Index

A

accept() (bsb.topology._layout.Layout method) Adapter (bsb.simulation.SimulationBackendPlugin attribute) AdapterError AdaptiveNeighbourhood (class in bsb.placement.particle) add() (bsb.simulation.results.SimulationResult method) add_after() (bsb._util.SortableByAfter method) add_locals() (bsb.cli.commands.BaseCommand method) add_parser_arguments() (bsb.cli.commands.BaseCommand method) add_parser_options() (bsb.cli.commands.BaseCommand method) add_particle() (bsb.placement.particle.ParticleSystem method) add_particles() (bsb.placement.particle.ParticleSystem method) add_progress_listener() (bsb.simulation.simulation.Simulation 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.fiber_intersection.FiberIntersection attribute) (bsb.connectivity.detailed.shared.Intersectional attribute) after (bsb.connectivity.strategy.ConnectionStrategy attribute) (bsb.placement.strategy.PlacementStrategy attribute) after() (in module bsb.config) after_connectivity (bsb.config.Configuration attribute) (bsb.core.Scaffold property) after_connectivity() (bsb.postprocessing.BidirectionalContact method) (bsb.postprocessing.MissingAxon method) (bsb.postprocessing.PostProcessingHook method) (bsb.postprocessing.SpoofDetails method) after_placement (bsb.config.Configuration attribute) (bsb.core.Scaffold property) after_placement() (bsb.postprocessing.AscendingAxonLengths method) (bsb.postprocessing.DCNRotations method) (bsb.postprocessing.LabelMicrozones method) (bsb.postprocessing.PostProcessingHook method)

all() (bsb.storage.interfaces.ConnectivityIterator method) (bsb.storage.interfaces.FileStore method) (bsb.storage.interfaces.MorphologyRepository method) AllenApiError AllenStructure (class in bsb.topology.partition) allow_zero_contacts (bsb.connectivity.detailed.touch_detection.TouchDetector attribute) AllToAll (class in bsb.connectivity.general) angle (bsb.placement.arrays.ParallelArrayPlacement attribute) any_() (in module bsb.config.types) append_additional() (bsb.storage.interfaces.PlacementSet method) append_data() (bsb.storage.interfaces.PlacementSet method) ArborError 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) AscendingAxonLengths (class in bsb.postprocessing) assert_indication() (bsb.placement.indicator.PlacementIndicator method) assert_samelen() (in module bsb._util) assert_support() (bsb.storage.Storage method) assert_voxelization() (bsb.connectivity.detailed.fiber_intersection.FiberIntersection method) attach_child() (bsb.morphologies.Branch method) attr (bsb.core.Scaffold attribute) attr() (in module bsb.config) attr_name (bsb.config.Configuration attribute) AttributeMissingError axis (bsb.simulation.targetting.CylindricalTargetting attribute) (bsb.topology.partition.Layer attribute) (bsb.topology.region.Stack attribute)

B

BaseCommand (class in bsb.cli.commands) BaseParser (class in bsb.cli.commands) before() (in module bsb.config) BidirectionalContact (class in bsb.postprocessing) boot() (bsb.connectivity.detailed.fiber_intersection.FiberTransform method) (bsb.placement.satellite.Satellite method) BootError bounded (bsb.placement.particle.ParticlePlacement attribute) bounds (bsb.voxels.VoxelSet property) box (bsb.storage.Chunk 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_iter() (in module bsb.morphologies) branches (bsb.morphologies.SubTree property) broadcast() (bsb.simulation.simulation.Simulation method) bsb module bsb._util module bsb.cell_types module bsb.cli module bsb.cli.commands module bsb.config module bsb.config.parsers module bsb.config.parsers.json module bsb.config.parsers.yaml module bsb.config.refs module bsb.config.templates module bsb.config.types module bsb.connectivity module bsb.connectivity.detailed module bsb.connectivity.detailed.fiber_intersection module bsb.connectivity.detailed.shared module bsb.connectivity.detailed.touch_detection module bsb.connectivity.detailed.voxel_intersection module bsb.connectivity.general module bsb.connectivity.strategy module bsb.core module bsb.exceptions module bsb.mixins module bsb.morphologies 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.particle module bsb.placement.satellite module bsb.placement.strategy module bsb.plugins module bsb.postprocessing module bsb.reporting module bsb.services 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.results module bsb.simulation.simulation module bsb.simulation.targetting module bsb.storage 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) 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) candidate_intersection() (bsb.connectivity.detailed.shared.Intersectional method) CastConfigurationError CastError casts (bsb.connectivity.detailed.fiber_intersection.QuiverTransform attribute) (bsb.connectivity.general.ExternalConnections attribute) (bsb.postprocessing.SpoofDetails attribute) catch_all() (in module bsb.config) ceil_arc_point() (bsb.morphologies.Branch method) cell_intersection_plane (bsb.connectivity.detailed.touch_detection.TouchDetector attribute) cell_intersection_radius (bsb.connectivity.detailed.touch_detection.TouchDetector attribute) 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.config.Configuration attribute) (bsb.connectivity.strategy.Hemitype attribute) (bsb.core.Scaffold property) (bsb.placement.strategy.PlacementStrategy 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) CfgReferenceError check_external_source() (bsb.connectivity.general.ExternalConnections method) children (bsb.morphologies.Branch property) (bsb.topology._layout.Layout property) (bsb.topology.region.Region attribute) Chunk (class in bsb.storage) 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 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) CLIError CLIOptionDescriptor (class in bsb.option) close_gaps() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) CodeImportError collapse() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) collect() (bsb.simulation.adapter.SimulatorAdapter method) colliding() (bsb.placement.particle.Neighbourhood method) color (bsb.cell_types.Plotting attribute) comm (bsb.storage.interfaces.Engine property)

CommandError compartment_intersection_plane (bsb.connectivity.detailed.touch_detection.TouchDetector attribute) compartment_intersection_radius (bsb.connectivity.detailed.touch_detection.TouchDetector attribute) CompartmentError CompilationError compile() (bsb.core.Scaffold method) components (bsb.config.Configuration attribute) compose_nodes() (in module bsb.config) concatenate() (bsb.voxels.VoxelSet class method) ConfigTemplateNotFoundError configuration (bsb.core.Scaffold property) Configuration (class in bsb.config) ConfigurationAttribute (class in bsb.config) ConfigurationError ConfigurationFormatError ConfigurationWarning connect() (bsb.connectivity.detailed.fiber_intersection.FiberIntersection method) (bsb.connectivity.detailed.touch_detection.TouchDetector method) (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection method) (bsb.connectivity.general.AllToAll method) (bsb.connectivity.general.Convergence method) (bsb.connectivity.general.ExternalConnections method) (bsb.connectivity.general.FixedIndegree method) (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.storage.interfaces.ConnectivitySet method) connect_cells() (bsb.connectivity.strategy.ConnectionStrategy method) connection_models (bsb.simulation.simulation.Simulation attribute) connection_type (bsb.simulation.connection.ConnectionModel attribute) ConnectionModel (class in bsb.simulation.connection) ConnectionStrategy (class in bsb.connectivity.strategy) ConnectionTargetting (class in bsb.simulation.targetting) connectivity (bsb.config.Configuration attribute) (bsb.core.Scaffold property) ConnectivityError ConnectivityIterator (class in bsb.storage.interfaces) ConnectivitySet (class in bsb.storage.interfaces) ConnectivityWarning contacts (bsb.connectivity.detailed.fiber_intersection.FiberIntersection attribute) (bsb.connectivity.detailed.touch_detection.TouchDetector attribute) (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection attribute) contains_labels() (bsb.morphologies.Branch method) 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_template() (in module bsb.config) count (bsb.placement.indicator.PlacementIndications attribute) count_morphologies() (bsb.storage.interfaces.PlacementSet method) count_ratio (bsb.placement.indicator.PlacementIndications attribute) create() (bsb.storage.interfaces.ConnectivitySet class method) (bsb.storage.interfaces.Engine method) (bsb.storage.interfaces.PlacementSet class method) (bsb.storage.Storage method) create_after() (bsb._util.SortableByAfter method) (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.placement.strategy.PlacementStrategy method) (bsb.simulation.component.SimulationComponent method) create_engine() (in module bsb.storage) create_entities() (bsb.core.Scaffold method) create_recorder() (bsb.simulation.results.SimulationResult method) create_topology() (in module bsb.topology) CriticalDataWarning crop() (bsb.voxels.VoxelSet method) crop_chunk() (bsb.voxels.VoxelSet method) 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 DCNRotations (class in bsb.postprocessing) default() (bsb.config.Configuration class method) default_vector (bsb.placement.distributor.VolumetricRotations attribute) defaults (bsb.connectivity.detailed.fiber_intersection.QuiverTransform attribute) (bsb.connectivity.general.ExternalConnections attribute) deg_to_radian (class in bsb.config.types) deintersect() (bsb.placement.particle.ParticleSystem method) density (bsb.placement.indicator.PlacementIndications attribute) density_key (bsb.placement.indicator.PlacementIndications attribute) density_ratio (bsb.placement.indicator.PlacementIndications attribute) DependencyError depth (bsb.topology._layout.RhomboidData property) detach() (bsb.morphologies.Branch method) detach_child() (bsb.morphologies.Branch method) DeviceConnectionError DeviceModel (class in bsb.simulation.device) devices (bsb.simulation.simulation.Simulation attribute) dict() (in module bsb.config) (in module bsb.config.types) dimensions (bsb.storage.Chunk property) (bsb.topology._layout.RhomboidData property) (bsb.topology.partition.Rhomboid attribute)

discover() (in module bsb.plugins) discover_engines() (in module bsb.storage) displace() (bsb.placement.particle.Particle method) displace_by() (bsb.placement.particle.Particle method) display_name (bsb.cell_types.Plotting attribute) distance() (in module bsb.placement.particle) 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 (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) DryrunError duration (bsb.simulation.simulation.Simulation attribute) dynamic() (in module bsb.config) DynamicClassError DynamicClassInheritanceError DynamicObjectNotFoundError

E

empty() (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 (bsb.placement.strategy.Entities attribute) Entities (class in bsb.placement.strategy) entity (bsb.cell_types.CellType attribute) EnvOptionDescriptor (class in bsb.option) equilateral (bsb.voxels.VoxelSet property)

error() (bsb.cli.commands.BaseParser method) euclidean_dist (bsb.morphologies.Branch property) evaluation (class in bsb.config.types) execute() (bsb.services.JobPool method) execute_handler() (bsb.cli.commands.BaseCommand method) 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) ExternalConnections (class in bsb.connectivity.general) ExternalSourceError

F

favor_cache (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection attribute) FiberIntersection (class in bsb.connectivity.detailed.fiber_intersection) FiberTransform (class in bsb.connectivity.detailed.fiber_intersection) file() (in module bsb.config) files (bsb.core.Scaffold property) (bsb.storage.Storage property) FileStore (class in bsb.storage.interfaces) fill() (bsb.placement.particle.LargeParticleSystem method) (bsb.placement.particle.ParticleSystem method) (bsb.voxels.VoxelSet class method) find_closest_point() (bsb.morphologies.Branch method) find_colliding_particles() (bsb.placement.particle.ParticleSystem method) find_file() (bsb.storage.interfaces.FileStore method) find_files() (bsb.storage.interfaces.FileStore method) find_id() (bsb.storage.interfaces.FileStore method) find_meta() (bsb.storage.interfaces.FileStore method) find_neighbourhood() (bsb.placement.particle.AdaptiveNeighbourhood method) (bsb.placement.particle.ParticleSystem method) (bsb.placement.particle.SmallestNeighbourhood method) find_structure() (bsb.topology.partition.AllenStructure class method) FixedIndegree (class in bsb.connectivity.general) FixedPositions (class in bsb.placement.strategy) FixtureError flag_dirty() (bsb.config.ConfigurationAttribute method) flag_pristine() (bsb.config.ConfigurationAttribute method) 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_content() (in module bsb.config) fractal_dim (bsb.morphologies.Branch property) fraction() (in module bsb.config.types) freeze() (bsb.placement.particle.ParticleSystem method) from_() (bsb.storage.interfaces.ConnectivityIterator method) from_content() (in module bsb.config) from_file() (bsb.morphologies.Morphology class method) (in module bsb.config) from_id() (bsb.storage.Chunk class method) from_json() (in module bsb.config) from_morphology() (bsb.voxels.VoxelSet class method) from_storage() (in module bsb.core) from_swc() (bsb.morphologies.Morphology class method) from_swc_data() (bsb.morphologies.Morphology class method) from_yaml() (in module bsb.config) function_ (class in bsb.config.types)

G

GatewayError generate() (bsb.placement.distributor.MorphologyGenerator method) GeneratedMorphology (class in bsb.storage.interfaces) geometry (bsb.placement.indicator.PlacementIndications attribute) get() (bsb.option.BsbOption method) (bsb.storage.interfaces.FileStore method) (in module bsb.options) get_after() (bsb._util.SortableByAfter method) (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.placement.satellite.Satellite method) (bsb.placement.strategy.PlacementStrategy method) (bsb.simulation.component.SimulationComponent method) get_all_chunks() (bsb.storage.interfaces.PlacementSet method) get_all_meta() (bsb.storage.interfaces.MorphologyRepository method) get_arc_point() (bsb.morphologies.Branch method) get_axial_distances() (bsb.morphologies.Branch method) get_branch_direction() (bsb.connectivity.detailed.fiber_intersection.QuiverTransform 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.Storage method) get_cli_tags() (bsb.option.BsbOption method) get_compartment_intersections() (bsb.connectivity.detailed.touch_detection.TouchDetector method) get_config_attributes() (in module bsb.config) get_config_diagram() (bsb.core.Scaffold method) get_config_path() (in module bsb.config) get_connectivity() (bsb.core.Scaffold method) get_connectivity_set() (bsb.core.Scaffold method) (bsb.storage.Storage method) get_connectivity_sets() (bsb.core.Scaffold method) (bsb.simulation.simulation.Simulation method) (bsb.storage.Storage method) get_data() (bsb.voxels.VoxelSet method) get_default() (bsb.config.ConfigurationAttribute method) (bsb.option.BsbOption method) get_dependencies() (bsb.topology.partition.Rhomboid method) (bsb.topology.region.Region method) get_dependency_pipelines() (bsb.core.Scaffold method) get_displacement_force() (bsb.placement.particle.Particle static method) get_encoding() (bsb.storage.interfaces.FileStore method) get_engine_node() (in module bsb.storage) get_engines() (in module bsb.storage) get_external_source() (bsb.connectivity.general.ExternalConnections method) get_global_chunks() (bsb.storage.interfaces.ConnectivitySet method) get_hint() (bsb.config.ConfigurationAttribute method) get_indicators() (bsb.placement.strategy.PlacementStrategy 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_locations() (bsb.simulation.targetting.LocationTargetting method) (bsb.simulation.targetting.SomaTargetting method) get_mask() (bsb.topology.partition.NrrdVoxels method) get_meta() (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_mtime() (bsb.storage.interfaces.FileStore method) get_node_name() (bsb.cell_types.CellType method) (bsb.cell_types.Plotting method) (bsb.config.Configuration method) (bsb.config.ConfigurationAttribute method) (bsb.connectivity.detailed.fiber_intersection.FiberIntersection method) (bsb.connectivity.detailed.touch_detection.TouchDetector method) (bsb.connectivity.detailed.voxel_intersection.VoxelIntersection method) (bsb.connectivity.general.Convergence method) (bsb.connectivity.general.FixedIndegree method) (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.connectivity.strategy.Hemitype 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.indicator.PlacementIndications method) (bsb.placement.particle.ParticlePlacement method) (bsb.placement.particle.RandomPlacement method) (bsb.placement.satellite.Satellite method) (bsb.placement.strategy.FixedPositions method) (bsb.placement.strategy.PlacementStrategy method) (bsb.postprocessing.LabelMicrozones method) (bsb.postprocessing.PostProcessingHook method) (bsb.simulation.cell.CellModel method) (bsb.simulation.component.SimulationComponent method) (bsb.simulation.connection.ConnectionModel method) (bsb.simulation.device.DeviceModel method) (bsb.simulation.simulation.Simulation 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.LocationTargetting method) (bsb.simulation.targetting.RepresentativesTargetting method) (bsb.simulation.targetting.SomaTargetting method) (bsb.simulation.targetting.SphericalTargetting method) (bsb.simulation.targetting.Targetting 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_options() (bsb.cli.commands.BaseCommand method) (bsb.cli.commands.RootCommand method) (in module bsb.options) get_ordered() (bsb._util.SortableByAfter method) (bsb.connectivity.strategy.ConnectionStrategy class method) (bsb.placement.strategy.PlacementStrategy class method) (bsb.simulation.component.SimulationComponent class method) get_original() (bsb.config.types.evaluation method) get_overlap() (bsb.placement.particle.Neighbourhood method) get_owner() (bsb.services.JobPool class method) get_packing_factor() (bsb.placement.particle.ParticleSystem method) get_parser() (bsb.cli.commands.RootCommand method) (in module bsb.config) get_particle_trace() (in module bsb.placement.particle) get_particles_trace() (in module bsb.placement.particle) 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.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_qualified_class_name() (in module bsb._util) get_radius() (bsb.placement.indicator.PlacementIndicator method) get_rank() (bsb.simulation.simulation.Simulation method) get_raw() (bsb.voxels.VoxelSet method) get_region_of_interest() (bsb.connectivity.detailed.shared.Intersectional method) (bsb.connectivity.general.AllToAll method) (bsb.connectivity.general.FixedIndegree method) (bsb.connectivity.strategy.ConnectionStrategy method) get_report_file() (in module bsb.reporting) get_root_regions() (in module bsb.topology) get_search_radius() (bsb.connectivity.detailed.touch_detection.TouchDetector method) get_simulation() (bsb.core.Scaffold method) get_simulation_adapter() (in module bsb.simulation) get_size() (bsb.simulation.simulation.Simulation method) (bsb.voxels.VoxelSet method) get_size_matrix() (bsb.voxels.VoxelSet method) get_storage_diagram() (bsb.core.Scaffold 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_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_type() (bsb.config.ConfigurationAttribute method) get_voxelset() (bsb.topology.partition.NrrdVoxels method) (bsb.topology.partition.Voxels method) guess() (bsb.placement.indicator.PlacementIndicator method) (bsb.placement.satellite.SatelliteIndicator 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_after() (bsb._util.SortableByAfter method) (bsb.connectivity.strategy.ConnectionStrategy method) (bsb.placement.strategy.PlacementStrategy method) (bsb.simulation.component.SimulationComponent method)

has_data (bsb.voxels.VoxelSet property) has_external_source (bsb.connectivity.general.ExternalConnections attribute) has_hook() (in module bsb.config) height (bsb.topology._layout.RhomboidData property) Hemitype (class in bsb.connectivity.strategy) HemitypeCollection (class in bsb.connectivity.strategy)

I

ichain() (in module bsb._util) (in module bsb.connectivity.detailed.voxel_intersection) id (bsb.storage.Chunk property) ids (bsb.simulation.targetting.ByIdTargetting attribute) immutable() (in module bsb._util) Implicit (class in bsb.placement.distributor) ImplicitNoRotations (class in bsb.placement.distributor) import_arb() (bsb.storage.interfaces.MorphologyRepository method) import_file() (bsb.storage.interfaces.MorphologyRepository method) import_swc() (bsb.storage.interfaces.MorphologyRepository method) in_() (in module bsb.config.types) in_classmap() (in module bsb.config.types) in_notebook() (in module bsb.reporting) 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.satellite.Satellite attribute) (bsb.placement.strategy.PlacementStrategy attribute) IndicatorError init() (bsb.storage.Storage method) init_engines() (in module bsb.storage) init_placement() (bsb.storage.Storage method) InputError insert_branch() (bsb.morphologies.Branch method) inside() (bsb.voxels.VoxelSet method) int() (in module bsb.config.types)

Interface (class in bsb.storage.interfaces) interpolate_branches() (bsb.connectivity.detailed.fiber_intersection.FiberIntersection method) intersect_cells() (bsb.connectivity.detailed.touch_detection.TouchDetector method) intersect_compartments() (bsb.connectivity.detailed.touch_detection.TouchDetector method) intersect_voxel_tree() (bsb.connectivity.detailed.fiber_intersection.FiberIntersection method) Intersectional (class in bsb.connectivity.detailed.shared) IntersectionDataNotFoundError introduce_arc_point() (bsb.morphologies.Branch method) introduce_point() (bsb.morphologies.Branch method) InvalidReferenceError InvertedRoI (class in bsb.mixins) is_after_satisfied() (bsb._util.SortableByAfter method) is_dirty() (bsb.config.ConfigurationAttribute method) is_empty (bsb.voxels.VoxelSet property) is_entities() (bsb.placement.strategy.PlacementStrategy method) is_main_process() (bsb.core.Scaffold method) (bsb.storage.Storage method) is_master() (bsb.services.JobPool method) is_module_option_set() (in module bsb.options) is_node_type() (bsb.config.ConfigurationAttribute method) 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_morphologies() (bsb.morphologies.MorphologySet method)

J

JobPool (class in bsb.services) JsonImportError

JsonParseError JsonParser (class in bsb.config.parsers.json) JsonReferenceError

K

KernelLockedError KernelWarning

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) label_satellites() (bsb.postprocessing.LabelMicrozones method) LabelMicrozones (class in bsb.postprocessing) labels (bsb.connectivity.strategy.Hemitype attribute) (bsb.morphologies.Branch property) (bsb.simulation.targetting.ByLabelTargetting attribute) labelsets (bsb.morphologies.Branch property) (bsb.morphologies.Morphology property) LargeParticleSystem (class in bsb.placement.particle) Layer (class in bsb.topology.partition) Layout (class in bsb.topology._layout) LayoutError ldc (bsb.storage.Chunk property) (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) listify_input() (in module bsb._util) 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_ids() (bsb.storage.interfaces.PlacementSet method) load_local_connections() (bsb.storage.interfaces.ConnectivitySet method) load_morphologies() (bsb.storage.interfaces.PlacementSet method) load_positions() (bsb.storage.interfaces.PlacementSet method) load_root_command() (in module bsb.cli.commands) load_rotations() (bsb.storage.interfaces.PlacementSet method) LocationTargetting (class in bsb.simulation.targetting)

M

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) max_displacement (bsb.morphologies.Branch property) 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.storage.Chunk property) (bsb.topology.partition.Rhomboid property) merge() (bsb.config.parsers.json.parsed_dict method) (bsb.core.Scaffold method) merge_dicts() (in module bsb._util) meta (bsb.storage.interfaces.StoredFile property) method (class in bsb.config.types) method_shortcut (class in bsb.config.types) MissingAxon (class in bsb.postprocessing) MissingMorphologyError MissingSourceError module bsb bsb._util bsb.cell_types bsb.cli bsb.cli.commands bsb.config bsb.config.parsers bsb.config.parsers.json bsb.config.parsers.yaml bsb.config.refs bsb.config.templates bsb.config.types bsb.connectivity bsb.connectivity.detailed bsb.connectivity.detailed.fiber_intersection bsb.connectivity.detailed.shared bsb.connectivity.detailed.touch_detection bsb.connectivity.detailed.voxel_intersection bsb.connectivity.general bsb.connectivity.strategy bsb.core bsb.exceptions bsb.mixins bsb.morphologies bsb.morphologies.selector bsb.option bsb.options bsb.placement bsb.placement.arrays bsb.placement.distributor bsb.placement.indicator bsb.placement.particle bsb.placement.satellite bsb.placement.strategy bsb.plugins bsb.postprocessing bsb.reporting bsb.services bsb.simulation bsb.simulation.adapter bsb.simulation.cell bsb.simulation.component bsb.simulation.connection bsb.simulation.device bsb.simulation.results bsb.simulation.simulation bsb.simulation.targetting bsb.storage bsb.storage.interfaces bsb.topology bsb.topology._layout bsb.topology.partition bsb.topology.region bsb.trees bsb.voxels

morpho_loader (bsb.connectivity.strategy.Hemitype attribute) morphologies (bsb.cell_types.CellType property) (bsb.config.Configuration attribute) (bsb.core.Scaffold property) (bsb.placement.distributor.DistributorsNode attribute) (bsb.placement.indicator.PlacementIndications attribute) (bsb.storage.Storage property) Morphology (class in bsb.morphologies) morphology_labels (bsb.connectivity.strategy.Hemitype attribute) MorphologyDataError MorphologyDistributor (class in bsb.placement.distributor) MorphologyError MorphologyGenerator (class in bsb.placement.distributor) MorphologyRepository (class in bsb.storage.interfaces) MorphologyRepositoryError MorphologySelector (class in bsb.morphologies.selector) MorphologySet (class in bsb.morphologies) MorphologyWarning move() (bsb.storage.interfaces.Engine method) (bsb.storage.Storage method) MPI (in module bsb.services) MPILock (in module bsb.services) 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.config.Configuration attribute) (bsb.connectivity.strategy.ConnectionStrategy attribute) (bsb.placement.strategy.PlacementStrategy attribute) (bsb.simulation.component.SimulationComponent attribute) (bsb.simulation.simulation.Simulation attribute) (bsb.topology.partition.Partition attribute) (bsb.topology.region.Region attribute) names (bsb.morphologies.selector.NameSelector attribute) NameSelector (class in bsb.morphologies.selector) ndarray (class in bsb.config.types) Neighbourhood (class in bsb.placement.particle) nested_iter_connections() (bsb.storage.interfaces.ConnectivitySet method) NestError NestKernelError

NestModelError NestModuleError network (bsb.config.Configuration attribute) (bsb.core.Scaffold property) NetworkDescription (class in bsb.storage.interfaces) NeuroMorphoSelector (class in bsb.morphologies.selector) NeuronError node() (in module bsb.config) node_name (bsb.config.Configuration attribute) NodeNotFoundError NoneReferenceError NoopLock (class in bsb.storage.interfaces) NoReferenceAttributeSignal NotParallel (class in bsb.mixins) NotSupported (class in bsb.storage) NrrdVoxels (class in bsb.topology.partition) number() (in module bsb.config.types)

O

obj_str_insert() (in module bsb._util) object_ (class in bsb.config.types) of_equal_size (bsb.voxels.VoxelSet property) on() (in module bsb.config) one() (bsb.voxels.VoxelSet class method) opacity (bsb.cell_types.Plotting attribute) open_storage() (in module bsb.storage) OptionDescriptor (class in bsb.option) OptionError or_() (in module bsb.config.types)

OrderError orientation (bsb.topology.partition.Rhomboid attribute) orientation_path (bsb.placement.distributor.VolumetricRotations attribute) orientation_resolution (bsb.placement.distributor.VolumetricRotations attribute) origin (bsb.simulation.targetting.CylindricalTargetting attribute) (bsb.simulation.targetting.SphericalTargetting attribute) (bsb.topology.partition.Rhomboid attribute) outgoing() (bsb.storage.interfaces.ConnectivityIterator method) overrides (bsb.placement.strategy.PlacementStrategy attribute) owner (bsb.services.JobPool property)

P

PackingError PackingWarning parallel (bsb.services.JobPool property) ParallelArrayPlacement (class in bsb.placement.arrays) ParallelIntegrityError ParameterError parameters (bsb.simulation.cell.CellModel attribute) parse() (bsb.config.parsers.yaml.YAMLParser method) parsed_dict (class in bsb.config.parsers.json) parsed_list (class in bsb.config.parsers.json) Parser (class in bsb.config.parsers) ParserError Particle (class in bsb.placement.particle) ParticlePlacement (class in bsb.placement.particle) ParticleSystem (class in bsb.placement.particle) ParticleVoxel (class in bsb.placement.particle) Partition (class in bsb.topology.partition) PartitionData (class in bsb.topology._layout) partitions (bsb.config.Configuration attribute) (bsb.core.Scaffold property) (bsb.placement.distributor.DistributionContext attribute) (bsb.placement.satellite.Satellite attribute) (bsb.placement.strategy.PlacementStrategy attribute) path_length (bsb.morphologies.Branch property) (bsb.morphologies.SubTree property) peek_exists() (bsb.storage.interfaces.Engine class method) per_planet (bsb.placement.satellite.Satellite attribute) pick() (bsb.morphologies.selector.MorphologySelector method) (bsb.morphologies.selector.NameSelector method) place() (bsb.placement.arrays.ParallelArrayPlacement method) (bsb.placement.particle.ParticlePlacement method) (bsb.placement.particle.RandomPlacement method) (bsb.placement.satellite.Satellite 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) place_type() (bsb.placement.satellite.Satellite method) placement (bsb.config.Configuration attribute) (bsb.connectivity.strategy.HemitypeCollection property) (bsb.core.Scaffold property)

PlacementError PlacementIndications (class in bsb.placement.indicator) PlacementIndicator (class in bsb.placement.indicator) PlacementRelationError PlacementSet (class in bsb.storage.interfaces) PlacementStrategy (class in bsb.placement.strategy) PlacementWarning placing() (bsb.placement.particle.LargeParticleSystem method) planar_density (bsb.placement.indicator.PlacementIndications attribute) planet_types (bsb.placement.satellite.Satellite attribute) plot_detailed_system() (in module bsb.placement.particle) plot_particle_system() (in module bsb.placement.particle) 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) positions (bsb.placement.particle.ParticleSystem property) (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) PostProcessingHook (class in bsb.postprocessing) postsynaptic (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.strategy.ConnectionStrategy attribute) progress() (bsb.simulation.simulation.Simulation method) ProgressEvent (class in bsb.simulation.simulation) ProjectOptionDescriptor (class in bsb.option) properties (bsb.placement.distributor.DistributorsNode attribute) property() (in module bsb.config) provide() (in module bsb.config) prune (bsb.placement.particle.ParticlePlacement attribute) prune() (bsb.placement.particle.ParticleSystem method)

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.services.JobPool method)

queue_chunk() (bsb.services.JobPool method) queue_connectivity() (bsb.services.JobPool method) queue_placement() (bsb.services.JobPool method) QuiverFieldWarning QuiverTransform (class in bsb.connectivity.detailed.fiber_intersection)

R

radii (bsb.morphologies.Branch property) radius (bsb.placement.indicator.PlacementIndications attribute) (bsb.simulation.targetting.CylindricalTargetting attribute) (bsb.simulation.targetting.SphericalTargetting attribute) RandomMorphologies (class in bsb.placement.distributor) RandomPlacement (class in bsb.placement.particle) RandomRotations (class in bsb.placement.distributor) raw (bsb.voxels.VoxelSet property) read() (in module bsb.options) read_only() (bsb.storage.interfaces.Engine method) (bsb.storage.Storage method) ReadOnlyManager (class in bsb.storage.interfaces) ReadOnlyOptionError readwrite() (bsb.storage.interfaces.Engine method) ReceptorSpecificationError recognizes() (bsb.storage.interfaces.Engine method) RedoError ref() (in module bsb.config) 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.config.Configuration attribute) (bsb.core.Scaffold property) register() (bsb.option.BsbOption class method) register_engine() (in module bsb.storage) register_option() (in module bsb.options) register_service() (in module bsb.services) regular (bsb.voxels.VoxelSet property) ReificationError relative_to (bsb.placement.indicator.PlacementIndications attribute) remove() (bsb.storage.interfaces.Engine method) (bsb.storage.interfaces.FileStore method) (bsb.storage.Storage method) remove_particles() (bsb.placement.particle.ParticleSystem method) renew() (bsb.storage.Storage method) report() (in module bsb.reporting) ReportListener (class in bsb.core) RepositoryWarning 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) required (bsb.connectivity.general.ExternalConnections attribute) RequirementError reset_displacement() (bsb.placement.particle.Particle method) reset_module_option() (in module bsb.options) resize() (bsb.core.Scaffold method) (bsb.voxels.VoxelSet method) resolution (bsb.connectivity.detailed.fiber_intersection.FiberIntersection attribute) resolve_neighbourhood() (bsb.placement.particle.ParticleSystem method) resolve_order() (bsb._util.SortableByAfter class method) restrict (bsb.placement.particle.ParticlePlacement attribute) rev_merge() (bsb.config.parsers.json.parsed_dict method) 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.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) rotation_matrix_from_vectors() (in module bsb._util) 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.simulation.adapter.SimulatorAdapter method) run_after_connectivity() (bsb.core.Scaffold method) run_after_placement() (bsb.core.Scaffold 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)

S

sanitize_ndarray() (in module bsb._util) Satellite (class in bsb.placement.satellite) SatelliteIndicator (class in bsb.placement.satellite) satisfy_after() (bsb._util.SortableByAfter method) save() (bsb.storage.interfaces.MorphologyRepository method) 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) ScriptOptionDescriptor (class in bsb.option) segments (bsb.morphologies.Branch property) select (bsb.morphologies.selector.MorphologySelector attribute) select() (bsb.storage.interfaces.MorphologyRepository method) SelectorError set_all_meta() (bsb.storage.interfaces.MorphologyRepository method) set_chunk_filter() (bsb.storage.interfaces.PlacementSet method) set_comm() (bsb.storage.interfaces.Engine method) set_communicator() (bsb.simulation.adapter.SimulatorAdapter method) set_label_filter() (bsb.morphologies.Morphology method) (bsb.storage.interfaces.PlacementSet method) set_module_option() (in module bsb.options) set_morphology_label_filter() (bsb.storage.interfaces.PlacementSet method) set_report_file() (in module bsb.reporting) setup_reporting() (in module bsb.reporting) shortform() (in module bsb.config.types) should_call_default() (bsb.config.ConfigurationAttribute method) simplify() (bsb.morphologies.Branch method) simplify_branches() (bsb.morphologies.Branch method) (bsb.morphologies.SubTree method) simulate() (bsb.simulation.adapter.SimulatorAdapter method) Simulation (bsb.simulation.SimulationBackendPlugin attribute) (class in bsb.simulation.simulation) SimulationBackendPlugin (class in bsb.simulation) SimulationComponent (class in bsb.simulation.component) SimulationError SimulationRecorder (class in bsb.simulation.results) SimulationResult (class in bsb.simulation.results) simulations (bsb.config.Configuration attribute) (bsb.core.Scaffold property) SimulationWarning simulator (bsb.simulation.simulation.Simulation attribute) SimulatorAdapter (class in bsb.simulation.adapter) size (bsb.morphologies.Branch property) (bsb.voxels.VoxelSet property) slot() (in module bsb.config) slug (bsb.option.CLIOptionDescriptor attribute) (bsb.option.EnvOptionDescriptor attribute) (bsb.option.ProjectOptionDescriptor attribute) (bsb.option.ScriptOptionDescriptor attribute)

SmallestNeighbourhood (class in bsb.placement.particle) snap_to_grid() (bsb.voxels.VoxelSet method) solve_collisions() (bsb.placement.particle.LargeParticleSystem method) (bsb.placement.particle.ParticleSystem method) SomaTargetting (class in bsb.simulation.targetting) SortableByAfter (class in bsb._util) 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_volume() (in module bsb.placement.particle) SphericalTargetting (class in bsb.simulation.targetting) spoof_connections() (bsb.postprocessing.SpoofDetails method) SpoofDetails (class in bsb.postprocessing) Stack (class in bsb.topology.region) stack_index (bsb.topology.partition.Layer attribute) start (bsb.morphologies.Branch property) start_progress() (bsb.simulation.simulation.Simulation method) step_progress() (bsb.simulation.simulation.Simulation method) storage (bsb.config.Configuration attribute) (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) (in module bsb.options) store_active_config() (bsb.storage.interfaces.FileStore method) (bsb.storage.Storage method) 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.PostProcessingHook 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) SubTree (class in bsb.morphologies) SuffixTakenError supports() (bsb.storage.Storage method) suppress_stdout() (in module bsb._util) surface() (bsb.topology.partition.Partition method) (bsb.topology.partition.Rhomboid method) (bsb.topology.partition.Voxels method) swap() (bsb.topology._layout.Layout method)

T

tag (bsb.storage.interfaces.ConnectivitySet attribute) (bsb.storage.interfaces.PlacementSet property) targets (bsb.postprocessing.LabelMicrozones attribute) Targetting (class in bsb.simulation.targetting) TestError 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_plot (bsb.connectivity.detailed.fiber_intersection.FiberIntersection attribute) to_swc() (bsb.morphologies.Morphology method) TopologyError TouchDetector (class in bsb.connectivity.detailed.touch_detection) TouchInformation (class in bsb.connectivity.detailed.touch_detection) transform_branch() (bsb.connectivity.detailed.fiber_intersection.FiberTransform method) (bsb.connectivity.detailed.fiber_intersection.QuiverTransform method)

transform_branches() (bsb.connectivity.detailed.fiber_intersection.FiberTransform method) transformation (bsb.connectivity.detailed.fiber_intersection.FiberIntersection attribute) translate() (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) TransmitterError tree() (bsb.config.ConfigurationAttribute method) TreeError type (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) (in module bsb._util) UnknownConfigAttrError UnknownGIDError UnknownStorageEngineError UnmanagedPartitionError

unregister() (bsb.option.BsbOption method) unregister_option() (in module bsb.options) UnresolvedClassCastError unset() (in module bsb.config) update_all_meta() (bsb.storage.interfaces.MorphologyRepository method) use_morphologies() (bsb.placement.indicator.PlacementIndicator method) UserUserDeprecationWarning

V

validate() (bsb.connectivity.detailed.fiber_intersection.QuiverTransform method) (bsb.connectivity.general.ExternalConnections method) (bsb.morphologies.selector.MorphologySelector method) (bsb.morphologies.selector.NameSelector method) (bsb.postprocessing.MissingAxon method) vector (bsb.morphologies.Branch 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) volume_scale (bsb.topology.partition.Layer attribute) VolumetricRotations (class in bsb.placement.distributor)

voxel_size (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) voxelize_branches() (bsb.connectivity.detailed.fiber_intersection.FiberIntersection 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)

warning_on_one_line() (in module bsb.reporting) WeakInverter (class in bsb.config.types) width (bsb.topology._layout.RhomboidData property) wrap_autoflush_stream() (in module bsb.reporting) write() (bsb.simulation.results.SimulationResult method)

X

x (bsb.topology._layout.RhomboidData property)

Y

y (bsb.topology._layout.RhomboidData property)

YAMLParser (class in bsb.config.parsers.yaml)

Z

z (bsb.topology._layout.RhomboidData property)