/
_barnes_hut_tsne.pyx
845 lines (783 loc) · 31.4 KB
/
_barnes_hut_tsne.pyx
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# cython: boundscheck=False
# cython: wraparound=False
# cython: cdivision=True
# Author: Christopher Moody <chrisemoody@gmail.com>
# Author: Nick Travers <nickt@squareup.com>
# Implementation by Chris Moody & Nick Travers
# See http://homepage.tudelft.nl/19j49/t-SNE.html for reference
# implementations and papers describing the technique
from libc.stdlib cimport malloc, free
from libc.stdio cimport printf
from libc.math cimport sqrt, log
cimport numpy as np
import numpy as np
cdef char* EMPTY_STRING = ""
cdef extern from "math.h":
float fabsf(float x) nogil
# Round points differing by less than this amount
# effectively ignoring differences near the 32bit
# floating point precision
cdef float EPSILON = 1e-6
# 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 extern from "time.h":
# Declare only what is necessary from `tm` structure.
ctypedef long clock_t
clock_t clock() nogil
double CLOCKS_PER_SEC
cdef extern from "cblas.h":
float snrm2 "cblas_snrm2"(int N, float *X, int incX) nogil
cdef struct Node:
# Keep track of the center of mass
float* barycenter
# If this is a leaf, the position of the point within this leaf
float* leaf_point_position
# The number of points including all
# nodes below this one
long cumulative_size
# Number of points at this node
long size
# Index of the point at this node
# Only defined for non-empty leaf nodes
long point_index
# level = 0 is the root node
# And each subdivision adds 1 to the level
long level
# Left edge of this node
float* left_edge
# The center of this node, equal to le + w/2.0
float* center
# The width of this node -- used to calculate the opening
# angle. Equal to width = re - le
float* width
# The value of the maximum width w
float max_width
# Does this node have children?
# Default to leaf until we add points
int is_leaf
# Array of pointers to pointers of children
Node **children
# Keep a pointer to the parent
Node *parent
# Pointer to the tree this node belongs too
Tree* tree
cdef struct Tree:
# Holds a pointer to the root node
Node* root_node
# Number of dimensions in the ouput
int n_dimensions
# Total number of cells
long n_cells
# Total number of points
long n_points
# Spit out diagnostic information?
int verbose
# How many cells per node? Should go as 2 ** n_dimensionss
int n_cell_per_node
cdef Tree* init_tree(float[:] left_edge, float[:] width, int n_dimensions,
int verbose) nogil:
# tree is freed by free_tree
cdef Tree* tree = <Tree*> malloc(sizeof(Tree))
tree.n_dimensions = n_dimensions
tree.n_cells = 0
tree.n_points = 0
tree.verbose = verbose
tree.root_node = create_root(left_edge, width, n_dimensions)
tree.root_node.tree = tree
tree.n_cells += 1
tree.n_cell_per_node = 2 ** n_dimensions
if DEBUGFLAG:
printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n",
left_edge[0], left_edge[1], left_edge[2])
printf("[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n",
width[0], width[1], width[2])
return tree
cdef Node* create_root(float[:] left_edge, float[:] width, int n_dimensions) nogil:
# Create a default root node
cdef int ax
cdef int n_cell_per_node = 2 ** n_dimensions
# root is freed by free_tree
root = <Node*> malloc(sizeof(Node))
root.is_leaf = 1
root.parent = NULL
root.level = 0
root.cumulative_size = 0
root.size = 0
root.point_index = -1
root.max_width = 0.0
root.width = <float*> malloc(sizeof(float) * n_dimensions)
root.left_edge = <float*> malloc(sizeof(float) * n_dimensions)
root.center = <float*> malloc(sizeof(float) * n_dimensions)
root.barycenter = <float*> malloc(sizeof(float) * n_dimensions)
root.leaf_point_position= <float*> malloc(sizeof(float) * n_dimensions)
root.children = NULL
for ax in range(n_dimensions):
root.width[ax] = width[ax]
root.left_edge[ax] = left_edge[ax]
root.center[ax] = 0.0
root.barycenter[ax] = 0.
root.leaf_point_position[ax] = -1
for ax in range(n_dimensions):
root.max_width = max(root.max_width, root.width[ax])
if DEBUGFLAG:
printf("[t-SNE] Created root node %p\n", root)
return root
cdef Node* create_child(Node *parent, int[3] offset) nogil:
# Create a new child node with default parameters
cdef int ax
# these children are freed by free_recursive
child = <Node *> malloc(sizeof(Node))
child.is_leaf = 1
child.parent = parent
child.level = parent.level + 1
child.size = 0
child.cumulative_size = 0
child.point_index = -1
child.tree = parent.tree
child.max_width = 0.0
child.width = <float*> malloc(sizeof(float) * parent.tree.n_dimensions)
child.left_edge = <float*> malloc(sizeof(float) * parent.tree.n_dimensions)
child.center = <float*> malloc(sizeof(float) * parent.tree.n_dimensions)
child.barycenter = <float*> malloc(sizeof(float) * parent.tree.n_dimensions)
child.leaf_point_position = <float*> malloc(sizeof(float) * parent.tree.n_dimensions)
child.children = NULL
for ax in range(parent.tree.n_dimensions):
child.width[ax] = parent.width[ax] / 2.0
child.left_edge[ax] = parent.left_edge[ax] + offset[ax] * parent.width[ax] / 2.0
child.center[ax] = child.left_edge[ax] + child.width[ax] / 2.0
child.barycenter[ax] = 0.
child.leaf_point_position[ax] = -1.
for ax in range(parent.tree.n_dimensions):
child.max_width = max(child.max_width, child.width[ax])
child.tree.n_cells += 1
return child
cdef Node* select_child(Node *node, float[3] pos, long index) nogil:
# Find which sub-node a position should go into
# And return the appropriate node
cdef int* offset = <int*> malloc(sizeof(int) * node.tree.n_dimensions)
cdef int ax, idx
cdef Node* child
cdef int error
for ax in range(node.tree.n_dimensions):
offset[ax] = (pos[ax] - (node.left_edge[ax] + node.width[ax] / 2.0)) > 0.
idx = offset2index(offset, node.tree.n_dimensions)
child = node.children[idx]
if DEBUGFLAG:
printf("[t-SNE] Offset [%i, %i] with LE [%f, %f]\n",
offset[0], offset[1], child.left_edge[0], child.left_edge[1])
free(offset)
return child
cdef inline void index2offset(int* offset, int index, int n_dimensions) nogil:
# Convert a 1D index into N-D index; useful for indexing
# children of a quadtree, octree, N-tree
# Quite likely there's a fancy bitshift way of doing this
# since the offset is equivalent to the binary representation
# of the integer index
# We read the offset array left-to-right
# such that the least significat bit is on the right
cdef int rem, k, shift
for k in range(n_dimensions):
shift = n_dimensions -k -1
rem = ((index >> shift) << shift)
offset[k] = rem > 0
if DEBUGFLAG:
printf("i2o index %i k %i rem %i offset", index, k, rem)
for j in range(n_dimensions):
printf(" %i", offset[j])
printf(" n_dimensions %i\n", n_dimensions)
index -= rem
cdef inline int offset2index(int* offset, int n_dimensions) nogil:
# Calculate the 1:1 index for a given offset array
# We read the offset array right-to-left
# such that the least significat bit is on the right
cdef int dim
cdef int index = 0
for dim in range(n_dimensions):
index += (2 ** dim) * offset[n_dimensions - dim - 1]
if DEBUGFLAG:
printf("o2i index %i dim %i offset", index, dim)
for j in range(n_dimensions):
printf(" %i", offset[j])
printf(" n_dimensions %i\n", n_dimensions)
return index
cdef void subdivide(Node* node) nogil:
# This instantiates 2**n_dimensions = n_cell_per_node nodes for the current node
cdef int idx = 0
cdef int* offset = <int*> malloc(sizeof(int) * node.tree.n_dimensions)
node.is_leaf = False
node.children = <Node**> malloc(sizeof(Node*) * node.tree.n_cell_per_node)
for idx in range(node.tree.n_cell_per_node):
index2offset(offset, idx, node.tree.n_dimensions)
node.children[idx] = create_child(node, offset)
free(offset)
cdef int insert(Node *root, float pos[3], long point_index, long depth, long
duplicate_count) nogil:
# Introduce a new point into the tree
# by recursively inserting it and subdividng as necessary
# Carefully treat the case of identical points at the same node
# by increasing the root.size and tracking duplicate_count
cdef Node *child
cdef long i
cdef int ax
cdef int not_identical = 1
cdef int n_dimensions = root.tree.n_dimensions
if DEBUGFLAG:
printf("[t-SNE] [d=%i] Inserting pos %i [%f, %f] duplicate_count=%i "
"into child %p\n", depth, point_index, pos[0], pos[1],
duplicate_count, root)
# Increment the total number points including this
# node and below it
root.cumulative_size += duplicate_count
# Evaluate the new center of mass, weighting the previous
# center of mass against the new point data
cdef double frac_seen = <double>(root.cumulative_size - 1) / (<double>
root.cumulative_size)
cdef double frac_new = 1.0 / <double> root.cumulative_size
# Assert that duplicate_count > 0
if duplicate_count < 1:
return -1
# Assert that the point is inside the left & right edges
for ax in range(n_dimensions):
root.barycenter[ax] *= frac_seen
if (pos[ax] > (root.left_edge[ax] + root.width[ax] + EPSILON)):
printf("[t-SNE] Error: point (%1.9e) is above right edge of node "
"(%1.9e)\n", pos[ax], root.left_edge[ax] + root.width[ax])
return -1
if (pos[ax] < root.left_edge[ax] - EPSILON):
printf("[t-SNE] Error: point (%1.9e) is below left edge of node "
"(%1.9e)\n", pos[ax], root.left_edge[ax])
return -1
for ax in range(n_dimensions):
root.barycenter[ax] += pos[ax] * frac_new
# If this node is unoccupied, fill it.
# Otherwise, we need to insert recursively.
# Two insertion scenarios:
# 1) Insert into this node if it is a leaf and empty
# 2) Subdivide this node if it is currently occupied
if (root.size == 0) & root.is_leaf:
# Root node is empty and a leaf
if DEBUGFLAG:
printf("[t-SNE] [d=%i] Inserting [%f, %f] into blank cell\n", depth,
pos[0], pos[1])
for ax in range(n_dimensions):
root.leaf_point_position[ax] = pos[ax]
root.point_index = point_index
root.size = duplicate_count
return 0
else:
# Root node is occupied or not a leaf
if DEBUGFLAG:
printf("[t-SNE] [d=%i] Node %p is occupied or is a leaf.\n", depth,
root)
printf("[t-SNE] [d=%i] Node %p leaf = %i. Size %i\n", depth, root,
root.is_leaf, root.size)
if root.is_leaf & (root.size > 0):
# is a leaf node and is occupied
for ax in range(n_dimensions):
not_identical &= (fabsf(pos[ax] - root.leaf_point_position[ax]) < EPSILON)
not_identical &= (root.point_index != point_index)
if not_identical == 1:
root.size += duplicate_count
if DEBUGFLAG:
printf("[t-SNE] Warning: [d=%i] Detected identical "
"points. Returning. Leaf now has size %i\n",
depth, root.size)
return 0
# If necessary, subdivide this node before
# descending
if root.is_leaf:
if DEBUGFLAG:
printf("[t-SNE] [d=%i] Subdividing this leaf node %p\n", depth,
root)
subdivide(root)
# We have two points to relocate: the one previously
# at this node, and the new one we're attempting
# to insert
if root.size > 0:
child = select_child(root, root.leaf_point_position, root.point_index)
if DEBUGFLAG:
printf("[t-SNE] [d=%i] Relocating old point to node %p\n",
depth, child)
insert(child, root.leaf_point_position, root.point_index, depth + 1, root.size)
# Insert the new point
if DEBUGFLAG:
printf("[t-SNE] [d=%i] Selecting node for new point\n", depth)
child = select_child(root, pos, point_index)
if root.size > 0:
# Remove the point from this node
for ax in range(n_dimensions):
root.leaf_point_position[ax] = -1
root.size = 0
root.point_index = -1
return insert(child, pos, point_index, depth + 1, 1)
cdef int insert_many(Tree* tree, float[:,:] pos_array) nogil:
# Insert each data point into the tree one at a time
cdef long nrows = pos_array.shape[0]
cdef long i
cdef int ax
cdef float row[3]
cdef long err = 0
for i in range(nrows):
for ax in range(tree.n_dimensions):
row[ax] = pos_array[i, ax]
if DEBUGFLAG:
printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1])
err = insert(tree.root_node, row, i, 0, 1)
if err != 0:
printf("[t-SNE] ERROR\n%s", EMPTY_STRING)
return err
tree.n_points += 1
return err
cdef int free_tree(Tree* tree) nogil:
cdef int check
cdef long* cnt = <long*> malloc(sizeof(long) * 3)
for i in range(3):
cnt[i] = 0
free_recursive(tree, tree.root_node, cnt)
check = cnt[0] == tree.n_cells
check &= cnt[2] == tree.n_points
free(tree)
free(cnt)
return check
cdef void free_post_children(Node *node) nogil:
free(node.width)
free(node.left_edge)
free(node.center)
free(node.barycenter)
free(node.leaf_point_position)
free(node)
cdef void free_recursive(Tree* tree, Node *root, long* counts) nogil:
# Free up all of the tree nodes recursively
# while counting the number of nodes visited
# and total number of data points removed
cdef int idx
cdef Node* child
if not root.is_leaf:
for idx in range(tree.n_cell_per_node):
child = root.children[idx]
free_recursive(tree, child, counts)
counts[0] += 1
if child.is_leaf:
counts[1] += 1
if child.size > 0:
counts[2] +=1
else:
free(child.children)
free_post_children(child)
if root == tree.root_node:
if not root.is_leaf:
free(root.children)
free_post_children(root)
cdef long count_points(Node* root, long count) nogil:
# Walk through the whole tree and count the number
# of points at the leaf nodes
if DEBUGFLAG:
printf("[t-SNE] Counting nodes at root node %p\n", root)
cdef Node* child
cdef int idx
if root.is_leaf:
count += root.size
if DEBUGFLAG :
printf("[t-SNE] %p is a leaf node, no children\n", root)
printf("[t-SNE] %i points in node %p\n", count, root)
return count
# Otherwise, get the children
for idx in range(root.tree.n_cell_per_node):
child = root.children[idx]
if DEBUGFLAG:
printf("[t-SNE] Counting points for child %p\n", child)
if child.is_leaf and child.size > 0:
if DEBUGFLAG:
printf("[t-SNE] Child has size %d\n", child.size)
count += child.size
elif not child.is_leaf:
if DEBUGFLAG:
printf("[t-SNE] Child is not a leaf. Descending\n%s", EMPTY_STRING)
count = count_points(child, count)
# else case is we have an empty leaf node
# which happens when we create a quadtree for
# one point, and then the other neighboring cells
# don't get filled in
if DEBUGFLAG:
printf("[t-SNE] %i points in this node\n", count)
return count
cdef float compute_gradient(float[:,:] val_P,
float[:,:] pos_reference,
np.int64_t[:,:] neighbors,
float[:,:] tot_force,
Node* root_node,
float theta,
float dof,
long start,
long stop) nogil:
# Having created the tree, calculate the gradient
# in two components, the positive and negative forces
cdef long i, coord
cdef int ax
cdef long n = pos_reference.shape[0]
cdef int n_dimensions = root_node.tree.n_dimensions
if root_node.tree.verbose > 11:
printf("[t-SNE] Allocating %i elements in force arrays\n",
n * n_dimensions * 2)
cdef float* sum_Q = <float*> malloc(sizeof(float))
cdef float* neg_f = <float*> malloc(sizeof(float) * n * n_dimensions)
cdef float* neg_f_fast = <float*> malloc(sizeof(float) * n * n_dimensions)
cdef float* pos_f = <float*> malloc(sizeof(float) * n * n_dimensions)
cdef clock_t t1, t2
cdef float sQ, error
sum_Q[0] = 0.0
t1 = clock()
compute_gradient_negative(val_P, pos_reference, neg_f, root_node, sum_Q,
dof, theta, start, stop)
t2 = clock()
if root_node.tree.verbose > 15:
printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1)))
sQ = sum_Q[0]
t1 = clock()
error = compute_gradient_positive(val_P, pos_reference, neighbors, pos_f,
n_dimensions, dof, sQ, start, root_node.tree.verbose)
t2 = clock()
if root_node.tree.verbose > 15:
printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1)))
for i in range(start, n):
for ax in range(n_dimensions):
coord = i * n_dimensions + ax
tot_force[i, ax] = pos_f[coord] - (neg_f[coord] / sum_Q[0])
free(sum_Q)
free(neg_f)
free(neg_f_fast)
free(pos_f)
return sQ
cdef float compute_gradient_positive(float[:,:] val_P,
float[:,:] pos_reference,
np.int64_t[:,:] neighbors,
float* pos_f,
int n_dimensions,
float dof,
float sum_Q,
np.int64_t start,
int verbose) nogil:
# Sum over the following expression for i not equal to j
# grad_i = p_ij (1 + ||y_i - y_j||^2)^-1 (y_i - y_j)
# This is equivalent to compute_edge_forces in the authors' code
# It just goes over the nearest neighbors instead of all the data points
# (unlike the non-nearest neighbors version of `compute_gradient_positive')
cdef:
int ax
long i, j, k
long K = neighbors.shape[1]
long n = val_P.shape[0]
float[3] buff
float D, Q, pij
float C = 0.0
float exponent = (dof + 1.0) / -2.0
cdef clock_t t1, t2
t1 = clock()
for i in range(start, n):
for ax in range(n_dimensions):
pos_f[i * n_dimensions + ax] = 0.0
for k in range(K):
j = neighbors[i, k]
# we don't need to exclude the i==j case since we've
# already thrown it out from the list of neighbors
D = 0.0
Q = 0.0
pij = val_P[i, j]
for ax in range(n_dimensions):
buff[ax] = pos_reference[i, ax] - pos_reference[j, ax]
D += buff[ax] ** 2.0
Q = (((1.0 + D) / dof) ** exponent)
D = pij * Q
Q /= sum_Q
C += pij * log((pij + EPSILON) / (Q + EPSILON))
for ax in range(n_dimensions):
pos_f[i * n_dimensions + ax] += D * buff[ax]
t2 = clock()
dt = ((float) (t2 - t1))
if verbose > 10:
printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt)
return C
cdef void compute_gradient_negative(float[:,:] val_P,
float[:,:] pos_reference,
float* neg_f,
Node *root_node,
float* sum_Q,
float dof,
float theta,
long start,
long stop) nogil:
if stop == -1:
stop = pos_reference.shape[0]
cdef:
int ax
long i, j
long n = stop - start
float* force
float* iQ
float* pos
float* dist2s
long* sizes
float* deltas
long* l
int n_dimensions = root_node.tree.n_dimensions
float qijZ, mult
long idx,
long dta = 0
long dtb = 0
clock_t t1, t2, t3
float* neg_force
iQ = <float*> malloc(sizeof(float))
force = <float*> malloc(sizeof(float) * n_dimensions)
pos = <float*> malloc(sizeof(float) * n_dimensions)
dist2s = <float*> malloc(sizeof(float) * n)
sizes = <long*> malloc(sizeof(long) * n)
deltas = <float*> malloc(sizeof(float) * n * n_dimensions)
l = <long*> malloc(sizeof(long))
neg_force= <float*> malloc(sizeof(float) * n_dimensions)
for i in range(start, stop):
# Clear the arrays
for ax in range(n_dimensions):
force[ax] = 0.0
neg_force[ax] = 0.0
pos[ax] = pos_reference[i, ax]
iQ[0] = 0.0
l[0] = 0
# Find which nodes are summarizing and collect their centers of mass
# deltas, and sizes, into vectorized arrays
t1 = clock()
compute_non_edge_forces(root_node, theta, i, pos, force, dist2s,
sizes, deltas, l)
t2 = clock()
# Compute the t-SNE negative force
# for the digits dataset, walking the tree
# is about 10-15x more expensive than the
# following for loop
exponent = (dof + 1.0) / -2.0
for j in range(l[0]):
qijZ = ((1.0 + dist2s[j]) / dof) ** exponent
sum_Q[0] += sizes[j] * qijZ
mult = sizes[j] * qijZ * qijZ
for ax in range(n_dimensions):
idx = j * n_dimensions + ax
neg_force[ax] += mult * deltas[idx]
t3 = clock()
for ax in range(n_dimensions):
neg_f[i * n_dimensions + ax] = neg_force[ax]
dta += t2 - t1
dtb += t3 - t2
if root_node.tree.verbose > 20:
printf("[t-SNE] Tree: %i clock ticks | ", dta)
printf("Force computation: %i clock ticks\n", dtb)
free(iQ)
free(force)
free(pos)
free(dist2s)
free(sizes)
free(deltas)
free(l)
free(neg_force)
cdef void compute_non_edge_forces(Node* node,
float theta,
long point_index,
float* pos,
float* force,
float* dist2s,
long* sizes,
float* deltas,
long* l) nogil:
# Compute the t-SNE force on the point in pos given by point_index
cdef:
Node* child
int i, j
int n_dimensions = node.tree.n_dimensions
long idx, idx1
float dist_check
# There are no points below this node if cumulative_size == 0
# so do not bother to calculate any force contributions
# Also do not compute self-interactions
if node.cumulative_size > 0 and not (node.is_leaf and (node.point_index ==
point_index)):
# Compute distance between node center of mass and the reference point
# I've tried rewriting this in terms of BLAS functions, but it's about
# 1.5x worse when we do so, probbaly because the vectors are small
idx1 = l[0] * n_dimensions
deltas[idx1] = pos[0] - node.barycenter[0]
idx = idx1
for i in range(1, n_dimensions):
idx += 1
deltas[idx] = pos[i] - node.barycenter[i]
# do np.sqrt(np.sum(deltas**2.0))
dist2s[l[0]] = snrm2(n_dimensions, &deltas[idx1], 1)
# Check whether we can use this node as a summary
# It's a summary node if the angular size as measured from the point
# is relatively small (w.r.t. to theta) or if it is a leaf node.
# If it can be summarized, we use the cell center of mass
# Otherwise, we go a higher level of resolution and into the leaves.
if node.is_leaf or ((node.max_width / dist2s[l[0]]) < theta):
# Compute the t-SNE force between the reference point and the
# current node
sizes[l[0]] = node.cumulative_size
dist2s[l[0]] = dist2s[l[0]] * dist2s[l[0]]
l[0] += 1
else:
# Recursively apply Barnes-Hut to child nodes
for idx in range(node.tree.n_cell_per_node):
child = node.children[idx]
if child.cumulative_size == 0:
continue
compute_non_edge_forces(child, theta,
point_index, pos, force, dist2s, sizes, deltas,
l)
cdef float compute_error(float[:, :] val_P,
float[:, :] pos_reference,
np.int64_t[:,:] neighbors,
float sum_Q,
int n_dimensions,
int verbose) nogil:
cdef int i, j, ax
cdef int I = neighbors.shape[0]
cdef int K = neighbors.shape[1]
cdef float pij, Q
cdef float C = 0.0
cdef clock_t t1, t2
cdef float dt, delta
t1 = clock()
for i in range(I):
for k in range(K):
j = neighbors[i, k]
pij = val_P[i, j]
Q = 0.0
for ax in range(n_dimensions):
delta = (pos_reference[i, ax] - pos_reference[j, ax])
Q += delta * delta
Q = (1.0 / (sum_Q + Q * sum_Q))
C += pij * log((pij + EPSILON) / (Q + EPSILON))
t2 = clock()
dt = ((float) (t2 - t1))
if verbose > 10:
printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt)
return C
def calculate_edge(pos_output):
# Make the boundaries slightly outside of the data
# to avoid floating point error near the edge
left_edge = np.min(pos_output, axis=0)
right_edge = np.max(pos_output, axis=0)
center = (right_edge + left_edge) * 0.5
width = np.maximum(np.subtract(right_edge, left_edge), EPSILON)
# Exagerate width to avoid boundary edge
width = width.astype(np.float32) * 1.001
left_edge = center - width / 2.0
right_edge = center + width / 2.0
return left_edge, right_edge, width
def gradient(float[:,:] pij_input,
float[:,:] pos_output,
np.int64_t[:,:] neighbors,
float[:,:] forces,
float theta,
int n_dimensions,
int verbose,
float dof = 1.0,
long skip_num_points=0):
# This function is designed to be called from external Python
# it passes the 'forces' array by reference and fills thats array
# up in-place
cdef float C
n = pos_output.shape[0]
left_edge, right_edge, width = calculate_edge(pos_output)
assert width.itemsize == 4
assert pij_input.itemsize == 4
assert pos_output.itemsize == 4
assert forces.itemsize == 4
m = "Number of neighbors must be < # of points - 1"
assert n - 1 >= neighbors.shape[1], m
m = "neighbors array and pos_output shapes are incompatible"
assert n == neighbors.shape[0], m
m = "Forces array and pos_output shapes are incompatible"
assert n == forces.shape[0], m
m = "Pij and pos_output shapes are incompatible"
assert n == pij_input.shape[0], m
m = "Pij and pos_output shapes are incompatible"
assert n == pij_input.shape[1], m
if verbose > 10:
printf("[t-SNE] Initializing tree of n_dimensions %i\n", n_dimensions)
cdef Tree* qt = init_tree(left_edge, width, n_dimensions, verbose)
if verbose > 10:
printf("[t-SNE] Inserting %i points\n", pos_output.shape[0])
err = insert_many(qt, pos_output)
assert err == 0, "[t-SNE] Insertion failed"
if verbose > 10:
# XXX: format hack to workaround lack of `const char *` type
# in the generated C code that triggers error with gcc 4.9
# and -Werror=format-security
printf("[t-SNE] Computing gradient\n%s", EMPTY_STRING)
sum_Q = compute_gradient(pij_input, pos_output, neighbors, forces,
qt.root_node, theta, dof, skip_num_points, -1)
C = compute_error(pij_input, pos_output, neighbors, sum_Q, n_dimensions,
verbose)
if verbose > 10:
# XXX: format hack to workaround lack of `const char *` type
# in the generated C code
# and -Werror=format-security
printf("[t-SNE] Checking tree consistency\n%s", EMPTY_STRING)
cdef long count = count_points(qt.root_node, 0)
m = ("Tree consistency failed: unexpected number of points=%i "
"at root node=%i" % (count, qt.root_node.cumulative_size))
assert count == qt.root_node.cumulative_size, m
m = "Tree consistency failed: unexpected number of points on the tree"
assert count == qt.n_points, m
free_tree(qt)
return C
# Helper functions
def check_quadtree(X, np.int64_t[:] counts):
"""
Helper function to access quadtree functions for testing
"""
X = X.astype(np.float32)
left_edge, right_edge, width = calculate_edge(X)
# Initialise a tree
qt = init_tree(left_edge, width, 2, 2)
# Insert data into the tree
insert_many(qt, X)
cdef long count = count_points(qt.root_node, 0)
counts[0] = count
counts[1] = qt.root_node.cumulative_size
counts[2] = qt.n_points
free_tree(qt)
return counts
cdef int helper_test_index2offset(int* check, int index, int n_dimensions):
cdef int* offset = <int*> malloc(sizeof(int) * n_dimensions)
cdef int error_check = 1
for i in range(n_dimensions):
offset[i] = 0
index2offset(offset, index, n_dimensions)
for i in range(n_dimensions):
error_check &= offset[i] == check[i]
free(offset)
return error_check
def test_index2offset():
ret = 1
ret &= helper_test_index2offset([1, 0, 1], 5, 3) == 1
ret &= helper_test_index2offset([0, 0, 0], 0, 3) == 1
ret &= helper_test_index2offset([0, 0, 1], 1, 3) == 1
ret &= helper_test_index2offset([0, 1, 0], 2, 3) == 1
ret &= helper_test_index2offset([0, 1, 1], 3, 3) == 1
ret &= helper_test_index2offset([1, 0, 0], 4, 3) == 1
return ret
def test_index_offset():
cdef int n_dimensions, idx, tidx, k
cdef int error_check = 1
cdef int* offset
for n_dimensions in range(2, 10):
offset = <int*> malloc(sizeof(int) * n_dimensions)
for k in range(n_dimensions):
offset[k] = 0
for idx in range(2 ** n_dimensions):
index2offset(offset, idx, n_dimensions)
tidx = offset2index(offset, n_dimensions)
error_check &= tidx == idx
assert error_check == 1
free(offset)
return error_check