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optics.go
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optics.go
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package govector
import (
"fmt"
"log"
"container/heap"
"time"
"github.com/vseledkin/govector/annoy"
"github.com/vseledkin/govector/index"
)
const (
UNDEFINED float32 = -1
)
type Point struct {
Item string
ReachabilityDistance float32
CoreDistance float32
Processed bool
NeiboursCount int
Vector []float32
}
func next(pq index.MinPriorityQueue) *Point {
for _, item := range pq {
if !item.Item.(*Point).Processed {
return item.Item.(*Point)
}
}
return nil
}
/*
ComputeClusters
epsilon - the maximum distance (radius) to consider
MinPts - the number of points required to form a cluster.
*/
func (m *Manifold) ComputeClusters(epsilon float32, MinPts int) {
/*defer func() {
if r := recover(); r != nil {
fmt.Println("Recovered in f", r)
fmt.Println("Failed to create index")
}
}()*/
//var max uint32 = 1000
var max uint32 = 100000
if m.WordCount() < max {
max = m.WordCount()
}
points := make([]interface{}, max)
log.Printf("Reading %d words", max)
var i uint32 = 0
m.VisitWords(func(key string) bool {
if len(key) == 0 {
panic(fmt.Errorf("Empty key"))
}
points[i] = &Point{key, UNDEFINED, UNDEFINED, false, 0, nil}
i++
if i == max {
return false
}
if i%1e4 == 0 {
log.Printf("Read %d words", i)
}
return true
})
log.Printf("Read %d words", i)
searchLimit := 200
idx := annoy.NewAnnoyIndexAngular(128)
start := time.Now()
for i, pp := range points {
v, e := m.GetVector(pp.(*Point).Item)
if e != nil {
panic(e)
}
pp.(*Point).Vector = v
idx.AddItem(i, pp.(*Point).Vector)
}
readTime := time.Now().Sub(start).Seconds()
start = time.Now()
idx.Build(16)
indexTime := time.Now().Sub(start).Seconds()
search := func(v []float32) ([]interface{}, []float32) {
var distances []float32
var near []int
var nearest []interface{}
idx.GetNnsByVector(v, searchLimit, -1, &near, &distances)
for i, j := range near {
if distances[i] > epsilon {
return nearest[:i], distances[:i]
}
nearest = append(nearest, points[j])
}
return nearest, distances
}
var orderedList []interface{}
// Optics
start = time.Now()
for _, pp := range points {
p := pp.(*Point)
//fmt.Printf("PROCESS: p -> %d-%s CoreD:%f ReachD:%f N:%d %v\n", j, p.Item, p.CoreDistance, p.ReachabilityDistance, p.NeiboursCount, p.Processed)
if p.Processed {
continue
}
N, distances := search(p.Vector)
//fmt.Printf("<<<<<<<<<\n")
//fmt.Printf("Near: %s are:\n", p.Item)
//for i, ppp := range N {
// fmt.Printf("%f %s\n", distances[i], ppp.(*Point).Item)
//}
p.Processed = true
p.NeiboursCount = len(N)
if len(N) >= MinPts {
p.CoreDistance = distances[MinPts-1]
p.ReachabilityDistance = 0 //p.CoreDistance // distance to itself is zero
}
//orderedList = append(orderedList, p)
if p.CoreDistance != UNDEFINED {
var seeds index.MinPriorityQueue
heap.Push(&seeds, &index.HeapItem{p, p.ReachabilityDistance, -1})
m.update(N, p, &seeds, epsilon, MinPts)
for q := next(seeds); q != nil; q = next(seeds) {
//for _, qhi := range seeds {
//q := heap.Pop(&seeds).(*index.HeapItem).Item.(*Point)
NQ, nqd := search(q.Vector)
//fmt.Printf(">>>>>>>>> %d\n", len(seeds))
//fmt.Printf("Near: %s are:\n", q.Item)
//for i, ppp := range NQ {
// fmt.Printf("%f %s\n", nqd[i], ppp.(*Point).Item)
//}
q.Processed = true
q.NeiboursCount = len(NQ)
if len(NQ) >= MinPts {
q.CoreDistance = nqd[MinPts-1]
}
//if q.ReachabilityDistance != UNDEFINED {
// heap.Push(&out, &index.HeapItem{q, q.ReachabilityDistance, -1})
//}
//orderedList = append(orderedList, q)
if q.CoreDistance != UNDEFINED {
m.update(NQ, q, &seeds, epsilon, MinPts)
}
}
for len(seeds) > 0 {
pout := heap.Pop(&seeds).(*index.HeapItem).Item.(*Point)
orderedList = append(orderedList, pout)
}
orderedList = append(orderedList, nil)
//fmt.Printf("Finish proc SEEDS l:%d\n", len(seeds))
}
/*
if len(nearestPoints) > MinPts {
fmt.Printf("%d-%s %f\n", j, p.(*Point).Item, p.(*Point).CoreDistance)
for i, np := range nearestPoints {
fmt.Printf("\t%d %s %f\n", i, np.(*Point).Item, distances[i])
}
}*/
}
//for j, p := range points {
// fmt.Printf("p -> %d-%s CoreD:%f ReachD:%f N:%d %v\n", j, p.(*Point).Item, p.(*Point).CoreDistance, p.(*Point).ReachabilityDistance, p.(*Point).NeiboursCount, p.(*Point).Processed)
//}
clusterTime := time.Now().Sub(start).Seconds()
fmt.Printf("--------\n")
outCount := 0
for _, p := range orderedList {
if p == nil {
fmt.Printf("------------------\n")
continue
}
if p.(*Point).ReachabilityDistance == UNDEFINED {
fmt.Printf("o -> %s %d\n", p.(*Point).Item, p.(*Point).NeiboursCount)
//fmt.Printf("o -> %s CoreD:%f ReachD:%f N:%d %v\n", p.(*Point).Item, p.(*Point).CoreDistance, p.(*Point).ReachabilityDistance, p.(*Point).NeiboursCount, p.(*Point).Processed)
} else {
fmt.Printf("o -> %d-%s CoreD:%f ReachD:%f N:%d %v\n", outCount, p.(*Point).Item, p.(*Point).CoreDistance, p.(*Point).ReachabilityDistance, p.(*Point).NeiboursCount, p.(*Point).Processed)
outCount++
}
}
fmt.Printf("Index time: %f s\n", indexTime)
fmt.Printf("Read time: %f s\n", readTime)
fmt.Printf("Cluster time: %f s\n", clusterTime)
}
func labeler(it *index.HeapItem) string {
return fmt.Sprintf("%s %v", it.Item.(*Point).Item, it.Item.(*Point).Processed)
}
func (m *Manifold) update(N []interface{}, P interface{}, seeds *index.MinPriorityQueue, epsilon float32, MinPts int) {
p := P.(*Point)
for _, oo := range N {
o := oo.(*Point)
if o.Processed {
continue
}
newReachDist := max(p.CoreDistance, m.Angular(p, o))
if o.ReachabilityDistance == UNDEFINED { // o is not in Seeds
o.ReachabilityDistance = newReachDist
//fmt.Printf("Add %s to SEEDS l:%d with RD %f\n", o.Item, len(*seeds), o.ReachabilityDistance)
heap.Push(seeds, &index.HeapItem{o, o.ReachabilityDistance, -1})
//seeds.Print(labeler)
} else {
if newReachDist < o.ReachabilityDistance { // o in Seeds, check for improvement
//fmt.Printf("Update RD of %s %v from %f to %f in l:%d \n", o.Item, o.Processed, o.ReachabilityDistance, newReachDist, len(*seeds))
o.ReachabilityDistance = newReachDist
/// find item position in pqueue
///var i int
///var hi *index.HeapItem
///var ok bool
//seeds.Print(labeler)
//for i, hi := range *seeds {
// fmt.Printf("\t%d %d %s %f %f\n", i, hi.Index, hi.Item.(*Point).Item, hi.Item.(*Point).ReachabilityDistance, hi.Dist)
// if hi.Item.(*Point).Item == o.Item {
// hi.Dist = o.ReachabilityDistance
// }
//}
hi := seeds.Find(o)
hi.Dist = o.ReachabilityDistance
heap.Fix(seeds, hi.Index)
//fmt.Printf("\n")
//seeds.Print(labeler)
//for i, hi := range *seeds {
// fmt.Printf("\t%d %d %s %f %f\n", i, hi.Index, hi.Item.(*Point).Item, hi.Item.(*Point).ReachabilityDistance, hi.Dist)
// if hi.Item.(*Point).Item == o.Item {
// hi.Dist = o.ReachabilityDistance
// }
//}
}
}
}
}