Placement sets

PlacementSets are constructed from the Storage and can be used to retrieve the positions, morphologies, rotations and additional datasets.

Note

Loading datasets from storage is an expensive operation. Store a local reference to the data you retrieve instead of making multiple calls.

Retrieving a PlacementSet

Multiple get_placement_set methods exist in several places as shortcuts to create the same PlacementSet. If the placement set does not exist, a DatesetNotFoundError is thrown.

from bsb import from_storage

network = from_storage("my_network.hdf5")
ps = network.get_placement_set("my_cell")
# Alternatives to obtain the same placement set:
ps = network.get_placement_set(network.cell_types.my_cell)
ps = network.cell_types.my_cell.get_placement_set()
ps = network.storage.get_placement_set(network.cell_types.my_cell)

Identifiers

Cells have no global identifiers, instead you use the indices of their data, i.e. the n-th position belongs to cell n, and so will the n-th rotation.

Positions

The positions of the cells can be retrieved using the load_positions() method.

for n, position in enumerate(ps.positions):
  print("I am", ps.tag, "number", n)
  print("My position is", position)

Morphologies

The positions of the cells can be retrieved using the load_morphologies() method.

for n, (pos, morpho) in enumerate(zip(ps.load_positions(), ps.load_morphologies())):
  print("I am", ps.tag, "number", n)
  print("My position is", position)

Warning

Loading morphologies is especially expensive.

load_morphologies() returns a MorphologySet. There are better ways to iterate over it using either soft caching or hard caching.

Rotations

The positions of the cells can be retrieved using the load_rotations() method.

Additional datasets

Not implemented yet.