102 lines
4.4 KiB
Cython
102 lines
4.4 KiB
Cython
# cython: boundscheck=False
|
|
# cython: wraparound=False
|
|
# cython: cdivision=True
|
|
#
|
|
# Author: Thomas Moreau <thomas.moreau.2010@gmail.com>
|
|
# Author: Olivier Grisel <olivier.grisel@ensta.fr>
|
|
|
|
# See quad_tree.pyx for details.
|
|
|
|
import numpy as np
|
|
cimport numpy as np
|
|
|
|
ctypedef np.npy_float32 DTYPE_t # Type of X
|
|
ctypedef np.npy_intp SIZE_t # Type for indices and counters
|
|
ctypedef np.npy_int32 INT32_t # Signed 32 bit integer
|
|
ctypedef np.npy_uint32 UINT32_t # Unsigned 32 bit integer
|
|
|
|
# This is effectively an ifdef statement in Cython
|
|
# It allows us to write printf debugging lines
|
|
# and remove them at compile time
|
|
cdef enum:
|
|
DEBUGFLAG = 0
|
|
|
|
cdef float EPSILON = 1e-6
|
|
|
|
# XXX: Careful to not change the order of the arguments. It is important to
|
|
# have is_leaf and max_width consecutive as it permits to avoid padding by
|
|
# the compiler and keep the size coherent for both C and numpy data structures.
|
|
cdef struct Cell:
|
|
# Base storage structure for cells in a QuadTree object
|
|
|
|
# Tree structure
|
|
SIZE_t parent # Parent cell of this cell
|
|
SIZE_t[8] children # Array pointing to childrens of this cell
|
|
|
|
# Cell description
|
|
SIZE_t cell_id # Id of the cell in the cells array in the Tree
|
|
SIZE_t point_index # Index of the point at this cell (only defined
|
|
# in non empty leaf)
|
|
bint is_leaf # Does this cell have children?
|
|
DTYPE_t squared_max_width # Squared value of the maximum width w
|
|
SIZE_t depth # Depth of the cell in the tree
|
|
SIZE_t cumulative_size # Number of points included in the subtree with
|
|
# this cell as a root.
|
|
|
|
# Internal constants
|
|
DTYPE_t[3] center # Store the center for quick split of cells
|
|
DTYPE_t[3] barycenter # Keep track of the center of mass of the cell
|
|
|
|
# Cell boundaries
|
|
DTYPE_t[3] min_bounds # Inferior boundaries of this cell (inclusive)
|
|
DTYPE_t[3] max_bounds # Superior boundaries of this cell (exclusive)
|
|
|
|
|
|
cdef class _QuadTree:
|
|
# The QuadTree object is a quad tree structure constructed by inserting
|
|
# recursively points in the tree and splitting cells in 4 so that each
|
|
# leaf cell contains at most one point.
|
|
# This structure also handle 3D data, inserted in trees with 8 children
|
|
# for each node.
|
|
|
|
# Parameters of the tree
|
|
cdef public int n_dimensions # Number of dimensions in X
|
|
cdef public int verbose # Verbosity of the output
|
|
cdef SIZE_t n_cells_per_cell # Number of children per node. (2 ** n_dimension)
|
|
|
|
# Tree inner structure
|
|
cdef public SIZE_t max_depth # Max depth of the tree
|
|
cdef public SIZE_t cell_count # Counter for node IDs
|
|
cdef public SIZE_t capacity # Capacity of tree, in terms of nodes
|
|
cdef public SIZE_t n_points # Total number of points
|
|
cdef Cell* cells # Array of nodes
|
|
|
|
# Point insertion methods
|
|
cdef int insert_point(self, DTYPE_t[3] point, SIZE_t point_index,
|
|
SIZE_t cell_id=*) nogil except -1
|
|
cdef SIZE_t _insert_point_in_new_child(self, DTYPE_t[3] point, Cell* cell,
|
|
SIZE_t point_index, SIZE_t size=*
|
|
) nogil
|
|
cdef SIZE_t _select_child(self, DTYPE_t[3] point, Cell* cell) nogil
|
|
cdef bint _is_duplicate(self, DTYPE_t[3] point1, DTYPE_t[3] point2) nogil
|
|
|
|
# Create a summary of the Tree compare to a query point
|
|
cdef long summarize(self, DTYPE_t[3] point, DTYPE_t* results,
|
|
float squared_theta=*, SIZE_t cell_id=*, long idx=*
|
|
) nogil
|
|
|
|
# Internal cell initialization methods
|
|
cdef void _init_cell(self, Cell* cell, SIZE_t parent, SIZE_t depth) nogil
|
|
cdef void _init_root(self, DTYPE_t[3] min_bounds, DTYPE_t[3] max_bounds
|
|
) nogil
|
|
|
|
# Private methods
|
|
cdef int _check_point_in_cell(self, DTYPE_t[3] point, Cell* cell
|
|
) nogil except -1
|
|
|
|
# Private array manipulation to manage the ``cells`` array
|
|
cdef int _resize(self, SIZE_t capacity) nogil except -1
|
|
cdef int _resize_c(self, SIZE_t capacity=*) nogil except -1
|
|
cdef int _get_cell(self, DTYPE_t[3] point, SIZE_t cell_id=*) nogil except -1
|
|
cdef np.ndarray _get_cell_ndarray(self)
|