304 lines
9.5 KiB
Cython
304 lines
9.5 KiB
Cython
# cython: cdivision=True
|
|
# cython: boundscheck=False
|
|
# cython: wraparound=False
|
|
|
|
# Authors: Gilles Louppe <g.louppe@gmail.com>
|
|
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
|
|
# Arnaud Joly <arnaud.v.joly@gmail.com>
|
|
# Jacob Schreiber <jmschreiber91@gmail.com>
|
|
#
|
|
#
|
|
# Licence: BSD 3 clause
|
|
|
|
from libc.stdlib cimport free
|
|
from libc.stdlib cimport malloc
|
|
from libc.stdlib cimport realloc
|
|
from libc.math cimport log as ln
|
|
|
|
import numpy as np
|
|
cimport numpy as np
|
|
np.import_array()
|
|
|
|
# =============================================================================
|
|
# Helper functions
|
|
# =============================================================================
|
|
|
|
cdef realloc_ptr safe_realloc(realloc_ptr* p, size_t nelems) except *:
|
|
# sizeof(realloc_ptr[0]) would be more like idiomatic C, but causes Cython
|
|
# 0.20.1 to crash.
|
|
cdef size_t nbytes = nelems * sizeof(p[0][0])
|
|
if nbytes / sizeof(p[0][0]) != nelems:
|
|
# Overflow in the multiplication
|
|
raise MemoryError("could not allocate (%d * %d) bytes"
|
|
% (nelems, sizeof(p[0][0])))
|
|
cdef realloc_ptr tmp = <realloc_ptr>realloc(p[0], nbytes)
|
|
if tmp == NULL:
|
|
raise MemoryError("could not allocate %d bytes" % nbytes)
|
|
|
|
p[0] = tmp
|
|
return tmp # for convenience
|
|
|
|
|
|
def _realloc_test():
|
|
# Helper for tests. Tries to allocate <size_t>(-1) / 2 * sizeof(size_t)
|
|
# bytes, which will always overflow.
|
|
cdef SIZE_t* p = NULL
|
|
safe_realloc(&p, <size_t>(-1) / 2)
|
|
if p != NULL:
|
|
free(p)
|
|
assert False
|
|
|
|
|
|
# rand_r replacement using a 32bit XorShift generator
|
|
# See http://www.jstatsoft.org/v08/i14/paper for details
|
|
cdef inline UINT32_t our_rand_r(UINT32_t* seed) nogil:
|
|
seed[0] ^= <UINT32_t>(seed[0] << 13)
|
|
seed[0] ^= <UINT32_t>(seed[0] >> 17)
|
|
seed[0] ^= <UINT32_t>(seed[0] << 5)
|
|
|
|
return seed[0] % (<UINT32_t>RAND_R_MAX + 1)
|
|
|
|
|
|
cdef inline np.ndarray sizet_ptr_to_ndarray(SIZE_t* data, SIZE_t size):
|
|
"""Encapsulate data into a 1D numpy array of intp's."""
|
|
cdef np.npy_intp shape[1]
|
|
shape[0] = <np.npy_intp> size
|
|
return np.PyArray_SimpleNewFromData(1, shape, np.NPY_INTP, data)
|
|
|
|
|
|
cdef inline SIZE_t rand_int(SIZE_t low, SIZE_t high,
|
|
UINT32_t* random_state) nogil:
|
|
"""Generate a random integer in [0; end)."""
|
|
return low + our_rand_r(random_state) % (high - low)
|
|
|
|
|
|
cdef inline double rand_uniform(double low, double high,
|
|
UINT32_t* random_state) nogil:
|
|
"""Generate a random double in [low; high)."""
|
|
return ((high - low) * <double> our_rand_r(random_state) /
|
|
<double> RAND_R_MAX) + low
|
|
|
|
|
|
cdef inline double log(double x) nogil:
|
|
return ln(x) / ln(2.0)
|
|
|
|
|
|
# =============================================================================
|
|
# Stack data structure
|
|
# =============================================================================
|
|
|
|
cdef class Stack:
|
|
"""A LIFO data structure.
|
|
|
|
Attributes
|
|
----------
|
|
capacity : SIZE_t
|
|
The elements the stack can hold; if more added then ``self.stack_``
|
|
needs to be resized.
|
|
|
|
top : SIZE_t
|
|
The number of elements currently on the stack.
|
|
|
|
stack : StackRecord pointer
|
|
The stack of records (upward in the stack corresponds to the right).
|
|
"""
|
|
|
|
def __cinit__(self, SIZE_t capacity):
|
|
self.capacity = capacity
|
|
self.top = 0
|
|
self.stack_ = <StackRecord*> malloc(capacity * sizeof(StackRecord))
|
|
if self.stack_ == NULL:
|
|
raise MemoryError()
|
|
|
|
def __dealloc__(self):
|
|
free(self.stack_)
|
|
|
|
cdef bint is_empty(self) nogil:
|
|
return self.top <= 0
|
|
|
|
cdef int push(self, SIZE_t start, SIZE_t end, SIZE_t depth, SIZE_t parent,
|
|
bint is_left, double impurity,
|
|
SIZE_t n_constant_features) nogil:
|
|
"""Push a new element onto the stack.
|
|
|
|
Returns 0 if successful; -1 on out of memory error.
|
|
"""
|
|
cdef SIZE_t top = self.top
|
|
cdef StackRecord* stack = NULL
|
|
|
|
# Resize if capacity not sufficient
|
|
if top >= self.capacity:
|
|
self.capacity *= 2
|
|
stack = <StackRecord*> realloc(self.stack_,
|
|
self.capacity * sizeof(StackRecord))
|
|
if stack == NULL:
|
|
# no free; __dealloc__ handles that
|
|
return -1
|
|
self.stack_ = stack
|
|
|
|
stack = self.stack_
|
|
stack[top].start = start
|
|
stack[top].end = end
|
|
stack[top].depth = depth
|
|
stack[top].parent = parent
|
|
stack[top].is_left = is_left
|
|
stack[top].impurity = impurity
|
|
stack[top].n_constant_features = n_constant_features
|
|
|
|
# Increment stack pointer
|
|
self.top = top + 1
|
|
return 0
|
|
|
|
cdef int pop(self, StackRecord* res) nogil:
|
|
"""Remove the top element from the stack and copy to ``res``.
|
|
|
|
Returns 0 if pop was successful (and ``res`` is set); -1
|
|
otherwise.
|
|
"""
|
|
cdef SIZE_t top = self.top
|
|
cdef StackRecord* stack = self.stack_
|
|
|
|
if top <= 0:
|
|
return -1
|
|
|
|
res[0] = stack[top - 1]
|
|
self.top = top - 1
|
|
|
|
return 0
|
|
|
|
|
|
# =============================================================================
|
|
# PriorityHeap data structure
|
|
# =============================================================================
|
|
|
|
cdef void heapify_up(PriorityHeapRecord* heap, SIZE_t pos) nogil:
|
|
"""Restore heap invariant parent.improvement > child.improvement from
|
|
``pos`` upwards. """
|
|
if pos == 0:
|
|
return
|
|
|
|
cdef SIZE_t parent_pos = (pos - 1) / 2
|
|
|
|
if heap[parent_pos].improvement < heap[pos].improvement:
|
|
heap[parent_pos], heap[pos] = heap[pos], heap[parent_pos]
|
|
heapify_up(heap, parent_pos)
|
|
|
|
|
|
cdef void heapify_down(PriorityHeapRecord* heap, SIZE_t pos,
|
|
SIZE_t heap_length) nogil:
|
|
"""Restore heap invariant parent.improvement > children.improvement from
|
|
``pos`` downwards. """
|
|
cdef SIZE_t left_pos = 2 * (pos + 1) - 1
|
|
cdef SIZE_t right_pos = 2 * (pos + 1)
|
|
cdef SIZE_t largest = pos
|
|
|
|
if (left_pos < heap_length and
|
|
heap[left_pos].improvement > heap[largest].improvement):
|
|
largest = left_pos
|
|
|
|
if (right_pos < heap_length and
|
|
heap[right_pos].improvement > heap[largest].improvement):
|
|
largest = right_pos
|
|
|
|
if largest != pos:
|
|
heap[pos], heap[largest] = heap[largest], heap[pos]
|
|
heapify_down(heap, largest, heap_length)
|
|
|
|
|
|
cdef class PriorityHeap:
|
|
"""A priority queue implemented as a binary heap.
|
|
|
|
The heap invariant is that the impurity improvement of the parent record
|
|
is larger then the impurity improvement of the children.
|
|
|
|
Attributes
|
|
----------
|
|
capacity : SIZE_t
|
|
The capacity of the heap
|
|
|
|
heap_ptr : SIZE_t
|
|
The water mark of the heap; the heap grows from left to right in the
|
|
array ``heap_``. The following invariant holds ``heap_ptr < capacity``.
|
|
|
|
heap_ : PriorityHeapRecord*
|
|
The array of heap records. The maximum element is on the left;
|
|
the heap grows from left to right
|
|
"""
|
|
|
|
def __cinit__(self, SIZE_t capacity):
|
|
self.capacity = capacity
|
|
self.heap_ptr = 0
|
|
self.heap_ = <PriorityHeapRecord*> malloc(capacity * sizeof(PriorityHeapRecord))
|
|
if self.heap_ == NULL:
|
|
raise MemoryError()
|
|
|
|
def __dealloc__(self):
|
|
free(self.heap_)
|
|
|
|
cdef bint is_empty(self) nogil:
|
|
return self.heap_ptr <= 0
|
|
|
|
cdef int push(self, SIZE_t node_id, SIZE_t start, SIZE_t end, SIZE_t pos,
|
|
SIZE_t depth, bint is_leaf, double improvement,
|
|
double impurity, double impurity_left,
|
|
double impurity_right) nogil:
|
|
"""Push record on the priority heap.
|
|
|
|
Returns 0 if successful; -1 on out of memory error.
|
|
"""
|
|
cdef SIZE_t heap_ptr = self.heap_ptr
|
|
cdef PriorityHeapRecord* heap = NULL
|
|
|
|
# Resize if capacity not sufficient
|
|
if heap_ptr >= self.capacity:
|
|
self.capacity *= 2
|
|
heap = <PriorityHeapRecord*> realloc(self.heap_,
|
|
self.capacity *
|
|
sizeof(PriorityHeapRecord))
|
|
if heap == NULL:
|
|
# no free; __dealloc__ handles that
|
|
return -1
|
|
self.heap_ = heap
|
|
|
|
# Put element as last element of heap
|
|
heap = self.heap_
|
|
heap[heap_ptr].node_id = node_id
|
|
heap[heap_ptr].start = start
|
|
heap[heap_ptr].end = end
|
|
heap[heap_ptr].pos = pos
|
|
heap[heap_ptr].depth = depth
|
|
heap[heap_ptr].is_leaf = is_leaf
|
|
heap[heap_ptr].impurity = impurity
|
|
heap[heap_ptr].impurity_left = impurity_left
|
|
heap[heap_ptr].impurity_right = impurity_right
|
|
heap[heap_ptr].improvement = improvement
|
|
|
|
# Heapify up
|
|
heapify_up(heap, heap_ptr)
|
|
|
|
# Increase element count
|
|
self.heap_ptr = heap_ptr + 1
|
|
return 0
|
|
|
|
cdef int pop(self, PriorityHeapRecord* res) nogil:
|
|
"""Remove max element from the heap. """
|
|
cdef SIZE_t heap_ptr = self.heap_ptr
|
|
cdef PriorityHeapRecord* heap = self.heap_
|
|
|
|
if heap_ptr <= 0:
|
|
return -1
|
|
|
|
# Take first element
|
|
res[0] = heap[0]
|
|
|
|
# Put last element to the front
|
|
heap[0], heap[heap_ptr - 1] = heap[heap_ptr - 1], heap[0]
|
|
|
|
# Restore heap invariant
|
|
if heap_ptr > 1:
|
|
heapify_down(heap, 0, heap_ptr - 1)
|
|
|
|
self.heap_ptr = heap_ptr - 1
|
|
|
|
return 0
|