Code

class cykdtree.PyKDTree

Construct a KDTree for a set of points.

Parameters:

• pts (np.ndarray of double) – (n,m) array of n coordinates in a m-dimensional domain.
• left_edge (np.ndarray of double) – (m,) domain minimum in each dimension.
• right_edge (np.ndarray of double) – (m,) domain maximum in each dimension.
• periodic (bool or np.ndarray of bool, optional) – Truth of the domain periodicity overall (if bool), or in each dimension (if np.ndarray). Defaults to False.
• leafsize (int, optional) – The maximum number of points that should be in a leaf. Defaults to 10000.
• nleaves (int, optional) – The number of leaves that should be in the resulting tree. If greater than 0, leafsize is adjusted to produce a tree with 2**(ceil(log2(nleaves))) leaves. Defaults to 0.

Raises:

ValueError – If leafsize < 2. This currectly segfaults.

npts

uint64 – Number of points in the tree.

ndim

uint32 – Number of dimensions points occupy.

num_leaves

uint32 – Number of leaves in the tree.

leafsize

uint32 – Maximum number of points a leaf can have.

leaves

list of cykdtree.PyNode – Tree leaves.

idx

np.ndarray of uint64 – Indices sorting the points by leaf.

left_edge

np.ndarray of double – (m,) domain minimum in each dimension.

right_edge

np.ndarray of double – (m,) domain maximum in each dimension.

domain_width

np.ndarray of double – (m,) domain width in each dimension.

periodic

np.ndarray of bool – Truth of domain periodicity in each dimension.

get()

Return the leaf containing a given position.

Parameters:pos (np.ndarray of double) – Coordinates. Returns:Leaf containing pos. Return type:cykdtree.PyNode Raises:ValueError – If pos is not contained withing the KDTree.

get_neighbor_ids()

Return the IDs of leaves containing & neighboring a given position.

Parameters:pos (np.ndarray of double) – Coordinates. Returns:Leaves containing/neighboring pos. Return type:np.ndarray of uint32 Raises:ValueError – If pos is not contained withing the KDTree.

leaf_idx()

Get array of indices for points in a leaf.

Parameters:leafid (np.uint32_t) – Unique index of the leaf in question. Returns:Indices of points belonging to leaf. Return type:np.ndarray of np.uint64_t

class cykdtree.PyNode

A container for leaf info.

npts

np.uint64_t – Number of points in this node.

ndim

np.uint32_t – Number of dimensions in domain.

num_leaves

np.uint32_t – Number of leaves in the tree containing this node.

start_idx

np.uint64_t – Index where indices for this node begin.

stop_idx

np.uint64_t – One passed the end of indices for this node.

left_edge

np.ndarray of float64 – Minimum bounds of this node in each dimension.

right_edge

np.ndarray of float64 – Maximum bounds of this node in each dimension.

periodic_left

np.ndarray of bool – Periodicity of minimum bounds.

periodic_right

np.ndarray of bool – Periodicity of maximum bounds.

domain_width

np.ndarray of float64 – Width of the total domain in each dimension.

left_neighbors

list of lists – Indices of neighbor leaves at the minimum bounds in each dimension.

right_neighbors

list of lists – Indices of neighbor leaves at the maximum bounds in each dimension.

neighbors

list of int – Indices of all neighboring leaves including this leaf.

slice

slice – Slice of kdtree indices contained by this node.

class cykdtree.PyKDTree

Construct a KDTree for a set of points.

Parameters:

• pts (np.ndarray of double) – (n,m) array of n coordinates in a m-dimensional domain.
• left_edge (np.ndarray of double) – (m,) domain minimum in each dimension.
• right_edge (np.ndarray of double) – (m,) domain maximum in each dimension.
• periodic (bool or np.ndarray of bool, optional) – Truth of the domain periodicity overall (if bool), or in each dimension (if np.ndarray). Defaults to False.
• leafsize (int, optional) – The maximum number of points that should be in a leaf. Defaults to 10000.
• nleaves (int, optional) – The number of leaves that should be in the resulting tree. If greater than 0, leafsize is adjusted to produce a tree with 2**(ceil(log2(nleaves))) leaves. Defaults to 0.

Raises:

ValueError – If leafsize < 2. This currectly segfaults.

npts

uint64 – Number of points in the tree.

ndim

uint32 – Number of dimensions points occupy.

num_leaves

uint32 – Number of leaves in the tree.

leafsize

uint32 – Maximum number of points a leaf can have.

leaves

list of cykdtree.PyNode – Tree leaves.

idx

np.ndarray of uint64 – Indices sorting the points by leaf.

left_edge

np.ndarray of double – (m,) domain minimum in each dimension.

right_edge

np.ndarray of double – (m,) domain maximum in each dimension.

domain_width

np.ndarray of double – (m,) domain width in each dimension.

periodic

np.ndarray of bool – Truth of domain periodicity in each dimension.

get()

Return the leaf containing a given position.

Parameters:pos (np.ndarray of double) – Coordinates. Returns:Leaf containing pos. Return type:cykdtree.PyNode Raises:ValueError – If pos is not contained withing the KDTree.

get_neighbor_ids()

Return the IDs of leaves containing & neighboring a given position.

Parameters:pos (np.ndarray of double) – Coordinates. Returns:Leaves containing/neighboring pos. Return type:np.ndarray of uint32 Raises:ValueError – If pos is not contained withing the KDTree.

leaf_idx()

Get array of indices for points in a leaf.

Parameters:leafid (np.uint32_t) – Unique index of the leaf in question. Returns:Indices of points belonging to leaf. Return type:np.ndarray of np.uint64_t

class cykdtree.PyNode

A container for leaf info.

npts

np.uint64_t – Number of points in this node.

ndim

np.uint32_t – Number of dimensions in domain.

num_leaves

np.uint32_t – Number of leaves in the tree containing this node.

start_idx

np.uint64_t – Index where indices for this node begin.

stop_idx

np.uint64_t – One passed the end of indices for this node.

left_edge

np.ndarray of float64 – Minimum bounds of this node in each dimension.

right_edge

np.ndarray of float64 – Maximum bounds of this node in each dimension.

periodic_left

np.ndarray of bool – Periodicity of minimum bounds.

periodic_right

np.ndarray of bool – Periodicity of maximum bounds.

domain_width

np.ndarray of float64 – Width of the total domain in each dimension.

left_neighbors

list of lists – Indices of neighbor leaves at the minimum bounds in each dimension.

right_neighbors

list of lists – Indices of neighbor leaves at the maximum bounds in each dimension.

neighbors

list of int – Indices of all neighboring leaves including this leaf.

slice

slice – Slice of kdtree indices contained by this node.