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#![warn(missing_docs)]
#![allow(clippy::deprecated_cfg_attr)]
#[cfg(any(test, feature = "dummy_point"))]
pub mod dummy_point;
mod heap;
mod infinite;
mod internal_neighbour;
mod internal_parameters;
mod node;
use internal_parameters::InternalParameters;
use node::Node;
use num_traits::{clamp_max, clamp_min, Bounded, Zero};
use ordered_float::Float;
pub use ordered_float::NotNan;
use std::{collections::BinaryHeap, ops::AddAssign};
use heap::CandidateHeap;
use internal_neighbour::InternalNeighbour;
pub trait Scalar: Float + AddAssign + std::fmt::Debug {}
impl<T: Float + AddAssign + std::fmt::Debug> Scalar for T {}
pub trait Point<T: Scalar>: Default {
fn set(&mut self, i: u32, value: NotNan<T>);
fn get(&self, i: u32) -> NotNan<T>;
const DIM: u32;
const DIM_BIT_COUNT: u32 = 32 - Self::DIM.leading_zeros();
const DIM_MASK: u32 = (1 << Self::DIM_BIT_COUNT) - 1;
const MAX_NODE_COUNT: u32 = ((1u64 << (32 - Self::DIM_BIT_COUNT)) - 1) as u32;
}
#[inline]
fn slice_dist2<T: Scalar, P: Point<T>>(lhs: &[NotNan<T>], rhs: &[NotNan<T>]) -> NotNan<T> {
let mut dist2 = NotNan::<T>::zero();
for index in 0..P::DIM {
let index = index as usize;
let diff = lhs[index] - rhs[index];
dist2 += diff * diff;
}
dist2
}
pub type Index = u32;
pub struct Neighbour<T: Scalar, P: Point<T>> {
pub point: P,
pub dist2: NotNan<T>,
pub index: Index,
}
pub enum CandidateContainer {
Linear,
BinaryHeap,
}
pub struct Parameters<T: Scalar> {
pub epsilon: T,
pub max_radius: T,
pub allow_self_match: bool,
pub sort_results: bool,
}
type Nodes<T, P> = Vec<Node<T, P>>;
#[derive(Debug)]
pub struct KDTree<T: Scalar, P: Point<T>> {
bucket_size: u32,
nodes: Nodes<T, P>,
points: Vec<NotNan<T>>,
indices: Vec<Index>,
}
impl<T: Scalar, P: Point<T>> KDTree<T, P> {
pub fn new(cloud: &[P]) -> Self {
KDTree::new_with_bucket_size(cloud, 8)
}
pub fn new_with_bucket_size(cloud: &[P], bucket_size: u32) -> Self {
if bucket_size < 2 {
panic!(
"Bucket size must be at least 2, but {} was passed",
bucket_size
);
}
if cloud.len() > u32::MAX as usize {
panic!(
"Point cloud is larger than maximum possible size {}",
u32::MAX
);
}
let estimated_node_count = (cloud.len() / (bucket_size as usize / 2)) as u32;
if estimated_node_count > P::MAX_NODE_COUNT {
panic!("Point cloud has a risk to have more nodes {} than the kd-tree allows {}. The kd-tree has {} bits for dimensions and {} bits for node indices", estimated_node_count, P::MAX_NODE_COUNT, P::DIM_BIT_COUNT, 32 - P::DIM_BIT_COUNT);
}
let mut build_points: Vec<_> = (0..cloud.len()).collect();
let mut tree = KDTree {
bucket_size,
nodes: Vec::with_capacity(estimated_node_count as usize),
points: Vec::with_capacity(cloud.len() * P::DIM as usize),
indices: Vec::with_capacity(cloud.len()),
};
tree.build_nodes(cloud, &mut build_points);
tree
}
pub fn knn(&self, k: u32, query: &P) -> Vec<Neighbour<T, P>> {
let candidate_container = if k <= 16 {
CandidateContainer::Linear
} else {
CandidateContainer::BinaryHeap
};
#[cfg_attr(rustfmt, rustfmt_skip)]
self.knn_advanced(
k, query,
candidate_container,
&Parameters {
epsilon: T::from(0.0).unwrap(),
max_radius: T::infinity(),
allow_self_match: true,
sort_results: true,
},
None,
)
}
pub fn knn_advanced(
&self,
k: u32,
query: &P,
candidate_container: CandidateContainer,
parameters: &Parameters<T>,
touch_statistics: Option<&mut u32>,
) -> Vec<Neighbour<T, P>> {
#[cfg_attr(rustfmt, rustfmt_skip)]
(match candidate_container {
CandidateContainer::Linear => Self::knn_generic_heap::<Vec<InternalNeighbour<T>>>,
CandidateContainer::BinaryHeap => Self::knn_generic_heap::<BinaryHeap<InternalNeighbour<T>>>
})(
self,
k, query,
parameters, touch_statistics
)
}
fn knn_generic_heap<H: CandidateHeap<T>>(
&self,
k: u32,
query: &P,
parameters: &Parameters<T>,
touch_statistics: Option<&mut u32>,
) -> Vec<Neighbour<T, P>> {
let query_as_vec: Vec<_> = (0..P::DIM).map(|i| query.get(i)).collect();
let Parameters {
epsilon,
max_radius,
allow_self_match,
sort_results,
} = *parameters;
let max_error = epsilon + T::from(1).unwrap();
let max_error2 = NotNan::new(max_error * max_error).unwrap();
let max_radius2 = NotNan::new(max_radius * max_radius).unwrap();
#[cfg_attr(rustfmt, rustfmt_skip)]
self.knn_internal::<H>(
k, &query_as_vec,
&InternalParameters { max_error2, max_radius2, allow_self_match },
sort_results, touch_statistics,
)
.into_iter()
.map(|n| self.externalise_neighbour(n))
.collect()
}
fn knn_internal<H: CandidateHeap<T>>(
&self,
k: u32,
query: &[NotNan<T>],
internal_parameters: &InternalParameters<T>,
sort_results: bool,
touch_statistics: Option<&mut u32>,
) -> Vec<InternalNeighbour<T>> {
let mut off = vec![NotNan::<T>::zero(); P::DIM as usize];
let mut heap = H::new_with_k(k);
#[cfg_attr(rustfmt, rustfmt_skip)]
let leaf_touched_count = self.recurse_knn(
k, query,
0, NotNan::<T>::zero(),
&mut heap, &mut off,
internal_parameters,
);
if let Some(touch_statistics) = touch_statistics {
*touch_statistics = leaf_touched_count;
}
if sort_results {
heap.into_sorted_vec()
} else {
heap.into_vec()
}
}
#[allow(clippy::too_many_arguments)]
fn recurse_knn<H: CandidateHeap<T>>(
&self,
k: u32,
query: &[NotNan<T>],
node: usize,
rd: NotNan<T>,
heap: &mut H,
off: &mut [NotNan<T>],
internal_parameters: &InternalParameters<T>,
) -> u32 {
self.nodes[node].dispatch_on_type(
heap,
|heap, split_dim, split_val, right_child| {
let mut rd = rd;
let split_dim = split_dim as usize;
let old_off = off[split_dim];
let new_off = query[split_dim] - split_val;
let left_child = node + 1;
let right_child = right_child as usize;
let InternalParameters {
max_radius2,
max_error2,
..
} = *internal_parameters;
if new_off > NotNan::<T>::zero() {
#[cfg_attr(rustfmt, rustfmt_skip)]
let mut leaf_visited_count = self.recurse_knn(
k, query,
right_child, rd,
heap, off,
internal_parameters,
);
rd += new_off * new_off - old_off * old_off;
if rd <= max_radius2 && rd * max_error2 < heap.furthest_dist2() {
off[split_dim] = new_off;
#[cfg_attr(rustfmt, rustfmt_skip)]
let new_visits= self.recurse_knn(
k, query,
left_child, rd,
heap, off,
internal_parameters,
);
leaf_visited_count += new_visits;
off[split_dim] = old_off;
}
leaf_visited_count
} else {
#[cfg_attr(rustfmt, rustfmt_skip)]
let mut leaf_visited_count = self.recurse_knn(
k, query,
left_child, rd,
heap, off,
internal_parameters,
);
rd += new_off * new_off - old_off * old_off;
if rd <= max_radius2 && rd * max_error2 < heap.furthest_dist2() {
off[split_dim] = new_off;
#[cfg_attr(rustfmt, rustfmt_skip)]
let new_visits = self.recurse_knn(
k, query,
right_child, rd,
heap, off,
internal_parameters,
);
leaf_visited_count += new_visits;
off[split_dim] = old_off;
}
leaf_visited_count
}
},
|heap, bucket_start_index, bucket_size| {
let bucket_end_index = bucket_start_index + bucket_size;
for bucket_index in bucket_start_index..bucket_end_index {
let point_index = (bucket_index * P::DIM) as usize;
let point = &self.points[point_index..point_index + (P::DIM as usize)];
let dist2 = slice_dist2::<T, P>(query, point);
let epsilon = NotNan::new(T::epsilon()).unwrap();
let InternalParameters {
max_radius2,
allow_self_match,
..
} = *internal_parameters;
if dist2 < max_radius2 && (allow_self_match || (dist2 > epsilon)) {
heap.add(dist2, bucket_index);
}
}
bucket_size
},
)
}
fn build_nodes(&mut self, cloud: &[P], build_points: &mut [usize]) -> usize {
let count = build_points.len() as u32;
let pos = self.nodes.len();
if count <= self.bucket_size {
let bucket_start_index = self.indices.len() as u32;
self.points.reserve(build_points.len() * P::DIM as usize);
self.indices.reserve(build_points.len());
for point_index in build_points {
let point_index = *point_index;
self.indices.push(point_index as u32);
for i in 0..P::DIM {
self.points.push(cloud[point_index].get(i));
}
}
self.nodes
.push(Node::new_leaf_node(bucket_start_index, count));
return pos;
}
let (min_bounds, max_bounds) = Self::get_build_points_bounds(cloud, build_points);
let split_dim = Self::max_delta_index(&min_bounds, &max_bounds);
let split_dim_u = split_dim as usize;
let split_val = (max_bounds[split_dim_u] + min_bounds[split_dim_u]) * T::from(0.5).unwrap();
let range = max_bounds[split_dim_u] - min_bounds[split_dim_u];
let (left_points, right_points) = if range == T::from(0).unwrap() {
build_points.split_at_mut(build_points.len() / 2)
} else {
partition::partition(build_points, |index| {
cloud[*index].get(split_dim) < split_val
})
};
debug_assert_ne!(left_points.len(), 0);
debug_assert_ne!(right_points.len(), 0);
self.nodes.push(Node::new_split_node(split_dim, split_val));
let left_child = self.build_nodes(cloud, left_points);
debug_assert_eq!(left_child, pos + 1);
let right_child = self.build_nodes(cloud, right_points);
self.nodes[pos].set_child_index(right_child as u32);
pos
}
fn get_build_points_bounds(
cloud: &[P],
build_points: &[usize],
) -> (Vec<NotNan<T>>, Vec<NotNan<T>>) {
let mut min_bounds = vec![NotNan::<T>::max_value(); P::DIM as usize];
let mut max_bounds = vec![NotNan::<T>::min_value(); P::DIM as usize];
for p_index in build_points {
let p = &cloud[*p_index];
for index in 0..P::DIM {
let index_u = index as usize;
min_bounds[index_u] = clamp_max(p.get(index), min_bounds[index_u]);
max_bounds[index_u] = clamp_min(p.get(index), max_bounds[index_u]);
}
}
(min_bounds, max_bounds)
}
fn max_delta_index(lower_bound: &[NotNan<T>], upper_bound: &[NotNan<T>]) -> u32 {
lower_bound
.iter()
.zip(upper_bound.iter())
.enumerate()
.max_by_key(|(_, (l, u))| *u - *l)
.unwrap()
.0 as u32
}
fn externalise_neighbour(&self, neighbour: InternalNeighbour<T>) -> Neighbour<T, P> {
let mut point = P::default();
let base_index = neighbour.index * P::DIM;
for i in 0..P::DIM {
point.set(i, self.points[(base_index + i) as usize]);
}
Neighbour {
point,
dist2: neighbour.dist2,
index: self.indices[neighbour.index as usize],
}
}
}
#[cfg(test)]
mod tests {
use crate::*;
use dummy_point::{cloud_random, rand_point, P2};
use float_cmp::approx_eq;
fn cloud3() -> Vec<P2> {
vec![P2::new(0., 0.), P2::new(-1., 3.), P2::new(2., -4.)]
}
fn point_dist2<T: Scalar, P: Point<T>>(lhs: &P, rhs: &P) -> NotNan<T> {
let mut dist2 = NotNan::<T>::zero();
for index in 0..P::DIM {
let diff = lhs.get(index) - rhs.get(index);
dist2 += diff * diff;
}
dist2
}
fn brute_force_1nn(cloud: &[P2], query: &P2) -> Neighbour<f32, P2> {
let mut best_dist2 = f32::infinity();
let mut best_index = 0;
for (index, point) in cloud.iter().enumerate() {
let dist2 = point_dist2(point, query).into_inner();
if dist2 < best_dist2 {
best_dist2 = dist2;
best_index = index;
}
}
Neighbour {
point: cloud[best_index],
dist2: NotNan::new(best_dist2).unwrap(),
index: best_index as u32,
}
}
fn brute_force_knn<H: CandidateHeap<f32>>(
cloud: &[P2],
query: &P2,
k: u32,
) -> Vec<Neighbour<f32, P2>> {
let mut h = H::new_with_k(k);
for (index, point) in cloud.iter().enumerate() {
let dist2 = point_dist2(point, query);
h.add(dist2, index as u32);
}
h.into_sorted_vec()
.into_iter()
.map(|n| {
let index = n.index as usize;
Neighbour {
point: cloud[index],
dist2: n.dist2,
index: n.index,
}
})
.collect()
}
#[test]
fn test_get_build_points_bounds() {
let cloud = cloud3();
let indices = vec![0, 1, 2];
let bounds = KDTree::get_build_points_bounds(&cloud, &indices);
assert_eq!(bounds.0, vec![-1., -4.]);
assert_eq!(bounds.1, vec![2., 3.]);
}
#[test]
fn test_max_delta_index() {
let b = |x: f32, y: f32| {
[
NotNan::<f32>::new(x).unwrap(),
NotNan::<f32>::new(y).unwrap(),
]
};
assert_eq!(
KDTree::<f32, P2>::max_delta_index(&b(0., 0.), &b(0., 1.)),
1
);
assert_eq!(
KDTree::<f32, P2>::max_delta_index(&b(0., 0.), &b(-1., 1.)),
1
);
assert_eq!(
KDTree::<f32, P2>::max_delta_index(&b(0., 0.), &b(-1., -2.)),
0
);
}
#[test]
fn test_new() {
let cloud = cloud3();
let tree = KDTree::new_with_bucket_size(&cloud, 2);
dbg!(tree);
}
#[test]
fn test_1nn_allow_self() {
let mut touch_sum = 0;
const PASS_COUNT: u32 = 20;
const QUERY_COUNT: u32 = 100;
const CLOUD_SIZE: u32 = 1000;
const PARAMETERS: Parameters<f32> = Parameters {
epsilon: 0.0,
max_radius: f32::INFINITY,
allow_self_match: true,
sort_results: true,
};
for _ in 0..PASS_COUNT {
let cloud = cloud_random(CLOUD_SIZE);
let tree = KDTree::new(&cloud);
for _ in 0..QUERY_COUNT {
let query = rand_point();
let mut touch_statistics = 0;
let nns_lin = tree.knn_advanced(
1,
&query,
CandidateContainer::Linear,
&PARAMETERS,
Some(&mut touch_statistics),
);
assert_eq!(nns_lin.len(), 1);
let nn_lin = &nns_lin[0];
assert_eq!(nn_lin.point, cloud[nn_lin.index as usize]);
touch_sum += touch_statistics;
let nns_bin =
tree.knn_advanced(1, &query, CandidateContainer::BinaryHeap, &PARAMETERS, None);
assert_eq!(nns_bin.len(), 1);
let nn_bin = &nns_bin[0];
assert_eq!(nn_bin.point, cloud[nn_bin.index as usize]);
let nn_bf = brute_force_1nn(&cloud, &query);
assert_eq!(nn_bf.point, cloud[nn_bf.index as usize]);
assert_eq!(
nn_bin.index, nn_bf.index,
"KDTree binary heap: mismatch indexes\nquery: {}\npoint {}, {}\nvs bf {}, {}",
query, nn_bin.dist2, nn_bin.point, nn_bf.dist2, nn_bf.point
);
assert_eq!(nn_lin.index, nn_bf.index, "\nKDTree linear heap: mismatch indexes\nquery: {}\npoint {}, {}\nvs bf {}, {}\n", query, nn_lin.dist2, nn_lin.point, nn_bf.dist2, nn_bf.point);
assert!(approx_eq!(f32, *nn_lin.dist2, *nn_bf.dist2, ulps = 2));
assert!(approx_eq!(f32, *nn_bin.dist2, *nn_bf.dist2, ulps = 2));
}
}
let touch_pct = (touch_sum * 100) as f32 / (PASS_COUNT * QUERY_COUNT * CLOUD_SIZE) as f32;
println!("Average tree point touched: {} %", touch_pct);
}
#[test]
fn test_knn_allow_self() {
const QUERY_COUNT: u32 = 100;
const CLOUD_SIZE: u32 = 1000;
const PARAMETERS: Parameters<f32> = Parameters {
epsilon: 0.0,
max_radius: f32::INFINITY,
allow_self_match: true,
sort_results: true,
};
let cloud = cloud_random(CLOUD_SIZE);
let tree = KDTree::new(&cloud);
for k in [1, 2, 3, 5, 7, 13] {
for _ in 0..QUERY_COUNT {
let query = rand_point();
let nns_bf_lin = brute_force_knn::<Vec<InternalNeighbour<f32>>>(&cloud, &query, k);
assert_eq!(nns_bf_lin.len(), k as usize);
let nns_bf_bin =
brute_force_knn::<BinaryHeap<InternalNeighbour<f32>>>(&cloud, &query, k);
assert_eq!(nns_bf_bin.len(), k as usize);
#[cfg_attr(rustfmt, rustfmt_skip)]
let nns_bin = tree.knn_advanced(
k, &query,
CandidateContainer::BinaryHeap,
&PARAMETERS,
None,
);
assert_eq!(nns_bin.len(), k as usize);
#[cfg_attr(rustfmt, rustfmt_skip)]
let nns_lin = tree.knn_advanced(
k, &query,
CandidateContainer::Linear,
&PARAMETERS,
None,
);
assert_eq!(nns_lin.len(), k as usize);
for i in 0..k as usize {
let nn_bf_lin = &nns_bf_lin[i];
let nn_bf_bin = &nns_bf_bin[i];
let nn_lin = &nns_lin[i];
let nn_bin = &nns_bin[i];
assert_eq!(nn_bf_lin.point, cloud[nn_bf_lin.index as usize]);
assert_eq!(nn_bf_bin.point, cloud[nn_bf_bin.index as usize]);
assert_eq!(nn_lin.point, cloud[nn_lin.index as usize]);
assert_eq!(nn_bin.point, cloud[nn_bin.index as usize]);
assert_eq!(nn_bf_bin.index, nn_bf_lin.index, "BF binary heap: mismatch indexes at {} on {}\nquery: {}\n bf bin {}, {}\nvs bf lin {}, {}\n", i, k, query, nn_bf_bin.dist2, nn_bf_bin.point, nn_bf_lin.dist2, nn_bf_lin.point);
assert_eq!(nn_lin.index, nn_bf_lin.index, "\nKDTree linear heap: mismatch indexes at {} on {}\nquery: {}\npoint {}, {}\nvs bf {}, {}\n", i, k, query, nn_lin.dist2, nn_lin.point, nn_bf_lin.dist2, nn_bf_lin.point);
assert_eq!(nn_bin.index, nn_bf_lin.index, "\nKDTree binary heap: mismatch indexes {} on {}\nquery: {}\npoint {}, {}\nvs bf {}, {}\n", i, k, query, nn_bin.dist2, nn_bin.point, nn_bf_lin.dist2, nn_bf_lin.point);
assert!(approx_eq!(
f32,
*nn_bf_bin.dist2,
*nn_bf_lin.dist2,
ulps = 2
));
assert!(approx_eq!(f32, *nn_lin.dist2, *nn_bf_lin.dist2, ulps = 2));
assert!(approx_eq!(f32, *nn_bin.dist2, *nn_bf_lin.dist2, ulps = 2));
}
}
}
}
}