siibra.volumes.volume

A specific mesh or 3D array.

Attributes

TypeDataset
VolumeData

Exceptions

ColorVolumeNotSupported

Method or function hasn't been implemented yet.

Classes

Subvolume	Wrapper class for exposing a z level of a 4D volume to be used like a 3D volume.
SubvolumeProvider	This provider wraps around an existing volume provider,
Volume	A volume is a specific mesh or 3D array,
VolumeProvider	Helper class that provides a standard way to create an ABC using

Module Contents

exception siibra.volumes.volume.ColorVolumeNotSupported

Method or function hasn’t been implemented yet.

class siibra.volumes.volume.Subvolume(parent_volume: Volume, z: int)

Wrapper class for exposing a z level of a 4D volume to be used like a 3D volume.

class siibra.volumes.volume.SubvolumeProvider(parent_provider: VolumeProvider, z: int)

This provider wraps around an existing volume provider, but is preconfigured to always fetch a fixed subvolume. The primary use is to provide a fixed z coordinate of a 4D volume provider as a 3D volume under the interface of a normal volume provider.

class UseCaching

fetch(**kwargs)

property boundingbox: siibra.locations.boundingbox.BoundingBox

provider

srctype

z

class siibra.volumes.volume.Volume(space_spec: dict, providers: List[VolumeProvider], name: str = '', variant: str = None, datasets: List[TypeDataset] = [])

A volume is a specific mesh or 3D array, which can be accessible via multiple providers in different formats.

fetch(format: str = None, **kwargs)

Fetch a volumetric or surface representation from one of the providers.

Parameters:

format (str, default=None) –

Requested format. If None, the first supported format matching in self.formats is tried, starting with volumetric formats. It can be explicitly specified as:

• ’surface’ or ‘mesh’ to fetch a surface format

• ’volumetric’ or ‘voxel’ to fetch a volumetric format

• supported format types, see SUPPORTED_FORMATS. This includes

’nii’, ‘zip/nii’, ‘neuroglancer/precomputed’, ‘gii-mesh’, ‘neuroglancer/precompmesh’, ‘gii-label’

Return type:

An image or mesh

IMAGE_FORMATS = ['nii', 'zip/nii', 'neuroglancer/precomputed']

MESH_FORMATS = ['neuroglancer/precompmesh', 'neuroglancer/precompmesh/surface', 'gii-mesh', 'gii-label',...

SUPPORTED_FORMATS = ['nii', 'zip/nii', 'neuroglancer/precomputed', 'neuroglancer/precompmesh',...

property boundingbox

datasets = []

property formats: Set[str]

property fragments: Dict[str, List[str]]

property name

Allows derived classes to implement a lazy name specification.

property providers

property provides_image

property provides_mesh

property space

variant = None

class siibra.volumes.volume.VolumeProvider

Helper class that provides a standard way to create an ABC using inheritance.

abstract fetch(*args, **kwargs) → VolumeData

property boundingbox: siibra.locations.boundingbox.BoundingBox

Abstractmethod:

property fragments: List[str]

siibra.volumes.volume.TypeDataset

siibra.volumes.volume.VolumeData