Using networks#

Greetings traveller, it seems you’ve created a network. Network files contain:

The configuration used to create them, so also all component definitions like cell types, topology, placement and connectivity blocks, and simulation config.
The morphologies that may be assigned to cells, their labels and properties.
The placement data such as positions, rotations, assigned morphologies and user-defined additional data.
The connectivity data that specifies which cells are connected, and the properties of those connections.

Here are some examples to help you on your way.

Creating networks#

Default network#

The default configuration contains a skeleton configuration, for an HDF5 storage, without any components in it. The file will be called something like scaffold_network_2022_06_29_10_10_10.hdf5, and will be created once you construct the Scaffold object:

from bsb.core import Scaffold

network = Scaffold()
network.compile()

Network from config#

You can also first load or create a config.Configuration object, and create a network from it, by passing it to the Scaffold:

from bsb.core import Scaffold
from bsb.config import Configuration

cfg = Configuration()
# Let's set a file name for the network
cfg.storage.root = "my_network.hdf5"
# And add a cell type
cfg.cell_types.add(
    "hero_cells",
    spatial=dict(
        radius=2,
        density=1e-3,
    ),
)

# After customizing your configuration, create a network from it.
network = Scaffold(cfg)
network.compile()

Loading a network from file#

You can load a stored network from file using bsb.core.from_storage():

from bsb.core import from_storage

network = from_storage("my_network.hdf5")

Accessing network data#

Configuration#

The configuration of a network is available as network.configuration, the root nodes such as cell_types, placement and others are available on network as well.

from bsb.core import from_storage

network = from_storage("network.hdf5")
print("My network was configured with", network.configuration)
print("My network has", len(network.configuration.cell_types), "cell types")
(
    # But to avoid some needless typing and repetition,
    network.cell_types is network.configuration.cell_types
    and network.placement is network.configuration.placement
    and "so on"
)

Placement data#

The placement data is available through the storage.interfaces.PlacementSet interface. This example shows how to access the cell positions of each population:

from bsb.core import from_storage
import numpy as np

network = from_storage("network.hdf5")
for cell_type in network.cell_types:
    ps = cell_type.get_placement_set()
    pos = ps.load_positions()
    print(len(pos), cell_type.name, "placed")
    # The positions are an (Nx3) numpy array
    print("The median cell is located at", np.median(pos, axis=0))