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Add kyroy/kdtree performance data #9

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Aug 5, 2022
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Add kyroy/kdtree performance data #9

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71 changes: 71 additions & 0 deletions container/kyroy/kyroy.go
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Original file line number Diff line number Diff line change
@@ -0,0 +1,71 @@
// Package kyroy is a wrapper around the @kyroy k-D tree implementation. This is
// used for performance testing.
package kyroy

import (
"github.com/downflux/go-geometry/nd/hyperrectangle"
"github.com/downflux/go-geometry/nd/vector"
"github.com/downflux/go-kd/filter"
"github.com/downflux/go-kd/point"
"github.com/kyroy/kdtree"
"github.com/kyroy/kdtree/points"
)

type KD[T point.P] kdtree.KDTree

func New[T point.P](data []T) *KD[T] {
var ps []kdtree.Point
for _, p := range data {
ps = append(ps, points.NewPoint([]float64(p.P()), p))
}
return (*KD[T])(kdtree.New(ps))
}

func (t *KD[T]) KNN(p vector.V, k int, f filter.F[T]) []T {
var data []T
for _, p := range (*kdtree.KDTree)(t).KNN(
points.NewPoint([]float64(p), nil),
k,
) {
if f(p.(*points.Point).Data.(T)) {
data = append(data, p.(*points.Point).Data.(T))
}
}
return data
}

func (t *KD[T]) Data() []T {
var data []T
for _, p := range (*kdtree.KDTree)(t).Points() {
data = append(data, p.(T))
}
return data
}

func (t *KD[T]) RangeSearch(q hyperrectangle.R, f filter.F[T]) []T {
var r [][2]float64
for i := vector.D(0); i < q.Min().Dimension(); i++ {
r = append(r, [2]float64{q.Min().X(i), q.Max().X(i)})
}

var data []T
for _, p := range (*kdtree.KDTree)(t).RangeSearch(r) {
if f(p.(*points.Point).Data.(T)) {
data = append(data, p.(*points.Point).Data.(T))
}
}
return data
}

func (t *KD[T]) Balance() { (*kdtree.KDTree)(t).Balance() }
func (t *KD[T]) Insert(p T) { (*kdtree.KDTree)(t).Insert(points.NewPoint([]float64(p.P()), p)) }

func (t *KD[T]) Remove(p vector.V, f filter.F[T]) (T, bool) {
v := (*kdtree.KDTree)(t).Remove(points.NewPoint([]float64(p), nil)).(*points.Point).Data.(T)
if !f(v) {
var blank T
(*kdtree.KDTree)(t).Insert(points.NewPoint([]float64(p), v))
return blank, false
}
return v, true
}
8 changes: 8 additions & 0 deletions container/kyroy/kyroy_test.go
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
package kyroy

import (
"github.com/downflux/go-kd/container"
"github.com/downflux/go-kd/point/mock"
)

var _ container.C[mock.P] = &KD[mock.P]{}
3 changes: 3 additions & 0 deletions go.mod
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Expand Up @@ -5,4 +5,7 @@ go 1.18
require (
github.com/downflux/go-geometry v0.10.2
github.com/google/go-cmp v0.5.8
github.com/kyroy/kdtree v0.0.0-20200419114247-70830f883f1d
)

require github.com/kyroy/priority-queue v0.0.0-20180327160706-6e21825e7e0c // indirect
11 changes: 11 additions & 0 deletions go.sum
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Original file line number Diff line number Diff line change
@@ -1,4 +1,15 @@
github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
github.com/downflux/go-geometry v0.10.2 h1:Z79Khzl6AKMSMLnM5xG75fEOL1fmIWlF14+8j+r01D0=
github.com/downflux/go-geometry v0.10.2/go.mod h1:XWTzSaMiRMAxupAR+cXAsa1Q75TCSp1Shc/ydsJ0xVE=
github.com/google/go-cmp v0.5.8 h1:e6P7q2lk1O+qJJb4BtCQXlK8vWEO8V1ZeuEdJNOqZyg=
github.com/google/go-cmp v0.5.8/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
github.com/jupp0r/go-priority-queue v0.0.0-20160601094913-ab1073853bde/go.mod h1:RDgD/dfPmIwFH0qdUOjw71HjtWg56CtyLIoHL+R1wJw=
github.com/kyroy/kdtree v0.0.0-20200419114247-70830f883f1d h1:1n5M/49q9H6QtNJiiVL/W5mqgT1UdlGQ7oLP+DkJ1vs=
github.com/kyroy/kdtree v0.0.0-20200419114247-70830f883f1d/go.mod h1:6oJGQK7VSg3RxSQ7QspgqpCmKjIbAslgT2wBXbFJUZw=
github.com/kyroy/priority-queue v0.0.0-20180327160706-6e21825e7e0c h1:1c7+XOOGQ19cXjZ1Ss/irljQxgPvb+8z+jNEprCXl20=
github.com/kyroy/priority-queue v0.0.0-20180327160706-6e21825e7e0c/go.mod h1:R477L6j2/dUcE0q0aftk0kR5Xt93W7g1066AodcJhEo=
github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4=
gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
56 changes: 46 additions & 10 deletions internal/perf/perf_test.go
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ import (
"github.com/downflux/go-geometry/nd/vector"
"github.com/downflux/go-kd/container"
"github.com/downflux/go-kd/container/bruteforce"
"github.com/downflux/go-kd/container/kyroy"
"github.com/downflux/go-kd/internal/perf/util"
"github.com/downflux/go-kd/kd"
"github.com/downflux/go-kd/point/mock"
Expand All @@ -22,15 +23,24 @@ func BenchmarkNew(b *testing.B) {
k vector.D
n int

// kyroy implementation does not take a leaf-size parameter.
kyroy bool

size int
}

var configs []config
for _, k := range util.BenchmarkKRange {
for _, n := range util.BenchmarkNRange {
configs = append(configs, config{
name: fmt.Sprintf("kyroy/K=%v/N=%v", k, n),
k: k,
n: n,
kyroy: true,
})
for _, size := range util.BenchmarkSizeRange {
configs = append(configs, config{
name: fmt.Sprintf("K=%v/N=%v/LeafSize=%v", k, n, size),
name: fmt.Sprintf("Real/K=%v/N=%v/LeafSize=%v", k, n, size),
k: k,
n: n,
size: size,
Expand All @@ -41,15 +51,24 @@ func BenchmarkNew(b *testing.B) {

for _, c := range configs {
ps := util.Generate(c.n, c.k)
b.Run(c.name, func(b *testing.B) {
for i := 0; i < b.N; i++ {
kd.New[*mock.P](kd.O[*mock.P]{
Data: ps,
K: c.k,
N: c.size,
})
}
})

if c.kyroy {
b.Run(c.name, func(b *testing.B) {
for i := 0; i < b.N; i++ {
kyroy.New[*mock.P](ps)
}
})
} else {
b.Run(c.name, func(b *testing.B) {
for i := 0; i < b.N; i++ {
kd.New[*mock.P](kd.O[*mock.P]{
Data: ps,
K: c.k,
N: c.size,
})
}
})
}
}
}

Expand Down Expand Up @@ -78,6 +97,15 @@ func BenchmarkKNN(b *testing.B) {
for _, f := range util.BenchmarkFRange {
knn := int(float64(n) * f)

// kyroy implementation does not take a
// leaf-size parameter.
configs = append(configs, config{
name: fmt.Sprintf("kyroy/K=%v/N=%v/KNN=%v", k, n, f),
t: kyroy.New[*mock.P](ps),
p: vector.V(make([]float64, k)),
knn: knn,
})

for _, size := range util.BenchmarkSizeRange {
configs = append(configs, config{
name: fmt.Sprintf("Real/K=%v/N=%v/LeafSize=%v/KNN=%v", k, n, size, f),
Expand Down Expand Up @@ -129,6 +157,14 @@ func BenchmarkRangeSearch(b *testing.B) {
for _, f := range util.BenchmarkFRange {
q := util.RH(k, f)

// kyroy implementation does not take a
// leaf-size parameter.
configs = append(configs, config{
name: fmt.Sprintf("kyroy/K=%v/N=%v/Coverage=%v", k, n, f),
t: kyroy.New[*mock.P](ps),
q: q,
})

for _, size := range util.BenchmarkSizeRange {
configs = append(configs, config{
name: fmt.Sprintf("Real/K=%v/N=%v/LeafSize=%v/Coverage=%v", k, n, size, f),
Expand Down