siibra.core.parcellation

Hierarchal brain regions and metadata.

Module Contents

Classes

Parcellation

Representation of a region with name and more optional attributes

ParcellationVersion

class siibra.core.parcellation.Parcellation(identifier: str, name: str, species: siibra.commons.Species | str, regions: List[siibra.core.region.Region] | siibra.core.region.Region = (), shortname: str = '', description: str = '', version: ParcellationVersion = None, modality: str = None, publications: list = [], datasets: list = [])
Inheritance diagram of siibra.core.parcellation.Parcellation

Representation of a region with name and more optional attributes

property id
property is_newest_version
__getitem__(regionspec: str | int)

Retrieve a region object from the parcellation by labelindex or partial name.

__lt__(other)

We sort parcellations by their version

static find_regions(region_spec: str, parents_only=True)

Find regions that match the given region specification in the subtree headed by each parcellation in the registry. .. note:

Use Region.find() to search for a region in an instance of a
parcellation.
Parameters:

  • regionspec (str) – a string with a possibly inexact name, which is matched both against the name and the identifier key,

  • parents_only (bool) – If true, children of matched parents will not be returned

Returns:

list of matching regions

Return type:

List[Region]

get_map(space=None, maptype: str | siibra.commons.MapType = MapType.LABELLED, spec: str = '')

Get the maps for the parcellation in the requested template space.

This might in general include multiple 3D volumes. For example, the Julich-Brain atlas provides two separate maps, one per hemisphere. Per default, multiple maps are concatenated into a 4D array, but you can choose to retrieve a dict of 3D volumes instead using return_dict=True.

Parameters:

  • space (Space or str) – template space specification

  • maptype (MapType) – Type of map requested (e.g., statistical or labelled). Use MapType.STATISTICAL to request probability maps. Defaults to MapType.LABELLED.

  • spec (str, optional) – In case of multiple matching maps for the given parcellation, space and type, use this field to specify keywords matching the desired parcellation map name. Otherwise, siibra will default to the first in the list of matches (and inform with a log message)

Returns:

A ParcellationMap representing the volumetric map or a SparseMap representing the list of statistical maps.

Return type:

parcellationmap.Map or SparseMap

get_region(regionspec: str | siibra.core.region.Region, find_topmost: bool = True, allow_tuple: bool = False)

Given a unique specification, return the corresponding region.

The spec could be a (possibly incomplete) name, or a region object. This method is meant to definitely determine a valid region. Therefore, if no match is found, it raises a ValueError. If multiple matches are found, the method tries to return only the common parent node. If there is no common parent, an exception is raised, except when allow_tuple=True - then a tuple of matched regions is returned.

Parameters:

  • regionspec (str, Region) –

    • a string with a possibly inexact name (matched both against the name and the identifier key)

    • a Region object

  • find_topmost (bool, default: True) – If True, will automatically return the parent of a decoded region the decoded region is its only child.

  • allow_tuple (bool, default: False) – If multiple candidates without a common parent are found, return a tuple of matches instead of raising an exception.

Returns:

A region object defined in the parcellation.

Note

If the spec exactly matched with more than one region, the first will be returned.

Return type:

Region

Raises:

  • RuntimeError – If the spec matches multiple regions

  • ValueError – If the spec cannot be matched against any region.

matches(spec)

Checks whether this region matches the given region specification.

Parameters:

regionspec (str, regex, Region) –

  • a string with a possibly inexact name, which is matched both against the name and the identifier key,

  • a regex applied to region names,

  • a region object

Returns:

If the regionspec matches to the Region.

Return type:

bool

class siibra.core.parcellation.ParcellationVersion(name, parcellation, collection=None, prev_id=None, next_id=None, deprecated=False)
__eq__(other)

Return self==value.

__iter__()
__lt__(other: ParcellationVersion)

< operator, useful for sorting by version FIXME: this is only by name, not recursing into parcellations, to avoid importing the registry here.

__repr__()

Return repr(self).

__str__()

Return str(self).