siibra.volumes.providers.nifti

Module Contents

Classes

NiftiProvider	Helper class that provides a standard way to create an ABC using
ZipContainedNiftiProvider	Helper class that provides a standard way to create an ABC using

class siibra.volumes.providers.nifti.NiftiProvider(src: str | Dict[str, str] | nibabel.Nifti1Image | Tuple[numpy.ndarray, numpy.ndarray])

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

property fragments

fetch(fragment: str = None, voi: siibra.locations.boundingbox.BoundingBox = None, label: int = None)

Loads and returns a Nifti1Image object

Parameters:

• fragment (str) – Optional name of a fragment volume to fetch, if any. For example, some volumes are split into left and right hemisphere fragments. see fragments()

• voi (BoundingBox) – optional specification of a volume of interest to fetch.

• label (int, default: None) – Optional: a label index can be provided. Then the mask of the 3D volume will be returned, where voxels matching this label are marked as “1”.

find_peaks(min_distance_mm=5)

Find peaks in the image data.

Parameters:

• min_distance_mm (float) – Minimum distance between peaks in mm

• Returns –

• -------- –

• PointSet –

get_boundingbox(clip=True, background=0, **fetch_kwargs) → siibra.locations.boundingbox.BoundingBox

Return the bounding box in physical coordinates of the union of fragments in this nifti volume.

Parameters:

• clip (bool, default: True) – Whether to clip the background of the volume.

• background (float, default: 0.0) – The background value to clip. .. note:: To use it, clip must be True.

• fetch_kwargs – Not used

get_shape(resolution_mm=None)

is_float()

class siibra.volumes.providers.nifti.ZipContainedNiftiProvider(src: str)

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