Blob tdigest.go
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// Package tdigest provides a highly accurate mergeable data-structure // for quantile estimation. // // Typical T-Digest use cases involve accumulating metrics on several // distinct nodes of a cluster and then merging them together to get // a system-wide quantile overview. Things such as: sensory data from // IoT devices, quantiles over enormous document datasets (think // ElasticSearch), performance metrics for distributed systems, etc. // // After you create (and configure, if desired) the digest: // digest, err := tdigest.New(tdigest.Compression(100)) // // You can then use it for registering measurements: // digest.Add(number) // // Estimating quantiles: // digest.Quantile(0.99) // // And merging with another digest: // digest.Merge(otherDigest) package tdigest import ( "fmt" "math" ) // TDigest is a quantile approximation data structure. type TDigest struct { summary *summary compression float64 count uint64 rng RNG } // New creates a new digest. // // By default the digest is constructed with a configuration that // should be useful for most use-cases. It comes with compression // set to 100 and uses a local random number generator for // performance reasons. func New(options ...tdigestOption) (*TDigest, error) { tdigest, err := newWithoutSummary(options...) if err != nil { return nil, err } tdigest.summary = newSummary(estimateCapacity(tdigest.compression)) return tdigest, nil } // Creates a tdigest instance without allocating a summary. func newWithoutSummary(options ...tdigestOption) (*TDigest, error) { tdigest := &TDigest{ compression: 100, count: 0, rng: newLocalRNG(1), } for _, option := range options { err := option(tdigest) if err != nil { return nil, err } } return tdigest, nil } func _quantile(index float64, previousIndex float64, nextIndex float64, previousMean float64, nextMean float64) float64 { delta := nextIndex - previousIndex previousWeight := (nextIndex - index) / delta nextWeight := (index - previousIndex) / delta return previousMean*previousWeight + nextMean*nextWeight } // Compression returns the TDigest compression. func (t *TDigest) Compression() float64 { return t.compression } // Quantile returns the desired percentile estimation. // // Values of p must be between 0 and 1 (inclusive), will panic otherwise. func (t *TDigest) Quantile(q float64) float64 { if q < 0 || q > 1 { panic("q must be between 0 and 1 (inclusive)") } if t.summary.Len() == 0 { return math.NaN() } else if t.summary.Len() == 1 { return t.summary.Mean(0) } index := q * float64(t.count-1) previousMean := math.NaN() previousIndex := float64(0) next, total := t.summary.FloorSum(index) if next > 0 { previousMean = t.summary.Mean(next - 1) previousIndex = total - float64(t.summary.Count(next-1)+1)/2 } for { nextIndex := total + float64(t.summary.Count(next)-1)/2 if nextIndex >= index { if math.IsNaN(previousMean) { // the index is before the 1st centroid if nextIndex == previousIndex { return t.summary.Mean(next) } // assume linear growth nextIndex2 := total + float64(t.summary.Count(next)) + float64(t.summary.Count(next+1)-1)/2 previousMean = (nextIndex2*t.summary.Mean(next) - nextIndex*t.summary.Mean(next+1)) / (nextIndex2 - nextIndex) } // common case: two centroids found, the result in in between return _quantile(index, previousIndex, nextIndex, previousMean, t.summary.Mean(next)) } else if next+1 == t.summary.Len() { // the index is after the last centroid nextIndex2 := float64(t.count - 1) nextMean2 := (t.summary.Mean(next)*(nextIndex2-previousIndex) - previousMean*(nextIndex2-nextIndex)) / (nextIndex - previousIndex) return _quantile(index, nextIndex, nextIndex2, t.summary.Mean(next), nextMean2) } total += float64(t.summary.Count(next)) previousMean = t.summary.Mean(next) previousIndex = nextIndex next++ } // unreachable } // boundedWeightedAverage computes the weighted average of two // centroids guaranteeing that the result will be between x1 and x2, // inclusive. // // Refer to https://github.com/caio/go-tdigest/pull/19 for more details func boundedWeightedAverage(x1 float64, w1 float64, x2 float64, w2 float64) float64 { if x1 > x2 { x1, x2, w1, w2 = x2, x1, w2, w1 } result := (x1*w1 + x2*w2) / (w1 + w2) return math.Max(x1, math.Min(result, x2)) } // AddWeighted registers a new sample in the digest. // // It's the main entry point for the digest and very likely the only // method to be used for collecting samples. The count parameter is for // when you are registering a sample that occurred multiple times - the // most common value for this is 1. // // This will emit an error if `value` is NaN of if `count` is zero. func (t *TDigest) AddWeighted(value float64, count uint64) (err error) { if count == 0 { return fmt.Errorf("Illegal datapoint <value: %.4f, count: %d>", value, count) } if t.summary.Len() == 0 { err = t.summary.Add(value, count) t.count = uint64(count) return err } begin := t.summary.Floor(value) if begin == -1 { begin = 0 } begin, end := t.findNeighbors(begin, value) closest := t.chooseMergeCandidate(begin, end, value, count) if closest == t.summary.Len() { err = t.summary.Add(value, count) if err != nil { return err } } else { c := float64(t.summary.Count(closest)) newMean := boundedWeightedAverage(t.summary.Mean(closest), c, value, float64(count)) t.summary.setAt(closest, newMean, uint64(c)+count) } t.count += uint64(count) if float64(t.summary.Len()) > 20*t.compression { err = t.Compress() } return err } // Count returns the total number of samples this digest represents // // The result represents how many times Add() was called on a digest // plus how many samples the digests it has been merged with had. // This is useful mainly for two scenarios: // // - Knowing if there is enough data so you can trust the quantiles // // - Knowing if you've registered too many samples already and // deciding what to do about it. // // For the second case one approach would be to create a side empty // digest and start registering samples on it as well as on the old // (big) one and then discard the bigger one after a certain criterion // is reached (say, minimum number of samples or a small relative // error between new and old digests). func (t TDigest) Count() uint64 { return t.count } // Add is an alias for AddWeighted(x,1) // Read the documentation for AddWeighted for more details. func (t *TDigest) Add(value float64) error { return t.AddWeighted(value, 1) } // Compress tries to reduce the number of individual centroids stored // in the digest. // // Compression trades off accuracy for performance and happens // automatically after a certain amount of distinct samples have been // stored. // // At any point in time you may call Compress on a digest, but you // may completely ignore this and it will compress itself automatically // after it grows too much. If you are minimizing network traffic // it might be a good idea to compress before serializing. func (t *TDigest) Compress() (err error) { if t.summary.Len() <= 1 { return nil } oldTree := t.summary t.summary = newSummary(estimateCapacity(t.compression)) t.count = 0 oldTree.shuffle(t.rng) oldTree.ForEach(func(mean float64, count uint64) bool { err = t.AddWeighted(mean, count) return err == nil }) return err } // Merge joins a given digest into itself. // // Merging is useful when you have multiple TDigest instances running // in separate threads and you want to compute quantiles over all the // samples. This is particularly important on a scatter-gather/map-reduce // scenario. func (t *TDigest) Merge(other *TDigest) (err error) { if other.summary.Len() == 0 { return nil } other.summary.Perm(t.rng, func(mean float64, count uint64) bool { err = t.AddWeighted(mean, count) return err == nil }) return err } // MergeDestructive joins a given digest into itself rendering // the other digest invalid. // // This works as Merge above but its faster. Using this method // requires caution as it makes 'other' useless - you must make // sure you discard it without making further uses of it. func (t *TDigest) MergeDestructive(other *TDigest) (err error) { if other.summary.Len() == 0 { return nil } other.summary.shuffle(t.rng) other.summary.ForEach(func(mean float64, count uint64) bool { err = t.AddWeighted(mean, count) return err == nil }) return err } // CDF computes the fraction in which all samples are less than // or equal to the given value. func (t *TDigest) CDF(value float64) float64 { if t.summary.Len() == 0 { return math.NaN() } else if t.summary.Len() == 1 { if value < t.summary.Mean(0) { return 0 } return 1 } // We have at least 2 centroids left := (t.summary.Mean(1) - t.summary.Mean(0)) / 2 right := left tot := 0.0 for i := 1; i < t.summary.Len()-1; i++ { prevMean := t.summary.Mean(i - 1) if value < prevMean+right { v := (tot + float64(t.summary.Count(i-1))*interpolate(value, prevMean-left, prevMean+right)) / float64(t.Count()) if v > 0 { return v } return 0 } tot += float64(t.summary.Count(i - 1)) left = right right = (t.summary.Mean(i+1) - t.summary.Mean(i)) / 2 } // last centroid, the summary length is at least two aIdx := t.summary.Len() - 2 aMean := t.summary.Mean(aIdx) if value < aMean+right { aCount := float64(t.summary.Count(aIdx)) return (tot + aCount*interpolate(value, aMean-left, aMean+right)) / float64(t.Count()) } return 1 } // Clone returns a deep copy of a TDigest. func (t *TDigest) Clone() *TDigest { return &TDigest{ summary: t.summary.Clone(), compression: t.compression, count: t.count, rng: t.rng, } } func interpolate(x, x0, x1 float64) float64 { return (x - x0) / (x1 - x0) } // ForEachCentroid calls the specified function for each centroid. // // Iteration stops when the supplied function returns false, or when all // centroids have been iterated. func (t *TDigest) ForEachCentroid(f func(mean float64, count uint64) bool) { t.summary.ForEach(f) } func (t TDigest) findNeighbors(start int, value float64) (int, int) { minDistance := math.MaxFloat64 lastNeighbor := t.summary.Len() for neighbor := start; neighbor < t.summary.Len(); neighbor++ { z := math.Abs(t.summary.Mean(neighbor) - value) if z < minDistance { start = neighbor minDistance = z } else if z > minDistance { lastNeighbor = neighbor break } } return start, lastNeighbor } func (t TDigest) chooseMergeCandidate(begin, end int, value float64, count uint64) int { closest := t.summary.Len() sum := t.summary.HeadSum(begin) var n float32 for neighbor := begin; neighbor != end; neighbor++ { c := float64(t.summary.Count(neighbor)) var q float64 if t.count == 1 { q = 0.5 } else { q = (sum + (c-1)/2) / float64(t.count-1) } k := 4 * float64(t.count) * q * (1 - q) / t.compression if c+float64(count) <= k { n++ if t.rng.Float32() < 1/n { closest = neighbor } } sum += c } return closest } // TrimmedMean returns the mean of the distribution between the two // percentiles p1 and p2. // // Values of p1 and p2 must be beetween 0 and 1 (inclusive) and p1 // must be less than p2. Will panic otherwise. func (t *TDigest) TrimmedMean(p1, p2 float64) float64 { if p1 < 0 || p1 > 1 { panic("p1 must be between 0 and 1 (inclusive)") } if p2 < 0 || p2 > 1 { panic("p2 must be between 0 and 1 (inclusive)") } if p1 >= p2 { panic("p1 must be lower than p2") } minCount := p1 * float64(t.count) maxCount := p2 * float64(t.count) var trimmedSum, trimmedCount, currCount float64 for i, mean := range t.summary.means { count := float64(t.summary.counts[i]) nextCount := currCount + count if nextCount <= minCount { currCount = nextCount continue } if currCount < minCount { count = nextCount - minCount } if nextCount > maxCount { count -= nextCount - maxCount } trimmedSum += count * mean trimmedCount += count if nextCount >= maxCount { break } currCount = nextCount } if trimmedCount == 0 { return 0 } return trimmedSum / trimmedCount } func estimateCapacity(compression float64) int { return int(compression) * 10 } |