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