Connectivity sets

The ConnectivitySet represents the ensemble of all connections established in your network. It is constructed from the bsb.storage.Storage and can be used to retrieve information about pre- and post-cell types, as well as the connections between them.

Retrieving a ConnectivitySet

It is possible to list all the ConnectivitySet stored in your scaffold, here, loaded from the network file "my_network.hdf5":

from bsb import from_storage

scaffold = from_storage("my_network.hdf5")

cs_list = scaffold.get_connectivity_sets()
for cs in cs_list:
  print (f"ConnectivitySet {cs.tag} has {len(cs)} connections")

Alternatively, is possible to load the set by its name:

cs = scaffold.get_connectivity_set("my_CS")

The cell type information is accessible through the attributes pre_type and post_type:

# Get the pre-/post-synaptic cell types
ct_pre = cs.pre_type
ct_pos = cs.pos_type

# Get the name of the pre-/post-synaptic cell types
print(f"My pre-type is {cs.pre_type_name}")
print(f"My post-type is {cs.post_type_name}")

Connections

A list of all the cell pairs for every ConnectivitySet can be loaded with the method bsb.storage.interfaces.ConnectivitySet.load_connections().

for (src_locs, dest_locs) in cs.load_connections():
    print(f"Cell id: {src_locs[0]} connects to cell {dest_locs[0]}")

Here, src_locs and dest_locs contains for each pair:

• the cell id

• the cell morphology branch id

• the cell morphology branch point id

Note

If the pre-/post-synaptic neuron does not have a morphology then their branch and point id in the connection is -1