src.object package

Submodules

src.object.function module

class src.object.function.Coordinate(*args, **metadata)

Bases: CoordinateMixin, ABC

Parameters:

• args (Any)

• metadata (Metadata)

class src.object.function.CoordinateMixin(*args, **metadata)

Bases: FunctionMixin, ABC

Parameters:

• args (Any)

• metadata (Metadata)

class src.object.function.Degree(*args, **metadata)

Bases: DegreeMixin, DenseArray

Parameters:

• args (Any)

• metadata (Metadata)

class src.object.function.DegreeMixin(*args, **metadata)

Bases: FunctionMixin, ABC

Parameters:

• args (Any)

• metadata (Metadata)

class src.object.function.FunctionMixin(*args, **metadata)

Bases: ObjectMixin, ABC

Parameters:

• args (Any)

• metadata (Metadata)

fixed_dtype

alias of float64

fixed_ndim: int = 2

metadata: Metadata

property nfuncs: int

property npts: int

class src.object.function.KNNDistance(*args, **metadata)

Bases: KNNDistanceMixin, DenseArray

Parameters:

• args (Any)

• metadata (Any)

class src.object.function.KNNDistanceMixin(*args, **metadata)

Bases: FunctionMixin, ABC

Parameters:

• args (Any)

• metadata (Any)

class src.object.function.LocalDistortion(*args, **metadata)

Bases: LocalDistortionMixin, DenseArray

Parameters:

• args (Any)

• metadata (Any)

class src.object.function.LocalDistortionMixin(*args, **metadata)

Bases: FunctionMixin, ABC

Parameters:

• args (Any)

• metadata (Any)

class src.object.function.NeighborCount(*args, **metadata)

Bases: NeighborCountMixin, DenseArray

Parameters:

• args (Any)

• metadata (Any)

class src.object.function.NeighborCountMixin(*args, **metadata)

Bases: FunctionMixin, ABC

Parameters:

• args (Any)

• metadata (Any)

fixed_dtype

alias of int64

src.object.geometry_matrix_mixin module

class src.object.geometry_matrix_mixin.GeometryMatrixMixin(*args, **metadata)

Bases: ObjectMixin, ABC

Mixin class providing common functionality for geometry-related matrices.

Adds default dimensionality of 2 of and default dtype of np.float64, along with convenience properties for querying matrix shape and point counts. Typically used as a base for distance, affinity, and Laplacian matrices.

Parameters:

• args (Any)

• metadata (Metadata)

fixed_dtype

alias of float64

fixed_ndim: int = 2

property from_npts: int

Number of points corresponding to the rows of the matrix.

Returns:

Number of rows in the matrix.

Return type:

int

property is_square: bool

Check if the matrix is square (number of rows equals number of columns).

Returns:

True if the matrix is square, False otherwise.

Return type:

bool

metadata: Metadata

property npts: int

Number of points in the matrix, assuming it is square.

Returns:

Number of points (rows or columns) if the matrix is square.

Return type:

int

Raises:

ValueError – If the matrix is not square.

property to_npts: int

Number of points corresponding to the columns of the matrix.

Returns:

Number of columns in the matrix.

Return type:

int

src.object.metadata module

class src.object.metadata.Metadata(name=None, dist_type=None, aff_type=None, lap_type=None, radius=None, eps=None, ks=None, radii=None, ds=None, degree_type=None, aff_minus_id=None)

Bases: object

Parameters:

• name (str | None)

• dist_type (Literal['euclidean', 'cityblock', 'sqeuclidean'] | None)

• aff_type (Literal['gaussian'] | None)

• lap_type (Literal['geometric', 'random_walk', 'symmetric'] | None)

• radius (float | None)

• eps (float | None)

• ks (Tuple[int, ...] | None)

• radii (Tuple[float, ...] | None)

• ds (Tuple[int, ...] | None)

• degree_type (Literal['adjacency', 'affinity'] | None)

• aff_minus_id (bool | None)

aff_minus_id: bool | None

aff_type: Literal['gaussian'] | None

degree_type: Literal['adjacency', 'affinity'] | None

dist_type: Literal['euclidean', 'cityblock', 'sqeuclidean'] | None

ds: Tuple[int, ...] | None

eps: float | None

ks: Tuple[int, ...] | None

lap_type: Literal['geometric', 'random_walk', 'symmetric'] | None

name: str | None

radii: Tuple[float, ...] | None

radius: float | None

update_with(other)

Return a new Metadata with non-None values from ‘other’ overriding self.

Parameters:

other (Metadata)

Return type:

Metadata

src.object.metadata.optional_tuple_of_floats(instance, attribute, value)

Parameters:

• instance (object)

• attribute (Attribute)

• value (Tuple[float, ...] | None)

Return type:

None

src.object.metadata.optional_tuple_of_ints(instance, attribute, value)

Parameters:

• instance (object)

• attribute (Attribute)

• value (Tuple[int, ...] | None)

Return type:

None

src.object.object_mixin module

class src.object.object_mixin.ObjectMixin(*args, **kwargs)

Bases: BaseArray, ABC

Abstract base class providing metadata handling and type/dimension validation.

Parameters:

• args (Any)

• kwargs (Any)

fixed_dtype: Type[np.generic]

fixed_ndim: int

metadata: Metadata

Module contents

class src.object.FunctionMixin(*args, **metadata)

Bases: ObjectMixin, ABC

Parameters:

• args (Any)

• metadata (Any)

fixed_dtype

alias of float64

fixed_ndim: int = 2

metadata: Metadata

property nfuncs: int

property npts: int

class src.object.GeometryMatrixMixin(*args, **metadata)

Bases: ObjectMixin, ABC

Mixin class providing common functionality for geometry-related matrices.

Adds default dimensionality of 2 of and default dtype of np.float64, along with convenience properties for querying matrix shape and point counts. Typically used as a base for distance, affinity, and Laplacian matrices.

Parameters:

• args (Any)

• metadata (Any)

fixed_dtype

alias of float64

fixed_ndim: int = 2

property from_npts: int

Number of points corresponding to the rows of the matrix.

Returns:

Number of rows in the matrix.

Return type:

int

property is_square: bool

Check if the matrix is square (number of rows equals number of columns).

Returns:

True if the matrix is square, False otherwise.

Return type:

bool

metadata: Metadata

property npts: int

Number of points in the matrix, assuming it is square.

Returns:

Number of points (rows or columns) if the matrix is square.

Return type:

int

Raises:

ValueError – If the matrix is not square.

property to_npts: int

Number of points corresponding to the columns of the matrix.

Returns:

Number of columns in the matrix.

Return type:

int

class src.object.Metadata(name=None, dist_type=None, aff_type=None, lap_type=None, radius=None, eps=None, ks=None, radii=None, ds=None, degree_type=None, aff_minus_id=None)

Bases: object

Parameters:

• name (str | None)

• dist_type (Literal['euclidean', 'cityblock', 'sqeuclidean'] | None)

• aff_type (Literal['gaussian'] | None)

• lap_type (Literal['geometric', 'random_walk', 'symmetric'] | None)

• radius (float | None)

• eps (float | None)

• ks (Tuple[int, ...] | None)

• radii (Tuple[float, ...] | None)

• ds (Tuple[int, ...] | None)

• degree_type (Literal['adjacency', 'affinity'] | None)

• aff_minus_id (bool | None)

aff_minus_id: bool | None

aff_type: Literal['gaussian'] | None

degree_type: Literal['adjacency', 'affinity'] | None

dist_type: Literal['euclidean', 'cityblock', 'sqeuclidean'] | None

ds: Tuple[int, ...] | None

eps: float | None

ks: Tuple[int, ...] | None

lap_type: Literal['geometric', 'random_walk', 'symmetric'] | None

name: str | None

radii: Tuple[float, ...] | None

radius: float | None

update_with(other)

Return a new Metadata with non-None values from ‘other’ overriding self.

Parameters:

other (Metadata)

Return type:

Metadata

class src.object.ObjectMixin(*args, **kwargs)

Bases: BaseArray, ABC

Abstract base class providing metadata handling and type/dimension validation.

Parameters:

• args (Any)

• kwargs (Any)

fixed_dtype: Type[np.generic]

fixed_ndim: int

metadata: Metadata