siibra.volumes.nifti

Handles reading and preparing nifti files.

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

Module Contents

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

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

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_shape(resolution_mm=None)

is_float()

property boundingbox

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

property fragments

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

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