bsb.connectivity.detailed package

Submodules

bsb.connectivity.detailed.fiber_intersection module

class bsb.connectivity.detailed.fiber_intersection.FiberIntersection(*args, _parent=None, _key=None, **kwargs)

Bases: Intersectional, ConnectionStrategy

FiberIntersection connection strategies voxelize a fiber and find its intersections with postsynaptic cells. It’s a specific case of VoxelIntersection.

For each presynaptic cell, the following steps are executed:

1. Extract the FiberMorphology

2. Interpolate points on the fiber until the spatial resolution is respected

3. transform

4. Interpolate points on the fiber until the spatial resolution is respected

5. Voxelize (generates the voxel_tree associated to this morphology)

6. Check intersections of presyn bounding box with all postsyn boxes

7. Check intersections of each candidate postsyn with current presyn voxel_tree

affinity

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

assert_voxelization(morphology, compartment_types)

connect()

contacts

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

get_node_name()

interpolate_branches(branches)

intersect_voxel_tree(from_voxel_tree, to_cloud, to_pos)

Similarly to intersect_clouds from VoxelIntersection, it finds intersecting voxels between a from_voxel_tree and a to_cloud set of voxels

Parameters:

• from_voxel_tree – tree built from the voxelization of all branches in the fiber (in absolute coordinates)

• to_cloud (VoxelCloud) – voxel cloud associated to a to_cell morphology

• to_pos (list) – 3-D position of to_cell neuron

resolution

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

to_plot

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

transformation

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

voxelize_branches(branches, position, bounding_box=None, voxel_tree=None, map=None, voxel_list=None)

class bsb.connectivity.detailed.fiber_intersection.FiberTransform

Bases: ABC

boot()

abstract transform_branch()

transform_branches(branches, offset=None)

class bsb.connectivity.detailed.fiber_intersection.QuiverTransform

Bases: FiberTransform

QuiverTransform applies transformation to a FiberMorphology, based on an orientation field in a voxelized volume. Used for parallel fibers.

casts = {'vol_res': <class 'float'>}

defaults = {'quivers': None, 'vol_res': 10.0, 'vol_start': [0.0, 0.0, 0.0]}

get_branch_direction(branch)

transform_branch(branch, offset)

Compute bending transformation of a fiber branch (discretized according to original compartments and configured resolution value). The transformation is a rotation of each segment/compartment of each fiber branch to align to the cross product between the orientation vector and the transversal direction vector (i.e. cross product between fiber morphology/parent branch orientation and branch direction): compartment[n+1].start = compartment[n].end cross_prod = orientation_vector X transversal_vector or transversal_vector X orientation_vector compartment[n+1].end = compartment[n+1].start + cross_prod * length_comp

Parameters:

branch (:~class:.morphologies.Branch) – a branch of the current fiber to be transformed

Returns:

a transformed branch

Return type:

:~class:.morphologies.Branch

validate()

bsb.connectivity.detailed.shared module

class bsb.connectivity.detailed.shared.Intersectional

Bases: object

affinity

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

candidate_intersection(target_coll, candidate_coll)

get_region_of_interest(chunk)

bsb.connectivity.detailed.touch_detection module

class bsb.connectivity.detailed.touch_detection.TouchDetector(*args, _parent=None, _key=None, **kwargs)

Bases: Intersectional, ConnectionStrategy

Connectivity based on intersection of detailed morphologies

allow_zero_contacts

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

cell_intersection_plane

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

cell_intersection_radius

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

compartment_intersection_plane

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

compartment_intersection_radius

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

connect(pre, post)

contacts

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

get_compartment_intersections(touch_info, from_pos, to_pos)

get_node_name()

get_search_radius(cell_type)

intersect_cells(touch_info)

intersect_compartments(touch_info, candidate_map)

class bsb.connectivity.detailed.touch_detection.TouchInformation(from_cell_type, from_cell_compartments, to_cell_type, to_cell_compartments)

Bases: object

bsb.connectivity.detailed.voxel_intersection module

class bsb.connectivity.detailed.voxel_intersection.VoxelIntersection(*args, _parent=None, _key=None, **kwargs)

Bases: Intersectional, ConnectionStrategy

This strategy finds overlap between voxelized morphologies.

cache

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

connect(pre, post)

contacts

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

favor_cache

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

get_node_name()

voxels_post

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

voxels_pre

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

bsb.connectivity.detailed.voxel_intersection.ichain(iterable, /)

Alternative chain() constructor taking a single iterable argument that evaluates lazily.

Module contents