Merge pull request #8 from azizkayumov/develop

reverse knn (preinsert + batchnn)

Cargo.toml

@@ -1,7 +1,11 @@
 [workspace]
 
 members = [
-    "lib",
+    "bench",
     "demo",
+    "lib",
 ]
 resolver = "2"
+
+[patch.crates-io]
+rindex = { path = "lib" }

bench/Cargo.toml

@@ -0,0 +1,16 @@
+[package]
+name = "bench"
+version = "0.1.0"
+edition = "2021"
+authors = ["Kayumov A.I. <[email protected]>"]
+
+[dev-dependencies]
+rindex = { path = "../lib" }
+rand = "0.8.5"
+rstar = "0.12.0"
+ordered-float = "3.4.0"
+criterion = "0.5.1"
+
+[[bench]]
+name = "main"
+harness = false

bench/benches/main.rs

@@ -0,0 +1,10 @@
+use criterion::{criterion_group, criterion_main};
+mod uniform;
+
+criterion_group!(
+    benches,
+    uniform::build,
+    uniform::query,
+    uniform::query_radius
+);
+criterion_main!(benches);

bench/benches/uniform/build.rs

@@ -0,0 +1,67 @@
+use crate::uniform::{DELETION_PROB, DIMENSION as D, K, NUM_OPERATIONS};
+use core::f64;
+use criterion::Criterion;
+use rand::{rngs::StdRng, Rng, SeedableRng};
+use rindex::Rindex;
+use rstar::RTree;
+
+pub fn benchmark(criterion: &mut Criterion) {
+    let mut group = criterion.benchmark_group("build");
+    //group.sample_size(10);
+
+    group.bench_function("rindex", |b| {
+        b.iter(|| {
+            build_rindex();
+        });
+    });
+
+    group.bench_function("rstar", |b| {
+        b.iter(|| {
+            build_rstar();
+        });
+    });
+}
+
+pub fn build_rindex() -> (Rindex<D>, Vec<(usize, [f64; D])>) {
+    let mut rng = StdRng::seed_from_u64(0);
+    let mut index = Rindex::new(10, K).expect("Failed to create Rindex");
+    let mut points = Vec::new();
+    for _ in 0..NUM_OPERATIONS {
+        let should_delete = rng.gen_bool(DELETION_PROB);
+        if should_delete && !points.is_empty() {
+            let idx = rng.gen_range(0..points.len());
+            let (point_id, _) = points.swap_remove(idx);
+            index.delete(point_id);
+        } else {
+            let mut point = [0.0; D];
+            for i in 0..D {
+                point[i] = rng.gen_range(-100.0..100.0);
+            }
+            let point_id = index.insert(point);
+            points.push((point_id, point));
+        }
+    }
+    (index, points)
+}
+
+pub fn build_rstar() -> (RTree<[f64; D]>, Vec<[f64; D]>) {
+    let mut rng = StdRng::seed_from_u64(0);
+    let mut rstar = rstar::RTree::new();
+    let mut points = Vec::new();
+    for _ in 0..NUM_OPERATIONS {
+        let should_delete = rng.gen_bool(DELETION_PROB);
+        if should_delete && !points.is_empty() {
+            let idx = rng.gen_range(0..points.len());
+            let point = points.swap_remove(idx);
+            rstar.remove(&point);
+        } else {
+            let mut point = [0.0; D];
+            for i in 0..D {
+                point[i] = rng.gen_range(-100.0..100.0);
+            }
+            rstar.insert(point);
+            points.push(point);
+        }
+    }
+    (rstar, points)
+}

bench/benches/uniform/mod.rs

@@ -0,0 +1,15 @@
+mod build;
+mod query;
+mod query_radius;
+
+// Benchmark parameters:
+pub const DIMENSION: usize = 2;
+pub const NUM_OPERATIONS: usize = 10000; // Number of operations to perform (insertions and deletions)
+pub const DELETION_PROB: f64 = 0.2; // Probability of deleting a point for simulating dynamic data
+pub const K: usize = 10; // Number of neighbors to query
+pub const RADIUS: f64 = 5.0; // Radius for range queries
+pub const RADIUS_SQUARED: f64 = RADIUS * RADIUS;
+
+pub use build::benchmark as build;
+pub use query::benchmark as query;
+pub use query_radius::benchmark as query_radius;

bench/benches/uniform/query.rs

@@ -0,0 +1,67 @@
+use crate::uniform::build::{build_rindex, build_rstar};
+use crate::uniform::{DIMENSION as D, K};
+use core::f64;
+use criterion::Criterion;
+use ordered_float::OrderedFloat;
+use rindex::Rindex;
+use rstar::RTree;
+use std::collections::BinaryHeap;
+
+pub fn benchmark(criterion: &mut Criterion) {
+    let mut group = criterion.benchmark_group("query");
+    //group.sample_size(10);
+
+    let (rindex, pts) = build_rindex();
+    group.bench_function("rindex", |b| {
+        b.iter(|| {
+            query_rindex(&rindex, &pts);
+        });
+    });
+
+    let (rstar, pts) = build_rstar();
+    group.bench_function("rstar", |b| {
+        b.iter(|| {
+            query_rstar(&rstar, &pts);
+        });
+    });
+
+    group.bench_function("list", |b| {
+        b.iter(|| {
+            query_list(&pts);
+        });
+    });
+}
+
+fn query_rindex(rindex: &Rindex<D>, points: &Vec<(usize, [f64; D])>) {
+    for (query_id, _) in points {
+        let (neighbors, _) = rindex.neighbors_of(*query_id);
+        assert_eq!(neighbors.len(), 10);
+    }
+}
+
+fn query_rstar(rstar: &RTree<[f64; D]>, points: &Vec<[f64; D]>) {
+    for query in points {
+        let mut iter = rstar.nearest_neighbor_iter(&query);
+        let results = iter.by_ref().take(K).collect::<Vec<_>>();
+        assert_eq!(results.len(), K);
+    }
+}
+
+fn query_list(points: &Vec<[f64; D]>) {
+    for query in points {
+        let mut results = BinaryHeap::from(vec![OrderedFloat(f64::INFINITY); K]);
+        for point in points {
+            let dist = query
+                .iter()
+                .zip(point.iter())
+                .map(|(a, b)| (a - b).powi(2))
+                .sum::<f64>()
+                .sqrt();
+            if dist < results.peek().unwrap().0 {
+                results.push(OrderedFloat(dist));
+                results.pop();
+            }
+        }
+        assert_eq!(results.len(), K);
+    }
+}

bench/benches/uniform/query_radius.rs

@@ -0,0 +1,65 @@
+use crate::uniform::build::{build_rindex, build_rstar};
+use crate::uniform::{DIMENSION as D, RADIUS, RADIUS_SQUARED};
+use core::f64;
+use criterion::Criterion;
+use rindex::Rindex;
+use rstar::RTree;
+
+pub fn benchmark(criterion: &mut Criterion) {
+    let mut group = criterion.benchmark_group("query_radius");
+    //group.sample_size(10);
+
+    let (rindex, pts) = build_rindex();
+    group.bench_function("rindex", |b| {
+        b.iter(|| {
+            query_range_rindex(&rindex, &pts);
+        });
+    });
+
+    let (rstar, pts) = build_rstar();
+    group.bench_function("rstar", |b| {
+        b.iter(|| {
+            query_range_rstar(&rstar, &pts);
+        });
+    });
+
+    group.bench_function("list", |b| {
+        b.iter(|| {
+            query_range_list(&pts);
+        });
+    });
+}
+
+fn query_range_rindex(rindex: &Rindex<D>, points: &Vec<(usize, [f64; D])>) {
+    for (query_id, query) in points {
+        let (neighbors, _) = rindex.query(&query, RADIUS);
+        assert!(neighbors.contains(query_id));
+    }
+}
+
+fn query_range_rstar(rstar: &RTree<[f64; D]>, points: &Vec<[f64; D]>) {
+    for query in points {
+        let result = rstar
+            .locate_within_distance(*query, RADIUS_SQUARED)
+            .collect::<Vec<_>>();
+        assert!(result.contains(&query));
+    }
+}
+
+fn query_range_list(points: &Vec<[f64; D]>) {
+    for query in points {
+        let mut results = Vec::new();
+        for point in points {
+            let dist = query
+                .iter()
+                .zip(point.iter())
+                .map(|(a, b)| (a - b).powi(2))
+                .sum::<f64>()
+                .sqrt();
+            if dist <= RADIUS {
+                results.push(dist);
+            }
+        }
+        assert!(results.contains(&0.0));
+    }
+}