Morphology repositories#

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

To access an MR, a Storage object is required:

from bsb.storage 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.core import from_storage

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

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

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

abstract all()[source]

Fetch all of the stored morphologies.

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

abstract get_all_meta()[source]: Get the metadata of all stored morphologies. :returns: Metadata dictionary :rtype: dict

abstract 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

abstract 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

import_arb(arbor_morpho, labels, name, overwrite=False, centering=True)[source]

Import and store an Arbor morphology object as a morphology in the repository.

Parameters:

arbor_morpho (arbor.morphology) – Arbor morphology.
name (str) – Key to store the morphology under.
overwrite (bool) – Overwrite any stored morphology that already exists under that name
centering (bool) – Whether the morphology should be centered on the geometric mean of the morphology roots. Usually the soma.

Returns:

The stored morphology

Return type:

StoredMorphology

import_file(file, name=None, overwrite=False)[source]

Import and store file contents as a morphology in the repository.

Parameters:

file – file-like object or path to the file.
name (str) – Key to store the morphology under.
overwrite (bool) – Overwrite any stored morphology that already exists under that name

Returns:

The stored morphology

Return type:

StoredMorphology

import_swc(file, name=None, overwrite=False)[source]

Import and store .swc file contents as a morphology in the repository.

Parameters:

file – file-like object or path to the file.
name (str) – Key to store the morphology under.
overwrite (bool) – Overwrite any stored morphology that already exists under that name

Returns:

The stored morphology

Return type:

StoredMorphology

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

abstract 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

abstract 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

abstract 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

abstract 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]

abstract set_all_meta(all_meta)[source]: Set the metadata of all stored morphologies. :param all_meta: Metadata dictionary. :type all_meta: dict

abstract update_all_meta(meta)[source]

Update the metadata of stored morphologies with the provided key values

Parameters:: meta (str) – Metadata dictionary.