siibra.locations.point

Singular coordinate defined on a space, possibly with an uncertainty.

Classes

Point

A single 3D point in reference space.

Module Contents

class siibra.locations.point.Point(coordinatespec, space=None, sigma_mm: float = 0.0)
Inheritance diagram of siibra.locations.point.Point

A single 3D point in reference space.

bigbrain_section()

Estimate the histological section number of BigBrain which corresponds to this point. If the point is given in another space, a warping to BigBrain space will be tried.

contained_in(other: siibra.locations.location.Location | nibabel.Nifti1Image)
contains(other: siibra.locations.location.Location | nibabel.Nifti1Image)
get_enclosing_cube(width_mm)

Create a bounding box centered around this point with the given width.

intersection(other: siibra.locations.location.Location | nibabel.Nifti1Image) → Point

All subclasses of Location must implement intersection, as it is required by SpatialFeature._test_mask()

intersects(other: siibra.locations.location.Location | nibabel.Nifti1Image) → bool

Returns true if this point lies in 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.

static parse(spec, unit='mm') → Tuple[float, float, float]

Converts a 3D coordinate specification into a 3D tuple of floats.

Parameters:

  • spec (Any of str, tuple(float,float,float)) – For string specifications, comma separation with decimal points are expected.

  • unit (str) – specification of the unit (only ‘mm’ supported so far)

Return type:

tuple(float, float, float)

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

Returns a new Point obtained by transforming the coordinate of this one with the given affine matrix.

Parameters:

  • affine (numpy 4x4 ndarray) – affine matrix

  • space (str, Space, or None) –

    Target reference space which is reached after applying the transform

    Note

    The consistency of this cannot be checked and is up to the user.

warp(space)

Creates a new point by warping this point to another space

property boundingbox
coordinate
property homogeneous

The homogenous coordinate of this point as a 4-tuple, obtained by appending ‘1’ to the original 3-tuple.

property id: str
sigma = 0.0
property volume

The volume of a point can be nonzero if it has a location uncertainty.