bsb.connectivity package

Subpackages

• bsb.connectivity.detailed package
  • Submodules
  • bsb.connectivity.detailed.fiber_intersection module
    • FiberIntersection
      • FiberIntersection.affinity
      • FiberIntersection.assert_voxelization()
      • FiberIntersection.connect()
      • FiberIntersection.contacts
      • FiberIntersection.get_node_name()
      • FiberIntersection.interpolate_branches()
      • FiberIntersection.intersect_voxel_tree()
      • FiberIntersection.resolution
      • FiberIntersection.to_plot
      • FiberIntersection.transformation
      • FiberIntersection.voxelize_branches()
    • FiberTransform
      • FiberTransform.boot()
      • FiberTransform.transform_branch()
      • FiberTransform.transform_branches()
    • QuiverTransform
      • QuiverTransform.casts
      • QuiverTransform.defaults
      • QuiverTransform.get_branch_direction()
      • QuiverTransform.transform_branch()
      • QuiverTransform.validate()
  • bsb.connectivity.detailed.shared module
    • Intersectional
      • Intersectional.affinity
      • Intersectional.candidate_intersection()
      • Intersectional.get_region_of_interest()
  • bsb.connectivity.detailed.touch_detection module
    • TouchDetector
      • TouchDetector.allow_zero_contacts
      • TouchDetector.cell_intersection_plane
      • TouchDetector.cell_intersection_radius
      • TouchDetector.compartment_intersection_plane
      • TouchDetector.compartment_intersection_radius
      • TouchDetector.connect()
      • TouchDetector.contacts
      • TouchDetector.get_compartment_intersections()
      • TouchDetector.get_node_name()
      • TouchDetector.get_search_radius()
      • TouchDetector.intersect_cells()
      • TouchDetector.intersect_compartments()
    • TouchInformation
  • bsb.connectivity.detailed.voxel_intersection module
    • VoxelIntersection
      • VoxelIntersection.cache
      • VoxelIntersection.connect()
      • VoxelIntersection.contacts
      • VoxelIntersection.favor_cache
      • VoxelIntersection.get_node_name()
      • VoxelIntersection.voxels_post
      • VoxelIntersection.voxels_pre
    • ichain()
  • Module contents

Submodules

bsb.connectivity.general module

class bsb.connectivity.general.AllToAll(*args, _parent=None, _key=None, **kwargs)

Bases: ConnectionStrategy

All to all connectivity between two neural populations

connect(pre, post)

get_region_of_interest(chunk)

class bsb.connectivity.general.Convergence(*args, _parent=None, _key=None, **kwargs)

Bases: ConnectionStrategy

Connect cells based on a convergence distribution, i.e. by connecting each source cell to X target cells.

connect()

convergence

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

get_node_name()

class bsb.connectivity.general.ExternalConnections(*args, _parent=None, _key=None, **kwargs)

Bases: ConnectionStrategy

Load the connection matrix from an external source.

casts = {'format': <class 'str'>, 'headers': <class 'bool'>, 'use_map': <class 'bool'>, 'warn_missing': <class 'bool'>}

check_external_source()

connect()

defaults = {'delimiter': ',', 'format': 'csv', 'headers': True, 'use_map': False, 'warn_missing': True}

get_external_source()

has_external_source = True

required = ['source']

validate()

class bsb.connectivity.general.FixedIndegree(*args, _parent=None, _key=None, **kwargs)

Bases: InvertedRoI, ConnectionStrategy

Connect a group of postsynaptic cell types to indegree uniformly random presynaptic cells from all the presynaptic cell types.

connect(pre, post)

get_node_name()

get_region_of_interest(chunk)

indegree

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

bsb.connectivity.strategy module

class bsb.connectivity.strategy.ConnectionStrategy(*args, _parent=None, _key=None, **kwargs)

Bases: ABC, SortableByAfter

after

Action to perform after connecting the neurons with the current strategy.

abstract connect(presyn_collection, postsyn_collection)

connect_cells(pre_set, post_set, src_locs, dest_locs, tag=None)

create_after()

get_after()

get_cell_types()

get_node_name()

classmethod get_ordered(objects)

abstract get_region_of_interest(chunk)

has_after()

name

Name used to refer to the connectivity strategy

postsynaptic

Postsynaptic (target) neuron population

presynaptic

Presynaptic (source) neuron population

queue(pool)

Specifies how to queue this connectivity strategy into a job pool. Can be overridden, the default implementation asks each partition to chunk itself and creates 1 placement job per chunk.

strategy

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

class bsb.connectivity.strategy.Hemitype(*args, _parent=None, _key=None, **kwargs)

Bases: object

Class used to represent one (pre- or postsynaptic) side of a connection rule.

cell_types

List of cell types to use in connection.

get_node_name()

labels

List of labels to filter the placement set by.

morpho_loader

Function to load the morphologies (MorphologySet) from a PlacementSet

morphology_labels

List of labels to filter the morphologies by.

class bsb.connectivity.strategy.HemitypeCollection(hemitype, roi)

Bases: object

property placement

Module contents