Morphology repositories¶

Morphology repositories (MRs) are an interface of the bsb.storage module and can be supported by the bsb.storage.interfaces.Engine so that morphologies can be stored inside the network storage.

To access an MR, a bsb.storage.Storage object is required:

from bsb import Storage

store = Storage("hdf5", "morphologies.hdf5")
mr = store.morphologies
print(mr.all())

Similarly, the built-in MR of a network is accessible as network.morphologies:

from bsb import from_storage

network = from_hdf("my_existing_model.hdf5")
mr = network.morphologies

You can use the bsb.storage.interfaces.MorphologyRepository.save() method to store Morphologies. If you don’t immediately need the whole morphology, you can bsb.storage.interfaces.MorphologyRepository.preload() it, otherwise you can load the entire thing with bsb.storage.interfaces.MorphologyRepository.load().

class bsb.storage.interfaces.MorphologyRepository(engine)[source]

abstractmethod all()[source]

Fetch all the stored morphologies.

Returns:: List of the stored morphologies.
Return type:: list[StoredMorphology]

abstractmethod get_all_meta()[source]

Get the metadata of all stored morphologies.

Returns:: Metadata dictionary
Return type:: dict

abstractmethod get_meta(name)[source]

Get the metadata of a stored morphology.

Parameters:: name (str) – Key of the stored morphology.
Returns:: Metadata dictionary
Return type:: dict

abstractmethod has(name)[source]

Check whether a morphology under the given name exists.

Parameters:: name (str) – Key of the stored morphology.
Returns:: Whether the key exists in the repo.
Return type:: bool

list()[source]: List all the names of the morphologies in the repository.

abstractmethod load(name)[source]

Load a stored morphology as a constructed morphology object.

Parameters:: name (str) – Key of the stored morphology.
Returns:: A morphology
Return type:: Morphology

abstractmethod preload(name)[source]

Load a stored morphology as a morphology loader.

Parameters:: name (str) – Key of the stored morphology.
Returns:: The stored morphology
Return type:: StoredMorphology

abstractmethod save(name, morphology, overwrite=False)[source]

Store a morphology.

Parameters:

name (str) – Key to store the morphology under.
morphology (bsb.morphologies.Morphology) – Morphology to store
overwrite (bool) – Overwrite any stored morphology that already exists under that name

Returns:

The stored morphology

Return type:

StoredMorphology

abstractmethod select(*selectors)[source]

Select stored morphologies.

Parameters:: selectors (list[bsb.morphologies.selector.MorphologySelector]) – Any number of morphology selectors.
Returns:: All stored morphologies that match at least one selector.
Return type:: list[StoredMorphology]

abstractmethod set_all_meta(all_meta)[source]

Set the metadata of all stored morphologies.

Parameters:: all_meta (dict) – Metadata dictionary.

abstractmethod update_all_meta(meta)[source]

Update the metadata of stored morphologies with the provided key values.

Parameters:: meta (str) – Metadata dictionary.