bsb.storage._files) FileStore (class in bsb.storage.interfaces) fill() (bsb.voxels.VoxelSet class method) filter() (bsb.simulation.targetting.FractionFilter static method) filter_by_labels() (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) find() (bsb.storage._files.FileScheme method) (bsb.storage._files.UriScheme method) (bsb.storage._files.UrlScheme method) find_closest_point() (bsb.morphologies.Branch method) find_file() (bsb.storage.interfaces.FileStore method) find_files() (bsb.storage.interfaces.FileStore method) find_id() (bsb.storage.interfaces.FileStore method) find_mbb() (bsb.connectivity.geometric.geometric_shapes.Cone method) (bsb.connectivity.geometric.geometric_shapes.Cuboid method) (bsb.connectivity.geometric.geometric_shapes.Cylinder method) (bsb.connectivity.geometric.geometric_shapes.Ellipsoid method) (bsb.connectivity.geometric.geometric_shapes.GeometricShape method) (bsb.connectivity.geometric.geometric_shapes.Parallelepiped method) (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) (bsb.connectivity.geometric.geometric_shapes.Sphere method) find_meta() (bsb.storage.interfaces.FileStore method) find_structure() (bsb.topology.partition.AllenStructure class method) finished (bsb.services.pool.Workflow property)

FixedIndegree (class in bsb.connectivity.general) FixedOutdegree (class in bsb.connectivity.general) FixedPositions (class in bsb.placement.strategy) FixedStepProgressController (class in bsb.simulation.adapter) flag_dirty() (bsb.config.ConfigurationAttribute method) flag_pristine() (bsb.config.ConfigurationAttribute method) flags (bsb.morphologies.parsers.parser.MorphIOParser attribute) flat_iter_connections() (bsb.storage.interfaces.ConnectivitySet method) flatten() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) flatten_labels() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) flatten_properties() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) flatten_radii() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) float() (in module bsb.config.types) floor_arc_point() (bsb.morphologies.Branch method) flush() (bsb.simulation.results.SimulationRecorder method) (bsb.simulation.results.SimulationResult method) format (bsb.storage.interfaces.Engine property) (bsb.storage.Storage property) format_configuration_content() (in module bsb.config) fractal_dim (bsb.morphologies.Branch property) fraction (bsb.simulation.targetting.FractionFilter attribute) fraction() (in module bsb.config.types) FractionFilter (class in bsb.simulation.targetting) free_stale_pool_cache() (in module bsb.services.pool) from_() (bsb.storage.interfaces.ConnectivityIterator method) from_morphology() (bsb.voxels.VoxelSet class method) from_storage() (in module bsb.core) fset() (bsb.config.ConfigurationAttribute method) func (bsb.storage._files.MorphologyOperation attribute) (bsb.storage._files.Operation attribute) function_ (class in bsb.config.types) FunctionJob (class in bsb.services.pool)

G

GatewayError gather() (bsb.services.mpi.MPIService method) generate() (bsb.config.parsers.ConfigurationParser method) (bsb.placement.distributor.MorphologyGenerator method) generate_point_cloud() (bsb.connectivity.geometric.geometric_shapes.Cone method) (bsb.connectivity.geometric.geometric_shapes.Cuboid method) (bsb.connectivity.geometric.geometric_shapes.Cylinder method) (bsb.connectivity.geometric.geometric_shapes.Ellipsoid method) (bsb.connectivity.geometric.geometric_shapes.GeometricShape method) (bsb.connectivity.geometric.geometric_shapes.Parallelepiped method) (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) (bsb.connectivity.geometric.geometric_shapes.Sphere method) generate_wireframe() (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) GeneratedMorphology (class in bsb.storage.interfaces) GeometricShape (class in bsb.connectivity.geometric.geometric_shapes) geometry (bsb.cell_types.PlacementIndications attribute) get() (bsb.morphologies.MorphologySet method) (bsb.option.BsbOption method) (bsb.storage.interfaces.FileStore method) get_all_chunks() (bsb.connectivity.strategy.Hemitype method) (bsb.storage.interfaces.PlacementSet method) get_all_meta() (bsb.storage.interfaces.MorphologyRepository method) get_all_post_chunks() (bsb.connectivity.strategy.ConnectionStrategy method) get_all_pre_chunks() (bsb.connectivity.strategy.ConnectionStrategy method) get_arc_point() (bsb.morphologies.Branch method) get_axial_distances() (bsb.morphologies.Branch method) get_base_url() (bsb.storage._files.NeuroMorphoScheme method) (bsb.storage._files.UrlScheme method) get_branches() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) get_cell_types() (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.core.Scaffold method) get_chunk_stats() (bsb.storage.interfaces.Engine method) (bsb.storage.interfaces.PlacementSet method) (bsb.storage.Storage method) get_cli_tags() (bsb.option.BsbOption method) get_communicator() (bsb.services.mpi.MPIService method) get_components() (bsb.simulation.simulation.Simulation method) get_config_attributes() (in module bsb.config) get_config_diagram() (bsb.core.Scaffold method) get_config_path() (in module bsb.config) get_configuration_parser() (in module bsb.config.parsers) get_connectivity() (bsb.core.Scaffold method) get_connectivity_set() (bsb.core.Scaffold method) (bsb.simulation.connection.ConnectionModel method) (bsb.storage.Storage method) get_connectivity_sets() (bsb.core.Scaffold method) (bsb.simulation.simulation.Simulation method) (bsb.storage.Storage method) get_content() (bsb.storage._files.FileDependency method) (bsb.storage._files.FileScheme method) (bsb.storage._files.UriScheme method) (bsb.storage._files.UrlScheme method) get_data() (bsb.storage._files.NrrdDependencyNode method) (bsb.voxels.VoxelSet method) get_default() (bsb.config.ConfigurationAttribute method) (bsb.option.BsbOption method) (bsb.options.ProfilingOption method) (bsb.options.VerbosityOption method) get_dependencies() (bsb.topology.partition.Rhomboid method) (bsb.topology.region.Region method) get_dependency_pipelines() (bsb.core.Scaffold method) get_deps() (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.mixins.HasDependencies method) (bsb.placement.strategy.PlacementStrategy method) get_encoding() (bsb.storage.interfaces.FileStore method) get_engine_node() (in module bsb.storage) get_engines() (in module bsb.storage) get_global_chunks() (bsb.storage.interfaces.ConnectivitySet method) get_header() (bsb.storage._files.NrrdDependencyNode method) get_hint() (bsb.config.ConfigurationAttribute method) get_indicators() (bsb.placement.strategy.PlacementStrategy method) get_indices() (bsb.morphologies.MorphologySet method) get_label_mask() (bsb.morphologies.Branch method) (bsb.morphologies.Morphology method) (bsb.storage.interfaces.PlacementSet method) get_labelled() (bsb.storage.interfaces.PlacementSet method) get_layout() (bsb.topology.partition.Layer method) (bsb.topology.partition.Partition method) (bsb.topology.partition.Rhomboid method) (bsb.topology.partition.Voxels method) (bsb.topology.region.Region method) (bsb.topology.region.Stack method) get_local_chunks() (bsb.storage.interfaces.ConnectivitySet method) get_local_path() (bsb.storage._files.FileScheme method) (bsb.storage._files.UriScheme method) (bsb.storage._files.UrlScheme method) get_locations() (bsb.simulation.targetting.BranchLocTargetting method) (bsb.simulation.targetting.LabelTargetting method) (bsb.simulation.targetting.LocationTargetting method) (bsb.simulation.targetting.SomaTargetting method) get_mask() (bsb.topology.partition.NrrdVoxels method) get_mbb() (bsb.connectivity.geometric.shape_shape_intersection.ShapeHemitype method) get_mbb_max() (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) get_mbb_min() (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) get_meta() (bsb.storage._files.FileDependency method) (bsb.storage._files.FileScheme method) (bsb.storage._files.NeuroMorphoScheme method) (bsb.storage._files.UriScheme method) (bsb.storage._files.UrlScheme method) (bsb.storage.interfaces.FileStore method) (bsb.storage.interfaces.MorphologyRepository method) (bsb.storage.interfaces.StoredMorphology method) get_model_of() (bsb.simulation.simulation.Simulation method) get_module_option() (in module bsb.options) get_morphologies() (bsb.cell_types.CellType method) get_morphology_name() (bsb.storage._files.MorphologyDependencyNode method) get_mtime() (bsb.storage.interfaces.FileStore method) get_next_checkpoint() (bsb.simulation.adapter.FixedStepProgressController method) (bsb.simulation.adapter.SimulatorAdapter method) get_nm_meta() (bsb.storage._files.NeuroMorphoScheme method) get_node_cache_items() (in module bsb.services.pool) get_node_name() (bsb.cell_types.CellType method) (bsb.cell_types.PlacementIndications method) (bsb.cell_types.Plotting method) (bsb.config.ConfigurationAttribute method) (bsb.config.Distribution method) (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection method) (bsb.connectivity.general.AllToAll method) (bsb.connectivity.general.Convergence method) (bsb.connectivity.general.FixedIndegree method) (bsb.connectivity.general.FixedOutdegree method) (bsb.connectivity.geometric.geometric_shapes.Cone method) (bsb.connectivity.geometric.geometric_shapes.Cuboid method) (bsb.connectivity.geometric.geometric_shapes.Cylinder method) (bsb.connectivity.geometric.geometric_shapes.Ellipsoid method) (bsb.connectivity.geometric.geometric_shapes.GeometricShape method) (bsb.connectivity.geometric.geometric_shapes.Parallelepiped method) (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) (bsb.connectivity.geometric.geometric_shapes.Sphere method) (bsb.connectivity.geometric.morphology_shape_intersection.MorphologyToShapeIntersection method) (bsb.connectivity.geometric.shape_morphology_intersection.ShapeToMorphologyIntersection method) (bsb.connectivity.geometric.shape_shape_intersection.ShapeHemitype method) (bsb.connectivity.geometric.shape_shape_intersection.ShapeToShapeIntersection method) (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.connectivity.strategy.Hemitype method) (bsb.morphologies.parsers.parser.BsbParser method) (bsb.morphologies.parsers.parser.MorphIOParser method) (bsb.morphologies.parsers.parser.MorphologyParser method) (bsb.morphologies.selector.MorphologySelector method) (bsb.morphologies.selector.NameSelector method) (bsb.morphologies.selector.NeuroMorphoSelector method) (bsb.placement.arrays.ParallelArrayPlacement method) (bsb.placement.distributor.Distributor method) (bsb.placement.distributor.DistributorsNode method) (bsb.placement.distributor.ExplicitNoRotations method) (bsb.placement.distributor.ImplicitNoRotations method) (bsb.placement.distributor.MorphologyDistributor method) (bsb.placement.distributor.MorphologyGenerator method) (bsb.placement.distributor.RandomMorphologies method) (bsb.placement.distributor.RandomRotations method) (bsb.placement.distributor.RotationDistributor method) (bsb.placement.distributor.RoundRobinMorphologies method) (bsb.placement.distributor.VolumetricRotations method) (bsb.placement.random.RandomPlacement method) (bsb.placement.strategy.Entities method) (bsb.placement.strategy.FixedPositions method) (bsb.placement.strategy.PlacementStrategy method) (bsb.postprocessing.AfterConnectivityHook method) (bsb.postprocessing.AfterPlacementHook method) (bsb.postprocessing.Relay method) (bsb.simulation.cell.CellModel method) (bsb.simulation.component.SimulationComponent method) (bsb.simulation.connection.ConnectionModel method) (bsb.simulation.device.DeviceModel method) (bsb.simulation.parameter.Parameter method) (bsb.simulation.parameter.ParameterValue method) (bsb.simulation.simulation.Simulation method) (bsb.simulation.targetting.BranchLocTargetting method) (bsb.simulation.targetting.ByIdTargetting method) (bsb.simulation.targetting.ByLabelTargetting method) (bsb.simulation.targetting.CellModelTargetting method) (bsb.simulation.targetting.CellTargetting method) (bsb.simulation.targetting.ConnectionTargetting method) (bsb.simulation.targetting.CylindricalTargetting method) (bsb.simulation.targetting.LabelTargetting method) (bsb.simulation.targetting.LocationTargetting method) (bsb.simulation.targetting.RepresentativesTargetting method) (bsb.simulation.targetting.SomaTargetting method) (bsb.simulation.targetting.SphericalTargetting method) (bsb.simulation.targetting.Targetting method) (bsb.storage._files.CodeDependencyNode method) (bsb.storage._files.FileDependencyNode method) (bsb.storage._files.MorphologyDependencyNode method) (bsb.storage._files.MorphologyOperation method) (bsb.storage._files.NrrdDependencyNode method) (bsb.storage._files.Operation method) (bsb.storage.interfaces.StorageNode method) (bsb.topology.partition.AllenStructure method) (bsb.topology.partition.Layer method) (bsb.topology.partition.NrrdVoxels method) (bsb.topology.partition.Partition method) (bsb.topology.partition.Rhomboid method) (bsb.topology.partition.Voxels method) (bsb.topology.region.Region method) (bsb.topology.region.RegionGroup method) (bsb.topology.region.Stack method)

get_option() (in module bsb.options) get_option_classes() (in module bsb.options) get_option_descriptor() (in module bsb.options) get_option_descriptors() (in module bsb.options) get_options() (bsb.cli.commands.BaseCommand method) (bsb.cli.commands.RootCommand method) get_original() (bsb.config.types.evaluation method) get_output_names() (bsb.connectivity.strategy.ConnectionStrategy method) get_owner() (bsb.services.pool.JobPool class method) get_parser() (bsb.cli.commands.RootCommand method) get_partitions() (in module bsb.topology) get_placement() (bsb.cell_types.CellType method) (bsb.core.Scaffold method) get_placement_of() (bsb.core.Scaffold method) get_placement_set() (bsb.cell_types.CellType method) (bsb.core.Scaffold method) (bsb.simulation.cell.CellModel method) (bsb.storage.Storage method) get_placement_sets() (bsb.core.Scaffold method) get_points_labelled() (bsb.morphologies.Branch method) get_project_option() (in module bsb.options) get_radius() (bsb.placement.indicator.PlacementIndicator method) get_rank() (bsb.services.mpi.MPIService method) get_raw() (bsb.voxels.VoxelSet method) get_region_of_interest() (bsb.connectivity.detailed.shared.Intersectional method) (bsb.connectivity.geometric.morphology_shape_intersection.MorphologyToShapeIntersection method) (bsb.connectivity.geometric.shape_morphology_intersection.ShapeToMorphologyIntersection method) (bsb.connectivity.geometric.shape_shape_intersection.ShapeToShapeIntersection method) (bsb.connectivity.strategy.ConnectionStrategy method) get_required_cache_items() (bsb.services.pool.JobPool method) get_root_regions() (in module bsb.topology) get_simulation() (bsb.core.Scaffold method) get_simulation_adapter() (in module bsb.simulation) get_size() (bsb.services.mpi.MPIService method) (bsb.voxels.VoxelSet method) get_size_matrix() (bsb.voxels.VoxelSet method) get_storage_diagram() (bsb.core.Scaffold method) get_stored_file() (bsb.storage._files.FileDependency method) (bsb.storage._files.FileDependencyNode method) get_structure_idset() (bsb.topology.partition.AllenStructure class method) get_structure_mask() (bsb.topology.partition.AllenStructure class method) get_structure_mask_condition() (bsb.topology.partition.AllenStructure class method) get_submissions_of() (bsb.services.pool.JobPool method) get_tags() (bsb.storage.interfaces.ConnectivitySet class method) get_targets() (bsb.simulation.targetting.ByIdTargetting method) (bsb.simulation.targetting.ByLabelTargetting method) (bsb.simulation.targetting.CellModelFilter method) (bsb.simulation.targetting.CellModelTargetting method) (bsb.simulation.targetting.CellTargetting method) (bsb.simulation.targetting.ConnectionTargetting method) (bsb.simulation.targetting.CylindricalTargetting method) (bsb.simulation.targetting.RepresentativesTargetting method) (bsb.simulation.targetting.SphericalTargetting method) (bsb.simulation.targetting.Targetting method) get_tmp_folder() (bsb.services.pool.JobPool class method) get_type() (bsb.config.ConfigurationAttribute method) get_unique_labels() (bsb.storage.interfaces.PlacementSet method) get_volume() (bsb.connectivity.geometric.geometric_shapes.Cone method) (bsb.connectivity.geometric.geometric_shapes.Cuboid method) (bsb.connectivity.geometric.geometric_shapes.Cylinder method) (bsb.connectivity.geometric.geometric_shapes.Ellipsoid method) (bsb.connectivity.geometric.geometric_shapes.GeometricShape method) (bsb.connectivity.geometric.geometric_shapes.Parallelepiped method) (bsb.connectivity.geometric.geometric_shapes.Sphere method) get_volumes() (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) get_voxelset() (bsb.topology.partition.NrrdVoxels method) (bsb.topology.partition.Voxels method) getter() (bsb.options.ProfilingOption method) (bsb.options.SimulationProgress method) (bsb.options.VerbosityOption method) guard() (bsb.services.mpilock.Fence method) guess() (bsb.placement.indicator.PlacementIndicator method) guess_cell_count() (bsb.placement.strategy.FixedPositions method) (bsb.placement.strategy.PlacementStrategy method)

H

handle_cli() (in module bsb.cli) handle_command() (in module bsb.cli) handler() (bsb.cli.commands.BsbCommand method) (bsb.cli.commands.RootCommand method) has() (bsb.storage.interfaces.FileStore method) (bsb.storage.interfaces.MorphologyRepository method)

has_data (bsb.voxels.VoxelSet property) has_hook() (in module bsb.config) HasDependencies (class in bsb.mixins) height (bsb.topology._layout.RhomboidData property) Hemitype (class in bsb.connectivity.strategy) HemitypeCollection (class in bsb.connectivity.strategy)

I

ids (bsb.simulation.targetting.ByIdTargetting attribute) implement() (bsb.simulation.component.SimulationComponent method) (bsb.simulation.device.DeviceModel method) implement_components() (bsb.simulation.adapter.SimulatorAdapter method) Implicit (class in bsb.placement.distributor) ImplicitNoRotations (class in bsb.placement.distributor) in_() (in module bsb.config.types) in_classmap() (in module bsb.config.types) incoming() (bsb.storage.interfaces.ConnectivityIterator method) IncompleteExternalMapError IncompleteMorphologyError indegree (bsb.connectivity.general.FixedIndegree attribute) index_of() (bsb.voxels.VoxelSet method) indication() (bsb.placement.indicator.PlacementIndicator method) indicator (bsb.placement.distributor.DistributionContext attribute) indicator_class (bsb.placement.strategy.PlacementStrategy attribute) IndicatorError init() (bsb.storage.Storage method) init_placement() (bsb.storage.Storage method) InputError insert_branch() (bsb.morphologies.Branch method) inside() (bsb.voxels.VoxelSet method) inside_mbox() (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) (in module bsb.connectivity.geometric.geometric_shapes) inside_shapes() (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) int() (in module bsb.config.types) Interface (class in bsb.storage.interfaces) Intersectional (class in bsb.connectivity.detailed.shared) IntersectionDataNotFoundError introduce_arc_point() (bsb.morphologies.Branch method)

introduce_point() (bsb.morphologies.Branch method) InvalidReferenceError inverted_flag (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) InvertedRoI (class in bsb.mixins) is_dirty() (bsb.config.ConfigurationAttribute method) is_empty (bsb.voxels.VoxelSet property) is_entities() (bsb.placement.strategy.PlacementStrategy method) is_flag (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) is_main() (bsb.services.pool.JobPool method) is_main_process() (bsb.core.Scaffold method) (bsb.storage.Storage method) is_module_option_set() (in module bsb.options) is_node_type() (bsb.config.ConfigurationAttribute method) is_optimized (bsb.morphologies.Morphology property) is_partition() (in module bsb.topology) is_region() (in module bsb.topology) is_root (bsb.morphologies.Branch property) is_set() (bsb.option.BsbOption method) (bsb.option.EnvOptionDescriptor method) (bsb.option.OptionDescriptor method) (bsb.option.ProjectOptionDescriptor method) (bsb.option.ScriptOptionDescriptor method) is_terminal (bsb.morphologies.Branch property) is_worker_process() (bsb.core.Scaffold method) iter() (bsb.morphologies.RotationSet method) iter_meta() (bsb.morphologies.MorphologySet method) iter_morphologies() (bsb.morphologies.MorphologySet method)

J

job (bsb.services.pool.PoolJobAddedProgress property) (bsb.services.pool.PoolJobUpdateProgress property) Job (class in bsb.services.pool) JOB_ADDED (bsb.services.pool.PoolProgressReason attribute) JOB_STATUS_CHANGE (bsb.services.pool.PoolProgressReason attribute) JobCancelledError JobErroredError

JobPool (class in bsb.services.pool) JobPoolContextError JobPoolError jobs (bsb.services.pool.JobPool property) (bsb.services.pool.PoolProgress property) JobSchedulingError JobStatus (class in bsb.services.pool)

K

key() (in module bsb.config.types)

keys (bsb.topology.partition.NrrdVoxels attribute) (bsb.voxels.VoxelData property)

L

label() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) (bsb.storage.interfaces.PlacementSet method) labels (bsb.connectivity.geometric.geometric_shapes.ShapesComposition attribute) (bsb.connectivity.strategy.Hemitype attribute) (bsb.morphologies.Branch property) (bsb.morphologies.SubTree property) (bsb.simulation.targetting.ByLabelTargetting attribute) (bsb.simulation.targetting.LabelTargetting attribute) labelsets (bsb.morphologies.Branch property) (bsb.morphologies.Morphology property) LabelTargetting (class in bsb.simulation.targetting) lambdas (bsb.connectivity.geometric.geometric_shapes.Ellipsoid attribute) Layer (class in bsb.topology.partition) Layout (class in bsb.topology._layout) LayoutError ldc (bsb.topology.partition.Rhomboid property) list() (bsb.storage.interfaces.MorphologyRepository method) (in module bsb.config) (in module bsb.config.types) list_labels() (bsb.morphologies.Branch method) (bsb.morphologies.Morphology method) list_or_scalar() (in module bsb.config.types) load() (bsb.storage.interfaces.FileStore method) (bsb.storage.interfaces.MorphologyRepository method) (bsb.storage.interfaces.StoredFile method) (bsb.storage.interfaces.StoredMorphology method) (bsb.storage.Storage method)

load_active_config() (bsb.storage.interfaces.FileStore method) (bsb.storage.Storage method) load_additional() (bsb.storage.interfaces.PlacementSet method) load_block_connections() (bsb.storage.interfaces.ConnectivitySet method) load_box_tree() (bsb.storage.interfaces.PlacementSet method) load_boxes() (bsb.storage.interfaces.PlacementSet method) load_connections() (bsb.storage.interfaces.ConnectivitySet method) load_controllers() (bsb.simulation.adapter.SimulatorAdapter method) load_ids() (bsb.storage.interfaces.PlacementSet method) load_local_connections() (bsb.storage.interfaces.ConnectivitySet method) load_morphologies() (bsb.storage.interfaces.PlacementSet method) load_object() (bsb.storage._files.CodeDependencyNode method) (bsb.storage._files.FileDependencyNode method) (bsb.storage._files.MorphologyDependencyNode method) (bsb.storage._files.NrrdDependencyNode method) load_positions() (bsb.storage.interfaces.PlacementSet method) load_root_command() (in module bsb.cli.commands) load_rotations() (bsb.storage.interfaces.PlacementSet method) local_count_ratio (bsb.cell_types.PlacementIndications attribute) LocationTargetting (class in bsb.simulation.targetting)

M

make_configuration_diagram() (in module bsb.config) mask_only (bsb.topology.partition.AllenStructure attribute) (bsb.topology.partition.NrrdVoxels attribute) mask_source (bsb.topology.partition.AllenStructure attribute) (bsb.topology.partition.NrrdVoxels attribute) mask_value (bsb.topology.partition.NrrdVoxels attribute) master (bsb.services.mpilock.MockedWindowController property) max_displacement (bsb.morphologies.Branch property) MAX_TIMEOUT_PING (bsb.services.pool.PoolProgressReason attribute) may_be_empty (bsb.placement.distributor.MorphologyDistributor attribute) (bsb.placement.distributor.MorphologyGenerator attribute) (bsb.placement.distributor.RandomMorphologies attribute) (bsb.placement.distributor.RoundRobinMorphologies attribute) mdc (bsb.topology.partition.Rhomboid property) merge() (bsb.core.Scaffold method) (bsb.morphologies.MorphologySet method) meta (bsb.morphologies.Morphology property) (bsb.storage.interfaces.StoredFile property) method (class in bsb.config.types) method_shortcut (class in bsb.config.types) MissingActiveConfigError MissingMorphologyError MissingSourceError MockedWindowController (class in bsb.services.mpilock) MockModule (class in bsb.services._util) module bsb bsb.cell_types bsb.cli bsb.cli.commands bsb.config bsb.config.parsers bsb.config.refs bsb.config.types bsb.connectivity bsb.connectivity.detailed bsb.connectivity.detailed.shared bsb.connectivity.detailed.voxel_intersection bsb.connectivity.general bsb.connectivity.geometric.geometric_shapes bsb.connectivity.geometric.morphology_shape_intersection bsb.connectivity.geometric.shape_morphology_intersection bsb.connectivity.geometric.shape_shape_intersection bsb.connectivity.strategy bsb.core bsb.exceptions bsb.mixins bsb.morphologies bsb.morphologies.parsers bsb.morphologies.parsers.parser bsb.morphologies.selector bsb.option bsb.options bsb.placement bsb.placement.arrays bsb.placement.distributor bsb.placement.indicator bsb.placement.random bsb.placement.strategy bsb.plugins bsb.postprocessing bsb.reporting bsb.services._util bsb.services.mpi bsb.services.mpilock bsb.services.pool bsb.simulation bsb.simulation.adapter bsb.simulation.cell bsb.simulation.component bsb.simulation.connection bsb.simulation.device bsb.simulation.parameter bsb.simulation.results bsb.simulation.simulation bsb.simulation.targetting bsb.storage bsb.storage._files bsb.storage.interfaces bsb.topology bsb.topology._layout bsb.topology.partition bsb.topology.region bsb.trees bsb.voxels

module (bsb.storage._files.CodeDependencyNode attribute) MorphIOParser (class in bsb.morphologies.parsers.parser) morpho_loader (bsb.connectivity.strategy.Hemitype attribute) morphologies (bsb.cell_types.CellType property) (bsb.cell_types.PlacementIndications attribute) (bsb.core.Scaffold property) (bsb.placement.distributor.DistributorsNode attribute) (bsb.storage.Storage property) Morphology (class in bsb.morphologies) morphology_labels (bsb.connectivity.strategy.Hemitype attribute) MorphologyDataError MorphologyDependencyNode (class in bsb.storage._files) MorphologyDistributor (class in bsb.placement.distributor) MorphologyError MorphologyGenerator (class in bsb.placement.distributor) MorphologyOperation (class in bsb.storage._files) MorphologyOperationCallable (class in bsb.storage._files) MorphologyParser (class in bsb.morphologies.parsers.parser) MorphologyRepository (class in bsb.storage.interfaces) MorphologyRepositoryError MorphologySelector (class in bsb.morphologies.selector) MorphologySet (class in bsb.morphologies) MorphologyToShapeIntersection (class in bsb.connectivity.geometric.morphology_shape_intersection) MorphologyWarning move() (bsb.storage.interfaces.Engine method) (bsb.storage.Storage method) MPILockModule (class in bsb.services.mpilock) MPIModule (class in bsb.services.mpi) MPIService (class in bsb.services.mpi) mtime (bsb.storage.interfaces.StoredFile property) mut_excl() (in module bsb.config.types)

N

n (bsb.simulation.targetting.RepresentativesTargetting attribute) name (bsb.cell_types.CellType attribute) (bsb.cli.commands.RootCommand attribute) (bsb.connectivity.strategy.ConnectionStrategy attribute) (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) (bsb.placement.strategy.PlacementStrategy attribute) (bsb.postprocessing.AfterConnectivityHook attribute) (bsb.postprocessing.AfterPlacementHook attribute) (bsb.services.pool.Job property) (bsb.services.pool.SubmissionContext property) (bsb.simulation.component.SimulationComponent attribute) (bsb.simulation.simulation.Simulation attribute) (bsb.storage._files.MorphologyDependencyNode attribute) (bsb.topology.partition.Partition attribute) (bsb.topology.region.Region attribute) names (bsb.morphologies.MorphologySet property) (bsb.morphologies.selector.NameSelector attribute) NameSelector (class in bsb.morphologies.selector)

ndarray (class in bsb.config.types) nested_iter_connections() (bsb.storage.interfaces.ConnectivitySet method) network (bsb.core.Scaffold property) NetworkDescription (class in bsb.storage.interfaces) NetworkNode (class in bsb.config._config) NeuroMorphoScheme (class in bsb.storage._files) NeuroMorphoSelector (class in bsb.morphologies.selector) next_phase() (bsb.services.pool.Workflow method) node() (in module bsb.config) NodeNotFoundError none() (in module bsb.config.types) NoneReferenceError NoopLock (class in bsb.storage.interfaces) NoReferenceAttributeSignal notify() (bsb.services.pool.JobPool method) NotParallel (class in bsb.mixins) NotSupported (class in bsb.storage) NrrdDependencyNode (class in bsb.storage._files) NrrdVoxels (class in bsb.topology.partition) number() (in module bsb.config.types)

O

object_ (class in bsb.config.types) of_equal_size (bsb.voxels.VoxelSet property) old_status (bsb.services.pool.PoolJobUpdateProgress property) on() (in module bsb.config) on_completion() (bsb.services.pool.Job method) one() (bsb.voxels.VoxelSet class method) opacity (bsb.cell_types.Plotting attribute) open_storage() (in module bsb.storage) Operation (class in bsb.storage._files) OperationCallable (class in bsb.storage._files) optimize() (bsb.morphologies.Morphology method) OptionDescriptor (class in bsb.option) OptionError or_() (in module bsb.config.types) orientation (bsb.topology.partition.Rhomboid attribute) orientation_path (bsb.placement.distributor.VolumetricRotations attribute)

orientation_resolution (bsb.placement.distributor.VolumetricRotations attribute) origin (bsb.connectivity.geometric.geometric_shapes.Cone attribute) (bsb.connectivity.geometric.geometric_shapes.Cuboid attribute) (bsb.connectivity.geometric.geometric_shapes.Cylinder attribute) (bsb.connectivity.geometric.geometric_shapes.Ellipsoid attribute) (bsb.connectivity.geometric.geometric_shapes.Parallelepiped attribute) (bsb.connectivity.geometric.geometric_shapes.Sphere attribute) (bsb.morphologies.SubTree property) (bsb.simulation.targetting.CylindricalTargetting attribute) (bsb.simulation.targetting.SphericalTargetting attribute) (bsb.topology.partition.Rhomboid attribute) outdegree (bsb.connectivity.general.FixedOutdegree attribute) outgoing() (bsb.storage.interfaces.ConnectivityIterator method) output_naming (bsb.connectivity.strategy.ConnectionStrategy attribute) overrides (bsb.placement.strategy.PlacementStrategy attribute) owner (bsb.services.pool.JobPool property)

P

PackageRequirement (class in bsb.config.types) PackageRequirementWarning PackingError PackingWarning parallel (bsb.services.pool.JobPool property) ParallelArrayPlacement (class in bsb.placement.arrays) Parallelepiped (class in bsb.connectivity.geometric.geometric_shapes) Parameter (class in bsb.simulation.parameter) ParameterError parameters (bsb.config.Distribution attribute) (bsb.simulation.cell.CellModel attribute) (bsb.storage._files.Operation attribute) ParameterValue (class in bsb.simulation.parameter) parent (bsb.morphologies.Branch property) parse() (bsb.config.parsers.ConfigurationParser method) (bsb.morphologies.parsers.parser.BsbParser method) (bsb.morphologies.parsers.parser.MorphIOParser method) (bsb.morphologies.parsers.parser.MorphologyParser method) parse_configuration_content() (in module bsb.config) parse_configuration_content_to_dict() (in module bsb.config) parse_configuration_file() (in module bsb.config) parse_content() (bsb.morphologies.parsers.parser.BsbParser method) parse_morphology_content() (in module bsb.morphologies.parsers) parse_morphology_file() (in module bsb.morphologies.parsers) parser (bsb.morphologies.parsers.parser.MorphologyParser attribute) (bsb.storage._files.MorphologyDependencyNode attribute) ParserError ParsesReferences (class in bsb.config.parsers) Partition (class in bsb.topology.partition) PartitionData (class in bsb.topology._layout) partitions (bsb.core.Scaffold property) (bsb.placement.distributor.DistributionContext attribute) (bsb.placement.indicator.PlacementIndicator property) (bsb.placement.strategy.PlacementStrategy attribute) path_length (bsb.morphologies.Branch property) (bsb.morphologies.SubTree property) peek_exists() (bsb.storage.interfaces.Engine class method) PENDING (bsb.services.pool.JobStatus attribute) phase (bsb.services.pool.Workflow property) phases (bsb.services.pool.Workflow property) pick() (bsb.morphologies.selector.MorphologySelector method) (bsb.morphologies.selector.NameSelector method) ping() (bsb.services.pool.JobPool method) pipeline (bsb.storage._files.MorphologyDependencyNode attribute) place() (bsb.placement.arrays.ParallelArrayPlacement method) (bsb.placement.random.RandomPlacement method) (bsb.placement.strategy.Entities method) (bsb.placement.strategy.FixedPositions method) (bsb.placement.strategy.PlacementStrategy method) place_cells() (bsb.core.Scaffold method) (bsb.placement.strategy.PlacementStrategy method) placement (bsb.connectivity.strategy.HemitypeCollection property) (bsb.core.Scaffold property) PlacementError PlacementIndications (class in bsb.cell_types) PlacementIndicator (class in bsb.placement.indicator) PlacementJob (class in bsb.services.pool) PlacementRelationError PlacementSet (class in bsb.storage.interfaces) PlacementStrategy (class in bsb.placement.strategy)

PlacementWarning planar_density (bsb.cell_types.PlacementIndications attribute) plotting (bsb.cell_types.CellType attribute) Plotting (class in bsb.cell_types) pluggable() (in module bsb.config) PluginError point_vectors (bsb.morphologies.Branch property) points (bsb.morphologies.Branch property) (bsb.morphologies.SubTree property) pool_cache() (in module bsb.services.pool) POOL_STATUS_CHANGE (bsb.services.pool.PoolProgressReason attribute) PoolJobAddedProgress (class in bsb.services.pool) PoolJobUpdateProgress (class in bsb.services.pool) PoolProgress (class in bsb.services.pool) PoolProgressReason (class in bsb.services.pool) PoolStatus (class in bsb.services.pool) PoolStatusProgress (class in bsb.services.pool) positional (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) positions (bsb.placement.strategy.FixedPositions attribute) post_prepare (bsb.simulation.simulation.Simulation attribute) post_type (bsb.storage.interfaces.ConnectivitySet attribute) post_type_name (bsb.storage.interfaces.ConnectivitySet attribute) postprocess() (bsb.postprocessing.AfterConnectivityHook method) (bsb.postprocessing.AfterPlacementHook method) (bsb.postprocessing.BidirectionalContact method) (bsb.postprocessing.Relay method) (bsb.postprocessing.SpoofDetails method) postsynaptic (bsb.connectivity.geometric.morphology_shape_intersection.MorphologyToShapeIntersection attribute) (bsb.connectivity.geometric.shape_shape_intersection.ShapeToShapeIntersection attribute) (bsb.connectivity.strategy.ConnectionStrategy attribute) pre_type (bsb.storage.interfaces.ConnectivitySet attribute) pre_type_name (bsb.storage.interfaces.ConnectivitySet attribute) preexisted (bsb.storage.Storage property) preload() (bsb.storage.interfaces.MorphologyRepository method) prepare() (bsb.simulation.adapter.SimulatorAdapter method) presynaptic (bsb.connectivity.geometric.shape_morphology_intersection.ShapeToMorphologyIntersection attribute) (bsb.connectivity.geometric.shape_shape_intersection.ShapeToShapeIntersection attribute) (bsb.connectivity.strategy.ConnectionStrategy attribute) ProfilingOption (class in bsb.options) ProgressEvent (class in bsb.simulation.simulation) project (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) ProjectOptionDescriptor (class in bsb.option) properties (bsb.morphologies.SubTree property) (bsb.placement.distributor.DistributorsNode attribute) property() (in module bsb.config) provide() (in module bsb.config) provide_locally() (bsb.storage._files.FileDependency method) (bsb.storage._files.FileDependencyNode method) provide_stream() (bsb.storage._files.FileDependency method) (bsb.storage._files.FileDependencyNode method) (bsb.storage._files.FileScheme method) (bsb.storage._files.UriScheme method) (bsb.storage._files.UrlScheme method) pruning_ratio (bsb.connectivity.geometric.morphology_shape_intersection.MorphologyToShapeIntersection attribute) (bsb.connectivity.geometric.shape_morphology_intersection.ShapeToMorphologyIntersection attribute) (bsb.connectivity.geometric.shape_shape_intersection.ShapeToShapeIntersection attribute)

Q

query() (bsb.trees.BoxTreeInterface method) queue() (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.mixins.InvertedRoI method) (bsb.placement.arrays.ParallelArrayPlacement method) (bsb.placement.strategy.Entities method) (bsb.placement.strategy.FixedPositions method) (bsb.placement.strategy.PlacementStrategy method) (bsb.postprocessing.AfterConnectivityHook method) (bsb.postprocessing.AfterPlacementHook method) (bsb.services.pool.JobPool method) (bsb.storage._files.MorphologyDependencyNode method)

queue_connectivity() (bsb.services.pool.JobPool method) queue_placement() (bsb.services.pool.JobPool method) QUEUED (bsb.services.pool.JobStatus attribute)

R

radii (bsb.morphologies.Branch property) (bsb.morphologies.SubTree property) radius (bsb.cell_types.PlacementIndications attribute) (bsb.connectivity.geometric.geometric_shapes.Cone attribute) (bsb.connectivity.geometric.geometric_shapes.Cylinder attribute) (bsb.connectivity.geometric.geometric_shapes.Sphere attribute) (bsb.simulation.targetting.CylindricalTargetting attribute) (bsb.simulation.targetting.SphericalTargetting attribute) raise_unhandled() (bsb.services.pool.JobPool method) RandomMorphologies (class in bsb.placement.distributor) RandomPlacement (class in bsb.placement.random) RandomRotations (class in bsb.placement.distributor) rank (bsb.services.mpilock.MockedWindowController property) raw (bsb.voxels.VoxelSet property) read() (bsb.services.mpilock.MockedWindowController method) read_only() (bsb.storage.interfaces.Engine method) (bsb.storage.Storage method) read_option() (in module bsb.options) readonly (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) ReadOnlyManager (class in bsb.storage.interfaces) ReadOnlyOptionError readwrite() (bsb.storage.interfaces.Engine method) reason (bsb.services.pool.PoolProgress property) recognizes() (bsb.storage.interfaces.Engine static method) RedoError ref() (in module bsb.config) Reference (class in bsb.config.refs) reflist() (in module bsb.config) region (bsb.topology.partition.Partition property) Region (class in bsb.topology.region) RegionGroup (class in bsb.topology.region) regions (bsb.core.Scaffold property) register() (bsb.option.BsbOption class method) register_listener() (bsb.core.Scaffold method) register_option() (in module bsb.options) register_pool_cached_item() (bsb.core.Scaffold method) regular (bsb.voxels.VoxelSet property) ReificationError relative_to (bsb.cell_types.PlacementIndications attribute) Relay (class in bsb.postprocessing) remove() (bsb.storage.interfaces.Engine method) (bsb.storage.interfaces.FileStore method) (bsb.storage.Storage method) remove_listener() (bsb.core.Scaffold method) renew() (bsb.storage.Storage method) report() (in module bsb.reporting) ReportListener (class in bsb.core) RepresentativesTargetting (class in bsb.simulation.targetting) require() (bsb.storage.interfaces.ConnectivitySet method) (bsb.storage.interfaces.PlacementSet class method)

require_connectivity_set() (bsb.core.Scaffold method) (bsb.storage.Storage method) require_placement_set() (bsb.storage.Storage method) RequirementError reset_module_option() (in module bsb.options) resize() (bsb.core.Scaffold method) (bsb.voxels.VoxelSet method) resolve_uri() (bsb.storage._files.NeuroMorphoScheme method) (bsb.storage._files.UrlScheme method) result (bsb.services.pool.Job property) Rhomboid (class in bsb.topology.partition) RhomboidData (class in bsb.topology._layout) root (bsb.storage.interfaces.Engine property) (bsb.storage.interfaces.StorageNode attribute) (bsb.storage.Storage property) root() (in module bsb.config) root_rotate() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) root_slug (bsb.storage.interfaces.Engine property) (bsb.storage.Storage property) RootCommand (class in bsb.cli.commands) rotate() (bsb.connectivity.geometric.geometric_shapes.Cone method) (bsb.connectivity.geometric.geometric_shapes.Cuboid method) (bsb.connectivity.geometric.geometric_shapes.Cylinder method) (bsb.connectivity.geometric.geometric_shapes.Ellipsoid method) (bsb.connectivity.geometric.geometric_shapes.GeometricShape method) (bsb.connectivity.geometric.geometric_shapes.Parallelepiped method) (bsb.connectivity.geometric.geometric_shapes.Sphere method) (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) (bsb.topology.partition.Partition method) (bsb.topology.partition.Rhomboid method) (bsb.topology.partition.Voxels method) (bsb.topology.region.Region method) (bsb.topology.region.RegionGroup method) (bsb.topology.region.Stack method) RotationDistributor (class in bsb.placement.distributor) rotations (bsb.placement.distributor.DistributorsNode attribute) RotationSet (class in bsb.morphologies) RoundRobinMorphologies (class in bsb.placement.distributor) run() (bsb.services.pool.Job method) (bsb.simulation.adapter.SimulatorAdapter method) run_after_connectivity() (bsb.core.Scaffold method) run_after_placement() (bsb.core.Scaffold method) run_checkpoint() (bsb.simulation.adapter.FixedStepProgressController method) run_connectivity() (bsb.core.Scaffold method) run_hook() (in module bsb.config) run_pipelines() (bsb.core.Scaffold method) run_placement() (bsb.core.Scaffold method) run_placement_strategy() (bsb.core.Scaffold method) run_simulation() (bsb.core.Scaffold method) RUNNING (bsb.services.pool.JobStatus attribute)

S

satisfy_fractions() (bsb.simulation.targetting.FractionFilter method) save() (bsb.storage.interfaces.MorphologyRepository method) scaffold (bsb.cell_types.CellType attribute) (bsb.cell_types.PlacementIndications attribute) (bsb.cell_types.Plotting attribute) (bsb.config.Distribution attribute) (bsb.connectivity.strategy.ConnectionStrategy attribute) (bsb.connectivity.strategy.Hemitype attribute) (bsb.morphologies.selector.MorphologySelector attribute) (bsb.placement.strategy.PlacementStrategy attribute) (bsb.simulation.simulation.Simulation attribute) (bsb.storage._files.FileDependencyNode attribute) (bsb.topology.partition.Partition attribute) (bsb.topology.region.Region attribute) Scaffold (class in bsb.core) ScaffoldError ScaffoldWarning scalar_expand() (in module bsb.config.types) scale() (bsb.topology.partition.Partition method) (bsb.topology.partition.Rhomboid method) (bsb.topology.partition.Voxels method) (bsb.topology.region.Region method) (bsb.topology.region.RegionGroup method) (bsb.topology.region.Stack method) schedule() (bsb.services.pool.JobPool method) scheduling (bsb.services.pool.JobPool property) SCHEDULING (bsb.services.pool.PoolStatus attribute) script (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) ScriptOptionDescriptor (class in bsb.option) segments (bsb.morphologies.Branch property) select (bsb.morphologies.selector.MorphologySelector attribute) select() (bsb.storage.interfaces.MorphologyRepository method) SelectorError serialize() (bsb.services.pool.Job method) set_all_meta() (bsb.storage.interfaces.MorphologyRepository method) set_chunk_filter() (bsb.storage.interfaces.PlacementSet method) set_comm() (bsb.storage.interfaces.Engine method) set_exception() (bsb.services.pool.Job method) set_label_filter() (bsb.morphologies.Morphology method) (bsb.morphologies.MorphologySet method) (bsb.storage.interfaces.PlacementSet method) set_module_option() (in module bsb.options) set_morphology_label_filter() (bsb.storage.interfaces.PlacementSet method) set_properties() (bsb.morphologies.Branch method) set_result() (bsb.services.pool.Job method) setter() (bsb.options.ProfilingOption method) (bsb.options.SimulationProgress method) (bsb.options.VerbosityOption method) sf() (bsb.config.Distribution method) ShapeHemitype (class in bsb.connectivity.geometric.shape_shape_intersection) shapes (bsb.connectivity.geometric.geometric_shapes.ShapesComposition attribute) shapes_composition (bsb.connectivity.geometric.shape_shape_intersection.ShapeHemitype attribute) ShapesComposition (class in bsb.connectivity.geometric.geometric_shapes) ShapeToMorphologyIntersection (class in bsb.connectivity.geometric.shape_morphology_intersection) ShapeToShapeIntersection (class in bsb.connectivity.geometric.shape_shape_intersection) share() (bsb.services.mpilock.Fence method) shortform() (in module bsb.config.types) should_call_default() (bsb.config.ConfigurationAttribute method) should_update() (bsb.storage._files.FileDependency method) (bsb.storage._files.FileScheme method) (bsb.storage._files.UriScheme method) (bsb.storage._files.UrlScheme method) side_length_1 (bsb.connectivity.geometric.geometric_shapes.Cuboid attribute) side_length_2 (bsb.connectivity.geometric.geometric_shapes.Cuboid attribute) side_vector_1 (bsb.connectivity.geometric.geometric_shapes.Parallelepiped attribute) side_vector_2 (bsb.connectivity.geometric.geometric_shapes.Parallelepiped attribute) side_vector_3 (bsb.connectivity.geometric.geometric_shapes.Parallelepiped attribute) simplify() (bsb.morphologies.Branch method) (bsb.morphologies.Morphology method) simplify_branches() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) simulate() (bsb.simulation.adapter.SimulatorAdapter method) simulation (bsb.simulation.component.SimulationComponent property) Simulation (bsb.simulation.SimulationBackendPlugin attribute) (class in bsb.simulation.simulation) SimulationBackendPlugin (class in bsb.simulation) SimulationComponent (class in bsb.simulation.component) SimulationData (class in bsb.simulation.adapter) SimulationError

SimulationProgress (class in bsb.options) SimulationRecorder (class in bsb.simulation.results) SimulationResult (class in bsb.simulation.results) simulations (bsb.core.Scaffold property) simulator (bsb.simulation.simulation.Simulation attribute) SimulatorAdapter (class in bsb.simulation.adapter) single_write() (bsb.services.mpilock.MockedWindowController method) size (bsb.morphologies.Branch property) (bsb.morphologies.SubTree property) (bsb.voxels.VoxelSet property) skip_boundary_labels (bsb.morphologies.parsers.parser.BsbParser attribute) slot() (in module bsb.config) slug (bsb.option.CLIOptionDescriptor attribute) (bsb.option.EnvOptionDescriptor attribute) (bsb.option.ProjectOptionDescriptor attribute) (bsb.option.ScriptOptionDescriptor attribute) snap_to_grid() (bsb.voxels.VoxelSet method) SomaTargetting (class in bsb.simulation.targetting) sort_deps() (bsb.mixins.HasDependencies class method) source (bsb.topology.partition.NrrdVoxels attribute) SourceQualityError sources (bsb.topology.partition.NrrdVoxels attribute) space_origin (bsb.placement.distributor.VolumetricRotations attribute) spacing_x (bsb.placement.arrays.ParallelArrayPlacement attribute) sparse (bsb.topology.partition.NrrdVoxels attribute) spatial (bsb.cell_types.CellType attribute) Sphere (class in bsb.connectivity.geometric.geometric_shapes) SphericalTargetting (class in bsb.simulation.targetting) spiketrains (bsb.simulation.results.SimulationResult property) spoof_connections() (bsb.postprocessing.SpoofDetails method) SpoofDetails (class in bsb.postprocessing) Stack (class in bsb.topology.region) start (bsb.morphologies.Branch property) status (bsb.services.pool.Job property) (bsb.services.pool.JobPool property) (bsb.services.pool.PoolJobUpdateProgress property) (bsb.services.pool.PoolProgress property) storage (bsb.core.Scaffold property) Storage (class in bsb.storage) storage_cfg (bsb.core.Scaffold property) StorageError StorageNode (class in bsb.storage.interfaces) store() (bsb.storage.interfaces.FileStore method) store_active_config() (bsb.storage.interfaces.FileStore method) (bsb.storage.Storage method) store_content() (bsb.storage._files.FileDependency method) (bsb.storage._files.MorphologyDependencyNode method) store_object() (bsb.storage._files.MorphologyDependencyNode method) store_option() (in module bsb.options) store_value() (bsb.config.types.WeakInverter method) StoredFile (class in bsb.storage.interfaces) StoredMorphology (class in bsb.storage.interfaces) str() (in module bsb.config.types) strategy (bsb.connectivity.strategy.ConnectionStrategy attribute) (bsb.placement.distributor.Distributor attribute) (bsb.placement.distributor.MorphologyDistributor attribute) (bsb.placement.distributor.RotationDistributor attribute) (bsb.placement.strategy.PlacementStrategy attribute) (bsb.postprocessing.AfterConnectivityHook attribute) (bsb.postprocessing.AfterPlacementHook attribute) (bsb.simulation.targetting.LocationTargetting attribute) (bsb.simulation.targetting.Targetting attribute) strict (bsb.topology.partition.NrrdVoxels attribute) struct_id (bsb.topology.partition.AllenStructure attribute) struct_name (bsb.topology.partition.AllenStructure attribute) SubmissionContext (class in bsb.services.pool) submitter (bsb.services.pool.Job property) (bsb.services.pool.SubmissionContext property) SubTree (class in bsb.morphologies) subtree() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) SUCCESS (bsb.services.pool.JobStatus attribute) supports() (bsb.storage.Storage method) surface() (bsb.topology.partition.Partition method) (bsb.topology.partition.Rhomboid method) (bsb.topology.partition.Voxels method) surface_function() (bsb.connectivity.geometric.geometric_shapes.Sphere method) surface_point() (bsb.connectivity.geometric.geometric_shapes.Ellipsoid method) swap() (bsb.topology._layout.Layout method) swap_axes() (bsb.morphologies.Morphology method) sync() (bsb.services.mpilock.MPILockModule method) sync_config() (bsb.core.Scaffold method)

T

tag (bsb.simulation.connection.ConnectionModel attribute) (bsb.storage.interfaces.ConnectivitySet attribute) (bsb.storage.interfaces.PlacementSet property) tags (bsb.morphologies.parsers.parser.BsbParser attribute) Targetting (class in bsb.simulation.targetting) thickness (bsb.topology.partition.Layer attribute) to() (bsb.storage.interfaces.ConnectivityIterator method) to_chunks() (bsb.topology.partition.Partition method) (bsb.topology.partition.Rhomboid method) (bsb.topology.partition.Voxels method) to_graph_array() (bsb.morphologies.Morphology method) to_swc() (bsb.morphologies.Morphology method) to_voxels() (bsb.topology.partition.Partition method) top_center (bsb.connectivity.geometric.geometric_shapes.Cuboid attribute) (bsb.connectivity.geometric.geometric_shapes.Cylinder attribute) TopologyError translate() (bsb.connectivity.geometric.geometric_shapes.Cone method) (bsb.connectivity.geometric.geometric_shapes.Cuboid method) (bsb.connectivity.geometric.geometric_shapes.Cylinder method) (bsb.connectivity.geometric.geometric_shapes.Ellipsoid method) (bsb.connectivity.geometric.geometric_shapes.GeometricShape method) (bsb.connectivity.geometric.geometric_shapes.Parallelepiped method) (bsb.connectivity.geometric.geometric_shapes.ShapesComposition method) (bsb.connectivity.geometric.geometric_shapes.Sphere method) (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) (bsb.topology.partition.Partition method) (bsb.topology.partition.Rhomboid method) (bsb.topology.partition.Voxels method) (bsb.topology.region.Region method) (bsb.topology.region.RegionGroup method) (bsb.topology.region.Stack method)

tree() (bsb.config.ConfigurationAttribute method) tree_of() (bsb.config.ConfigurationAttribute method) TreeError type (bsb.connectivity.geometric.geometric_shapes.GeometricShape attribute) (bsb.simulation.parameter.Parameter attribute) (bsb.simulation.parameter.ParameterValue attribute) (bsb.simulation.targetting.CellTargetting attribute) (bsb.simulation.targetting.ConnectionTargetting attribute) (bsb.simulation.targetting.Targetting attribute) (bsb.topology.partition.Partition attribute) (bsb.topology.region.Region attribute) TypeHandler (class in bsb.config.types) TypeHandlingError

U

UnfitClassCastError unique() (bsb.voxels.VoxelSet method) UnknownConfigAttrError UnknownGIDError UnknownStorageEngineError UnmanagedPartitionError unregister() (bsb.option.BsbOption method) unregister_option() (in module bsb.options) UnresolvedClassCastError unset() (in module bsb.config) up() (bsb.config.refs.Reference method) update() (bsb.storage._files.FileDependency method)

update_all_meta() (bsb.storage.interfaces.MorphologyRepository method) uri (bsb.storage._files.FileDependency property) UriScheme (class in bsb.storage._files) UrlScheme (class in bsb.storage._files) use_action (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) use_bar() (bsb.simulation.adapter.FixedStepProgressController method) use_extend (bsb.options.ProfilingOption attribute) (bsb.options.SimulationProgress attribute) (bsb.options.VerbosityOption attribute) use_morphologies() (bsb.placement.indicator.PlacementIndicator method)

V

v0 (bsb.connectivity.geometric.geometric_shapes.Ellipsoid attribute) v1 (bsb.connectivity.geometric.geometric_shapes.Ellipsoid attribute) v2 (bsb.connectivity.geometric.geometric_shapes.Ellipsoid attribute) validate() (bsb.morphologies.selector.MorphologySelector method) (bsb.morphologies.selector.NameSelector method) value (bsb.simulation.parameter.Parameter attribute) vector (bsb.morphologies.Branch property) VerbosityOption (class in bsb.options) versions (bsb.storage.interfaces.Engine property) versor (bsb.morphologies.Branch property) view_support() (in module bsb.storage) volume (bsb.voxels.VoxelSet property) volume() (bsb.topology.partition.Partition method) (bsb.topology.partition.Rhomboid method) (bsb.topology.partition.Voxels method)

VolumetricRotations (class in bsb.placement.distributor) voxel_size (bsb.connectivity.geometric.geometric_shapes.ShapesComposition attribute) (bsb.topology.partition.AllenStructure attribute) (bsb.topology.partition.NrrdVoxels attribute) voxel_size() (in module bsb.config.types) VoxelData (class in bsb.voxels) VoxelIntersection (class in bsb.connectivity.detailed.voxel_intersection) voxelize() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) Voxels (class in bsb.topology.partition) voxels_post (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection attribute) voxels_pre (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection attribute) voxelset (bsb.topology.partition.Voxels property) VoxelSet (class in bsb.voxels) VoxelSetError

W

walk() (bsb.morphologies.Branch method) walk_node_attributes() (in module bsb.config) walk_nodes() (in module bsb.config) warn() (in module bsb.reporting) WeakInverter (class in bsb.config.types) width (bsb.topology._layout.RhomboidData property) window() (bsb.services.mpi.MPIService method) wireframe_points() (bsb.connectivity.geometric.geometric_shapes.Cone method) (bsb.connectivity.geometric.geometric_shapes.Cuboid method) (bsb.connectivity.geometric.geometric_shapes.Cylinder method) (bsb.connectivity.geometric.geometric_shapes.Ellipsoid method) (bsb.connectivity.geometric.geometric_shapes.GeometricShape method) (bsb.connectivity.geometric.geometric_shapes.Parallelepiped method) (bsb.connectivity.geometric.geometric_shapes.Sphere method)

workflow (bsb.services.pool.JobPool property) (bsb.services.pool.PoolProgress property) Workflow (class in bsb.services.pool) WorkflowError write() (bsb.services.mpilock.MockedWindowController method) (bsb.simulation.results.SimulationResult method)

X

x (bsb.simulation.targetting.BranchLocTargetting attribute) (bsb.topology._layout.RhomboidData property)

Y

y (bsb.topology._layout.RhomboidData property)

Z

z (bsb.topology._layout.RhomboidData property)