siibra.locations.pointset

A set of coordinates on a reference space.

Module Contents

Classes

PointSet

A set of 3D points in the same reference space,

Functions

from_points(→ PointSet)

Create a PointSet from an iterable of Points.
class siibra.locations.pointset.PointSet(coordinates: List[Tuple] | numpy.ndarray, space=None, sigma_mm: int | float | List[int | float] = 0, labels: List[int | float | tuple] = None)
Inheritance diagram of siibra.locations.pointset.PointSet

A set of 3D points in the same reference space, defined by a list of coordinates.

property boundingbox

Return the bounding box of these points. TODO revisit the numerical margin of 1e-6, should not be necessary.

property centroid
property coordinates: numpy.ndarray
property has_constant_sigma: bool
property homogeneous

Access the list of 3D point as an Nx4 array of homogeneous coordinates.

property label_colors

return a color for the given label.

property sigma: List[int | float]

The list of sigmas corresponding to the points.

property volume
__eq__(other: PointSet)

Required to provide comparison and making the object hashable

__getitem__(index: int)
__hash__()

Return hash(self).

__iter__()

Return an iterator over the coordinate locations.

__len__()

The number of points in this PointSet.

__str__()

Return str(self).

as_list()

Return the point set as a list of 3D tuples.

find_clusters(min_fraction=1 / 200, max_fraction=1 / 8)
intersection(other: siibra.locations.location.Location)

Return the subset of points that are inside the given mask.

NOTE: The affine matrix of the image must be set to warp voxels coordinates into the reference space of this Bounding Box.

transform(affine: numpy.ndarray, space=None)

Returns a new PointSet obtained by transforming the coordinates of this one with the given affine matrix.

Parameters:

  • affine (numpy 4x4 ndarray) – affine matrix

  • space (reference space (id, name, or Space)) – Target reference space which is reached after applying the transform. Note that the consistency of this cannot be checked and is up to the user.

warp(space, chunksize=1000)

Creates a new point set by warping its points to another space

siibra.locations.pointset.from_points(points: List[siibra.locations.point.Point], newlabels: List[int | float | tuple] = None) → PointSet

Create a PointSet from an iterable of Points.

Parameters:

  • points (Iterable[point.Point]) –

  • newlabels (List[int], optional) – Use these labels instead of the original labels of the points.

Return type:

PointSet