/
labelidx.go
1817 lines (1699 loc) · 54.4 KB
/
labelidx.go
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package labelmap
import (
"bytes"
"compress/gzip"
"encoding/binary"
"encoding/json"
"fmt"
"io"
"math"
"net/http"
"os"
"sort"
"sync"
"sync/atomic"
pb "google.golang.org/protobuf/proto"
"github.com/coocood/freecache"
"github.com/janelia-flyem/dvid/datastore"
"github.com/janelia-flyem/dvid/datatype/common/labels"
"github.com/janelia-flyem/dvid/datatype/common/proto"
"github.com/janelia-flyem/dvid/dvid"
"github.com/janelia-flyem/dvid/server"
"github.com/janelia-flyem/dvid/storage"
lz4 "github.com/janelia-flyem/go/golz4-updated"
)
const (
numIndexShards = 64
)
var (
indexCache *freecache.Cache
indexMu [numIndexShards]sync.RWMutex
metaAttempts uint64
metaHits uint64
mutcache map[dvid.UUID]storage.OrderedKeyValueDB
)
// Initialize establishes the in-memory labelmap and other supporting
// data systems if specified in the server configuration:
// - index caching if cache size is specified in the server config.
// - mutation cache for label indices if specified in server config.
func (d *Data) Initialize() {
numBytes := server.CacheSize("labelmap")
if indexCache == nil {
if numBytes > 0 {
indexCache = freecache.NewCache(numBytes)
mbs := numBytes >> 20
dvid.Infof("Created freecache of ~ %d MB for labelmap instances.\n", mbs)
}
} else if numBytes == 0 {
indexCache = nil
} else {
indexCache.Clear()
}
mutcachePath := server.MutcachePath(d.DataName())
if mutcachePath != "" {
// Setup database support for mutation cache for this instance
engine := storage.GetEngine("badger")
var cfg dvid.Config
cfg.Set("path", mutcachePath)
store, _, err := engine.NewStore(dvid.StoreConfig{Config: cfg, Engine: "badger"})
if err != nil {
dvid.Criticalf("can't initialize Badger: %v\n", err)
} else {
okvDB, ok := store.(storage.OrderedKeyValueDB)
if !ok {
dvid.Criticalf("can't get proper ordered keyvalue DB for mutation cache %q for data %q\n", mutcachePath, d.DataName())
} else {
if mutcache == nil {
mutcache = make(map[dvid.UUID]storage.OrderedKeyValueDB)
}
mutcache[d.DataUUID()] = okvDB
}
}
}
ancestry, err := datastore.GetBranchVersions(d.RootUUID(), "")
if err != nil {
dvid.Criticalf("Unable to get ancestry of master branch: %v\n", err)
return
}
if len(ancestry) == 0 {
dvid.Infof("No versions in master branch -- not loading labelmap %q\n", d.DataName())
return
}
masterLeafV, err := datastore.VersionFromUUID(ancestry[0])
if err != nil {
dvid.Criticalf("Unable to get version ID from master leaf UUID %s: %v\n", ancestry[0], err)
}
if _, err := getMapping(d, masterLeafV); err != nil {
dvid.Criticalf("Unable to initialize in-memory labelmap for data %q: %v\n", d.DataName(), err)
}
}
func (d *Data) getMutcache(v dvid.VersionID, mutID uint64, label uint64) (*labels.Index, error) {
if mutcache == nil {
return nil, nil
}
db, found := mutcache[d.DataUUID()]
if !found {
return nil, nil
}
ctx := datastore.NewVersionedCtx(d, v)
tkey1 := newMutcacheKey(label, mutID)
tkey2 := newMutcacheKey(label, 0)
var idx *labels.Index
db.ProcessRange(ctx, tkey1, tkey2, nil, func(chunk *storage.Chunk) error {
label, curMutID, err := decodeMutcacheKey(chunk.K)
if err != nil {
return err
}
idx = new(labels.Index)
if err := pb.Unmarshal(chunk.V, idx); err != nil {
return err
}
dvid.Infof("Mutcache label %d mutid %d > %d\n", label, mutID, curMutID)
return fmt.Errorf("found mutcache")
})
return idx, nil
}
func (d *Data) addMutcache(v dvid.VersionID, mutID uint64, indices ...*labels.Index) error {
if mutcache == nil {
return nil
}
db, found := mutcache[d.DataUUID()]
if !found {
return nil
}
ctx := datastore.NewVersionedCtx(d, v)
for _, idx := range indices {
tkey := newMutcacheKey(idx.Label, mutID)
idxBytes, err := pb.Marshal(idx)
if err != nil {
return fmt.Errorf("unable to marshal index for label %d before caching: %v", idx.Label, err)
}
if err := db.Put(ctx, tkey, idxBytes); err != nil {
return err
}
}
return nil
}
// indexKey is a three tuple (instance id, version, label)
type indexKey struct {
data dvid.Data
version dvid.VersionID
label uint64
}
func (k indexKey) Bytes() []byte {
b := make([]byte, 16)
copy(b[0:4], k.data.InstanceID().Bytes())
copy(b[4:8], k.version.Bytes())
binary.LittleEndian.PutUint64(b[8:16], k.label)
return b
}
func (k indexKey) VersionedCtx() *datastore.VersionedCtx {
return datastore.NewVersionedCtx(k.data, k.version)
}
// TODO -- allow check of the cache as well.
func (d *Data) labelIndexExists(v dvid.VersionID, label uint64) (bool, error) {
ctx := datastore.NewVersionedCtx(d, v)
store, err := datastore.GetKeyValueDB(d)
if err != nil {
return false, err
}
return store.Exists(ctx, NewLabelIndexTKey(label))
}
// returns nil if no Meta is found.
// should only call getCachedLabelIndex external to this file.
func getLabelIndex(ctx *datastore.VersionedCtx, label uint64) (*labels.Index, error) {
// timedLog := dvid.NewTimeLog()
store, err := datastore.GetKeyValueDB(ctx.Data())
if err != nil {
return nil, err
}
compressed, err := store.Get(ctx, NewLabelIndexTKey(label))
if err != nil {
return nil, err
}
if len(compressed) == 0 {
// timedLog.Infof("retrieved empty index for label %d", label)
return nil, nil
}
val, _, err := dvid.DeserializeData(compressed, true)
if err != nil {
return nil, err
}
idx := new(labels.Index)
if err := pb.Unmarshal(val, idx); err != nil {
return nil, err
}
if idx.Label == 0 {
idx.Label = label
}
// timedLog.Infof("retrieved label %d index with %d blocks", label, len(idx.Blocks))
return idx, nil
}
func getLabelIndexCompressed(store storage.KeyValueGetter, ctx *datastore.VersionedCtx, label uint64) ([]byte, error) {
compressed, err := store.Get(ctx, NewLabelIndexTKey(label))
if err != nil {
return nil, err
}
if len(compressed) == 0 {
// timedLog.Infof("retrieved empty index for label %d", label)
return nil, nil
}
return compressed, nil
}
func getProtoLabelIndices(ctx *datastore.VersionedCtx, dataIn []byte) (numLabels int, dataOut []byte, err error) {
var labelList []uint64
if err = json.Unmarshal(dataIn, &labelList); err != nil {
err = fmt.Errorf("expected JSON label list: %v", err)
return
}
numLabels = len(labelList)
if numLabels > 50000 {
err = fmt.Errorf("only 50,000 label indices can be returned at a time, %d given", len(labelList))
return
}
var indices proto.LabelIndices
indices.Indices = make([]*proto.LabelIndex, len(labelList))
for i, label := range labelList {
var idx *labels.Index
if idx, err = getLabelIndex(ctx, label); err != nil {
err = fmt.Errorf("could not get label %d index in position %d: %v", label, i, err)
return
}
if idx != nil {
indices.Indices[i] = &(idx.LabelIndex)
} else {
index := proto.LabelIndex{
Label: label,
}
indices.Indices[i] = &index
}
}
if dataOut, err = pb.Marshal(&indices); err != nil {
err = fmt.Errorf("could not serialize %d label indices: %v", len(labelList), err)
}
return
}
// batch mode put/delete using protobuf indices without caching
func putProtoLabelIndices(ctx *datastore.VersionedCtx, dataIn []byte) (numAdded, numDeleted int, err error) {
data := ctx.Data()
var store storage.KeyValueDB
if store, err = datastore.GetKeyValueDB(data); err != nil {
err = fmt.Errorf("data %q had error getting KeyValue store: %v", data.DataName(), err)
return
}
indices := new(proto.LabelIndices)
if err = pb.Unmarshal(dataIn, indices); err != nil {
return
}
var maxLabel uint64
for i, protoIdx := range indices.Indices {
if protoIdx == nil {
err = fmt.Errorf("indices included a nil index in position %d", i)
return
}
if protoIdx.Label == 0 {
err = fmt.Errorf("index %d had label 0, which is a reserved label", i)
return
}
if len(protoIdx.Blocks) == 0 {
if err = deleteLabelIndex(ctx, protoIdx.Label); err != nil {
return
}
numDeleted++
continue
}
numAdded++
idx := labels.Index{LabelIndex: *protoIdx}
if err = putLabelIndex(store, ctx, data, &idx); err != nil {
return
}
if idx.Label > maxLabel {
maxLabel = idx.Label
}
}
// handle updating the max label
d, ok := data.(*Data)
if !ok {
err = fmt.Errorf("unable to update max label during PUT label index due to bad data ptr for %q", data.DataName())
return
}
_, err = d.updateMaxLabel(ctx.VersionID(), maxLabel)
return
}
// puts label index and doesn't calc max label
// Note: should only call putCachedLabelIndex external to this file so recent changes get cached.
func putLabelIndex(store storage.KeyValueDB, ctx *datastore.VersionedCtx, data dvid.Data, idx *labels.Index) error {
tk := NewLabelIndexTKey(idx.Label)
serialization, err := pb.Marshal(idx)
if err != nil {
return fmt.Errorf("error trying to serialize index for label set %d, data %q: %v", idx.Label, data.DataName(), err)
}
compressFormat, _ := dvid.NewCompression(dvid.LZ4, dvid.DefaultCompression)
compressed, err := dvid.SerializeData(serialization, compressFormat, dvid.NoChecksum)
if err != nil {
return fmt.Errorf("error trying to LZ4 compress label %d indexing in data %q", idx.Label, data.DataName())
}
if err := store.Put(ctx, tk, compressed); err != nil {
return fmt.Errorf("unable to store indices for label %d, data %s: %v", idx.Label, data.DataName(), err)
}
return err
}
// puts label index and stores max label.
// Note: should only call putCachedLabelIndex external to this file so recent changes get cached.
func putLabelIndexAndMax(ctx *datastore.VersionedCtx, idx *labels.Index) error {
// timedLog := dvid.NewTimeLog()
store, err := datastore.GetOrderedKeyValueDB(ctx.Data())
if err != nil {
return fmt.Errorf("data %q PutLabelMeta had error initializing store: %v", ctx.Data().DataName(), err)
}
tk := NewLabelIndexTKey(idx.Label)
serialization, err := pb.Marshal(idx)
if err != nil {
return fmt.Errorf("error trying to serialize index for label set %d, data %q: %v", idx.Label, ctx.Data().DataName(), err)
}
compressFormat, _ := dvid.NewCompression(dvid.LZ4, dvid.DefaultCompression)
compressed, err := dvid.SerializeData(serialization, compressFormat, dvid.NoChecksum)
if err != nil {
return fmt.Errorf("error trying to LZ4 compress label %d indexing in data %q", idx.Label, ctx.Data().DataName())
}
if err := store.Put(ctx, tk, compressed); err != nil {
return fmt.Errorf("unable to store indices for label %d, data %s: %v", idx.Label, ctx.Data().DataName(), err)
}
d, ok := ctx.Data().(*Data)
if !ok {
return fmt.Errorf("Unable to update max label during PUT label index due to bad data ptr")
}
_, err = d.updateMaxLabel(ctx.VersionID(), idx.Label)
// timedLog.Infof("stored label %d index with %d blocks", idx.Label, len(idx.Blocks))
return err
}
func deleteLabelIndex(ctx *datastore.VersionedCtx, label uint64) error {
store, err := datastore.GetOrderedKeyValueDB(ctx.Data())
if err != nil {
return fmt.Errorf("data %q delete label set index had error initializing store: %v", ctx.Data().DataName(), err)
}
tk := NewLabelIndexTKey(label)
if err := store.Delete(ctx, tk); err != nil {
return fmt.Errorf("unable to delete indices for label %d, data %s: %v", label, ctx.Data().DataName(), err)
}
return nil
}
// only returns error if we can't get index from storage, not if we can't get it from cache
func getCachedLabelIndex(d dvid.Data, v dvid.VersionID, label uint64) (*labels.Index, error) {
atomic.AddUint64(&metaAttempts, 1)
k := indexKey{data: d, version: v, label: label}
var err error
var idxBytes []byte
if indexCache != nil {
idxBytes, err = indexCache.Get(k.Bytes())
if err != nil && err != freecache.ErrNotFound {
dvid.Errorf("cache get of index for label %d failed due to error: %v\n", label, err)
idxBytes = nil
}
}
var idx *labels.Index
if idxBytes != nil {
idx = new(labels.Index)
if err = pb.Unmarshal(idxBytes, idx); err != nil {
return nil, err
}
atomic.AddUint64(&metaHits, 1)
return idx, nil
}
idx, err = getLabelIndex(k.VersionedCtx(), label)
if err != nil {
return nil, err
}
if idx == nil {
return nil, nil
}
if indexCache != nil {
idxBytes, err := pb.Marshal(idx)
if err != nil {
dvid.Errorf("unable to marshal label %d index for %q: %v\n", label, d.DataName(), err)
} else if err := indexCache.Set(k.Bytes(), idxBytes, 0); err != nil {
dvid.Errorf("unable to set label %d index cache for %q: %v\n", label, d.DataName(), err)
}
}
if idx.Label != label {
dvid.Criticalf("label index for data %q, label %d has internal label value %d\n", d.DataName(), label, idx.Label)
idx.Label = label
}
return idx, nil
}
// only returns error if we can't persist index, not if we can't cache
func putCachedLabelIndex(d dvid.Data, v dvid.VersionID, idx *labels.Index) error {
ctx := datastore.NewVersionedCtx(d, v)
if err := putLabelIndexAndMax(ctx, idx); err != nil {
return err
}
if indexCache != nil {
idxBytes, err := pb.Marshal(idx)
if err != nil {
dvid.Errorf("unable to marshal index for label %d before caching: %v\n", idx.Label, err)
return nil
}
k := indexKey{data: d, version: v, label: idx.Label}.Bytes()
if err = indexCache.Set(k, idxBytes, 0); err != nil {
dvid.Errorf("unable to cache index for label %d: %v\n", idx.Label, err)
}
}
return nil
}
func deleteCachedLabelIndex(d dvid.Data, v dvid.VersionID, label uint64) error {
ctx := datastore.NewVersionedCtx(d, v)
if err := deleteLabelIndex(ctx, label); err != nil {
return err
}
if indexCache != nil {
k := indexKey{data: d, version: v, label: label}.Bytes()
indexCache.Del(k)
}
return nil
}
////////////////////////
//
///////////////////////////////////////////////////////////////////////////
// The following public functions are concurrency-safe and support caching.
// GetSupervoxels returns the set of supervoxel ids that compose the given label.
// Used in other datatypes private interfaces (e.g., tarsupervoxels) and generally useful
// for other packages.
func (d *Data) GetSupervoxels(v dvid.VersionID, label uint64) (labels.Set, error) {
idx, err := GetLabelIndex(d, v, label, false)
if err != nil {
return nil, err
}
if idx == nil || len(idx.Blocks) == 0 {
return nil, err
}
return idx.GetSupervoxels(), nil
}
// GetLabelIndex gets label set index data from storage for a given data instance and version.
// If isSupervoxel is true, the label is interpreted as a supervoxel and the label set index
// containing the given supervoxel is returned. Concurrency-safe access and supports caching.
// If a label has been mapped to another, a nil Index is returned.
func GetLabelIndex(d dvid.Data, v dvid.VersionID, label uint64, isSupervoxel bool) (*labels.Index, error) {
if isSupervoxel {
mapping, err := getMapping(d, v)
if err != nil {
return nil, err
}
if mapping != nil {
if mapped, found := mapping.MappedLabel(v, label); found {
if mapped == 0 {
return nil, fmt.Errorf("cannot get label for supervoxel %d, which has been split and doesn't exist anymore", label)
}
label = mapped
}
}
}
shard := label % numIndexShards
indexMu[shard].RLock()
idx, err := getCachedLabelIndex(d, v, label)
indexMu[shard].RUnlock()
return idx, err
}
// GetSupervoxelBlocks gets the blocks corresponding to a supervoxel id.
func GetSupervoxelBlocks(d dvid.Data, v dvid.VersionID, supervoxel uint64) (dvid.IZYXSlice, error) {
idx, err := GetLabelIndex(d, v, supervoxel, true)
if err != nil {
return nil, err
}
if idx == nil {
return nil, nil
}
var blocks dvid.IZYXSlice
for zyx, svc := range idx.Blocks {
if svc != nil && svc.Counts != nil {
sz, found := svc.Counts[supervoxel]
if found && sz > 0 {
blocks = append(blocks, labels.BlockIndexToIZYXString(zyx))
}
}
}
return blocks, nil
}
// GetLabelSize returns the # of voxels in the given label. If isSupervoxel = true, the given
// label is interpreted as a supervoxel id and the size is of a supervoxel. If a label doesn't
// exist, a zero (not error) is returned.
func GetLabelSize(d dvid.Data, v dvid.VersionID, label uint64, isSupervoxel bool) (uint64, error) {
idx, err := GetLabelIndex(d, v, label, isSupervoxel)
if err != nil {
return 0, err
}
if idx == nil {
return 0, nil
}
if isSupervoxel {
return idx.GetSupervoxelCount(label), nil
}
return idx.NumVoxels(), nil
}
func getSupervoxelSizes(d dvid.Data, v dvid.VersionID, supervoxels []uint64) ([]uint64, error) {
svmap, err := getMapping(d, v)
if err != nil {
return nil, fmt.Errorf("couldn't get mapping for data %q, version %d: %v", d.DataName(), v, err)
}
labelsets := make(map[uint64][]uint64) // maps labels -> set of supervoxels in it.
labels, _, err := svmap.MappedLabels(v, supervoxels)
if err != nil {
return nil, err
}
for i, label := range labels {
labelsets[label] = append(labelsets[label], supervoxels[i])
}
sizemap := make(map[uint64]uint64, len(supervoxels))
for label, svlist := range labelsets {
idx, err := GetLabelIndex(d, v, label, false)
if err != nil {
return nil, err
}
if idx == nil {
for _, sv := range svlist {
sizemap[sv] = 0
}
} else {
svcounts := idx.GetSupervoxelCounts()
for _, sv := range svlist {
sizemap[sv] = svcounts[sv]
}
}
}
sizes := make([]uint64, len(supervoxels))
for i, sv := range supervoxels {
sizes[i] = sizemap[sv]
}
return sizes, nil
}
// GetLabelSizes returns the # of voxels in the given labels. If isSupervoxel = true, the given
// labels are interpreted as supervoxel ids and the sizes are of a supervoxel. If a label doesn't
// exist, a zero (not error) is returned.
func GetLabelSizes(d dvid.Data, v dvid.VersionID, labels []uint64, isSupervoxel bool) (sizes []uint64, err error) {
if isSupervoxel {
return getSupervoxelSizes(d, v, labels)
}
sizes = make([]uint64, len(labels))
for i, label := range labels {
idx, err := GetLabelIndex(d, v, label, false)
if err != nil {
return nil, err
}
if idx == nil {
sizes[i] = 0
} else {
sizes[i] = idx.NumVoxels()
}
}
return sizes, nil
}
// GetBoundedIndex gets bounded label index data from storage for a given data instance.
func GetBoundedIndex(d dvid.Data, v dvid.VersionID, label uint64, bounds dvid.Bounds, isSupervoxel bool) (*labels.Index, error) {
idx, err := GetLabelIndex(d, v, label, isSupervoxel)
if err != nil {
return nil, err
}
if idx == nil {
return nil, nil
}
if bounds.Block != nil && bounds.Block.IsSet() {
if err = idx.FitToBounds(bounds.Block); err != nil {
return nil, err
}
}
return idx, nil
}
// DeleteLabelIndex deletes the index for a given label set.
func DeleteLabelIndex(d dvid.Data, v dvid.VersionID, label uint64) error {
shard := label % numIndexShards
indexMu[shard].Lock()
err := deleteCachedLabelIndex(d, v, label)
indexMu[shard].Unlock()
return err
}
// PutLabelIndex persists a label index data for a given data instance and
// version. If the given index is nil, the index is deleted. Concurrency-safe
// and supports caching.
func PutLabelIndex(d dvid.Data, v dvid.VersionID, label uint64, idx *labels.Index) error {
if idx == nil {
return DeleteLabelIndex(d, v, label)
}
shard := label % numIndexShards
indexMu[shard].Lock()
idx.Label = label
err := putCachedLabelIndex(d, v, idx)
indexMu[shard].Unlock()
return err
}
type proximityJSON struct {
Block dvid.ChunkPoint3d
Distance int
}
// TODO: Flesh out this stub for /proximity endpoint.
func (d *Data) getProximity(ctx *datastore.VersionedCtx, idx1, idx2 *labels.Index) (jsonBytes []byte, err error) {
// Find all blocks shared by the two indices
// For each intersecting block, determine distance between labels and add to output.
return
}
// CleaveIndex modifies the label index to remove specified supervoxels and create another
// label index for this cleaved body.
func (d *Data) cleaveIndex(v dvid.VersionID, op labels.CleaveOp, info dvid.ModInfo) (cleavedSize, remainSize uint64, err error) {
shard := op.Target % numIndexShards
indexMu[shard].Lock()
defer indexMu[shard].Unlock()
var idx *labels.Index
if idx, err = getCachedLabelIndex(d, v, op.Target); err != nil {
return
}
if idx == nil {
err = fmt.Errorf("cannot cleave non-existent label %d", op.Target)
return
}
idx.LastMutId = op.MutID
idx.LastModUser = info.User
idx.LastModTime = info.Time
idx.LastModApp = info.App
if err := d.addMutcache(v, op.MutID, idx); err != nil {
dvid.Criticalf("unable to add cleaved mutid %d index %d: %v\n", op.MutID, op.Target, err)
}
supervoxels := idx.GetSupervoxels()
for _, supervoxel := range op.CleavedSupervoxels {
if _, found := supervoxels[supervoxel]; !found {
err = fmt.Errorf("cannot cleave supervoxel %d, which does not exist in label %d", supervoxel, op.Target)
return
}
delete(supervoxels, supervoxel)
}
if len(supervoxels) == 0 {
err = fmt.Errorf("cannot cleave all supervoxels from the label %d", op.Target)
return
}
// create a new label index to contain the cleaved supervoxels.
// we don't have to worry about mutex here because it's a new index.
var cidx *labels.Index
cleavedSize, remainSize, cidx = idx.Cleave(op.CleavedLabel, op.CleavedSupervoxels)
cidx.LastMutId = op.MutID
cidx.LastModUser = info.User
cidx.LastModTime = info.Time
cidx.LastModApp = info.App
if err = putCachedLabelIndex(d, v, cidx); err != nil {
return
}
err = putCachedLabelIndex(d, v, idx)
return
}
// ChangeLabelIndex applies changes to a label's index and then stores the result.
// Supervoxel size changes for blocks should be passed into the function. The passed
// SupervoxelDelta can contain more supervoxels than the label index.
func ChangeLabelIndex(d dvid.Data, v dvid.VersionID, label uint64, delta labels.SupervoxelChanges) error {
shard := label % numIndexShards
indexMu[shard].Lock()
defer indexMu[shard].Unlock()
idx, err := getCachedLabelIndex(d, v, label)
if err != nil {
return err
}
if idx == nil {
idx = new(labels.Index)
idx.Label = label
}
if err := idx.ModifyBlocks(label, delta); err != nil {
return err
}
if len(idx.Blocks) == 0 {
return deleteCachedLabelIndex(d, v, label)
}
return putCachedLabelIndex(d, v, idx)
}
// getMergedIndex gets index data for all labels in a set with possible bounds.
func (d *Data) getMergedIndex(v dvid.VersionID, mutID uint64, lbls labels.Set, bounds dvid.Bounds) (*labels.Index, error) {
if len(lbls) == 0 {
return nil, nil
}
idx := new(labels.Index)
for label := range lbls {
idx2, err := GetLabelIndex(d, v, label, false)
if err != nil {
return nil, err
}
if err := d.addMutcache(v, mutID, idx2); err != nil {
dvid.Criticalf("unable to add merge mutid %d index %d: %v\n", mutID, label, err)
}
if bounds.Block != nil && bounds.Block.IsSet() {
if err := idx2.FitToBounds(bounds.Block); err != nil {
return nil, err
}
}
if err := idx.Add(idx2); err != nil {
return nil, err
}
}
return idx, nil
}
// given supervoxels with given mapping and whether they were actually in in-memory SVMap, check
// label indices to see if supervoxels really are present in assigned bodies.
func (d *Data) verifyMappings(ctx *datastore.VersionedCtx, supervoxels, mapped []uint64, found []bool) (verified []uint64, err error) {
numSupervoxels := len(supervoxels)
if numSupervoxels != len(mapped) {
return nil, fmt.Errorf("length of supervoxels list (%d) not equal to length of provided mappings (%d)", numSupervoxels, len(mapped))
}
if numSupervoxels != len(found) {
return nil, fmt.Errorf("length of supervoxels list (%d) not equal to length of provided found mappings (%d)", numSupervoxels, len(found))
}
bodySupervoxels := make(map[uint64]labels.Set)
for i, supervoxel := range supervoxels {
if supervoxel != 0 && !found[i] { // we are uncertain whether this is a real or implicit supervoxel that may not exist
bodysvs, bodyfound := bodySupervoxels[mapped[i]]
if !bodyfound {
bodysvs = labels.Set{supervoxel: struct{}{}}
} else {
bodysvs[supervoxel] = struct{}{}
}
bodySupervoxels[mapped[i]] = bodysvs
}
}
wasVerified := make(map[uint64]bool, numSupervoxels)
for label, bodysvs := range bodySupervoxels {
shard := label % numIndexShards
indexMu[shard].RLock()
idx, err := getCachedLabelIndex(d, ctx.VersionID(), label)
indexMu[shard].RUnlock()
if err != nil {
return nil, err
}
svpresent := idx.SupervoxelsPresent(bodysvs)
for supervoxel, present := range svpresent {
wasVerified[supervoxel] = present
}
}
verified = make([]uint64, numSupervoxels)
for i, label := range mapped {
if found[i] || wasVerified[supervoxels[i]] {
verified[i] = label
} else {
verified[i] = 0
}
}
return
}
// computes supervoxel split on a label index, returning the split index and the slice of blocks
// that were modified.
func (d *Data) splitSupervoxelIndex(v dvid.VersionID, info dvid.ModInfo, op labels.SplitSupervoxelOp, idx *labels.Index) (dvid.IZYXSlice, error) {
idx.LastMutId = op.MutID
idx.LastModUser = info.User
idx.LastModTime = info.Time
idx.LastModApp = info.App
// modify the index to reflect old supervoxel -> two new supervoxels.
var svblocks dvid.IZYXSlice
for zyx, svc := range idx.Blocks {
origNumVoxels, found := svc.Counts[op.Supervoxel]
if found { // split supervoxel is in this block
delete(svc.Counts, op.Supervoxel)
izyx := labels.BlockIndexToIZYXString(zyx)
svblocks = append(svblocks, izyx)
rles, found := op.Split[izyx]
if found { // part of split
splitNumVoxels, _ := rles.Stats()
svc.Counts[op.SplitSupervoxel] = uint32(splitNumVoxels)
if splitNumVoxels > uint64(origNumVoxels) {
return nil, fmt.Errorf("tried to split %d voxels from supervoxel %d, but label index only has %d voxels", splitNumVoxels, op.Supervoxel, origNumVoxels)
}
if splitNumVoxels != uint64(origNumVoxels) {
svc.Counts[op.RemainSupervoxel] = origNumVoxels - uint32(splitNumVoxels)
}
} else { // part of remainder
svc.Counts[op.RemainSupervoxel] = origNumVoxels
}
}
}
return svblocks, nil
}
// SplitIndex modifies the split label's index and creates a new index for the split portion.
func (d *Data) splitIndex(v dvid.VersionID, info dvid.ModInfo, op labels.SplitOp, idx *labels.Index, splitMap dvid.BlockRLEs, blockSplits blockSplitsMap) error {
idx.LastMutId = op.MutID
idx.LastModUser = info.User
idx.LastModTime = info.Time
idx.LastModApp = info.App
sidx := new(labels.Index)
sidx.LastMutId = op.MutID
sidx.LastModUser = info.User
sidx.LastModTime = info.Time
sidx.LastModApp = info.App
sidx.Label = op.NewLabel
sidx.Blocks = make(map[uint64]*proto.SVCount, len(blockSplits))
for zyx, indexsvc := range idx.Blocks {
splitCount, inSplitBlock := blockSplits[zyx]
var splitsvc *proto.SVCount
if inSplitBlock {
splitsvc = new(proto.SVCount)
splitsvc.Counts = make(map[uint64]uint32, len(splitCount))
}
for supervoxel, svOrigCount := range indexsvc.Counts {
var svWasSplit bool
var svSplitCount labels.SVSplitCount
if inSplitBlock {
svSplitCount, svWasSplit = splitCount[supervoxel]
if svWasSplit {
if svSplitCount.Voxels > svOrigCount {
return fmt.Errorf("block %s had %d voxels written over supervoxel %d in label %d split yet this supervoxel only had %d voxels from index", labels.BlockIndexToIZYXString(zyx), svSplitCount.Voxels, supervoxel, op.Target, svOrigCount)
}
splitsvc.Counts[svSplitCount.Split] = svSplitCount.Voxels
if svOrigCount > svSplitCount.Voxels {
indexsvc.Counts[svSplitCount.Remain] = svOrigCount - svSplitCount.Voxels
}
delete(indexsvc.Counts, supervoxel)
}
}
if !svWasSplit {
// see if split anywhere
svsplit, found := op.SplitMap[supervoxel]
if found {
indexsvc.Counts[svsplit.Remain] = svOrigCount
delete(indexsvc.Counts, supervoxel)
}
}
}
if inSplitBlock {
sidx.Blocks[zyx] = splitsvc
}
if len(indexsvc.Counts) == 0 {
delete(idx.Blocks, zyx)
}
}
if err := putCachedLabelIndex(d, v, idx); err != nil {
return fmt.Errorf("modify split index for data %q, label %d: %v", d.DataName(), op.Target, err)
}
if err := putCachedLabelIndex(d, v, sidx); err != nil {
return fmt.Errorf("create new split index for data %q, label %d: %v", d.DataName(), op.NewLabel, err)
}
return nil
}
///////////////////////////////////////
// block-level analysis of mutation to get supervoxel changes in a block. accumulates data for
// a given mutation into a map per mutation which will then be flushed for each supervoxel meta
// k/v pair at end of mutation.
func (d *Data) handleBlockMutate(v dvid.VersionID, ch chan blockChange, mut MutatedBlock) {
if !d.IndexedLabels {
return
}
bc := blockChange{
bcoord: mut.BCoord,
}
if d.IndexedLabels {
// if mut.Prev == nil {
// dvid.Infof("block mutate %s has no previous block\n", mut.Prev)
// } else {
// dvid.Infof("block mutate %s: prev labels %v\n", mut.BCoord, mut.Prev.Labels)
// }
bc.delta = mut.Data.CalcNumLabels(mut.Prev)
}
ch <- bc
}
// block-level analysis of label ingest to do indexing
func (d *Data) handleBlockIndexing(v dvid.VersionID, ch chan blockChange, mut IngestedBlock) {
if !d.IndexedLabels {
return
}
bc := blockChange{
bcoord: mut.BCoord,
}
if d.IndexedLabels {
bc.delta = mut.Data.CalcNumLabels(nil)
}
ch <- bc
}
// Goroutines accepts block-level changes and segregates all changes by supervoxel, and then
// sends supervoxel-specific changes to concurrency-handling label indexing functions.
type blockChange struct {
bcoord dvid.IZYXString
delta map[uint64]int32
}
// goroutine(s) that aggregates supervoxel changes across blocks for one mutation, then calls
// mutex-guarded label index mutation routine.
func (d *Data) aggregateBlockChanges(v dvid.VersionID, svmap *VCache, ch <-chan blockChange) {
mappedVersions := svmap.getMappedVersionsDist(v)
labelset := make(labels.Set)
svChanges := make(labels.SupervoxelChanges)
var maxLabel uint64
for change := range ch {
for supervoxel, delta := range change.delta {
blockChanges, found := svChanges[supervoxel]
if !found {
blockChanges = make(map[dvid.IZYXString]int32)
svChanges[supervoxel] = blockChanges
}
blockChanges[change.bcoord] += delta
if supervoxel > maxLabel {
maxLabel = supervoxel
}
label, _ := svmap.mapLabel(supervoxel, mappedVersions)
labelset[label] = struct{}{}
}
}
go func() {
if _, err := d.updateMaxLabel(v, maxLabel); err != nil {
dvid.Errorf("max label change during block aggregation for %q: %v\n", d.DataName(), err)
}
}()
if d.IndexedLabels {
for label := range labelset {
if err := ChangeLabelIndex(d, v, label, svChanges); err != nil {
dvid.Errorf("indexing label %d: %v\n", label, err)
}
}
}
}
type labelBlock struct {
index dvid.IZYXString
data []byte
}
type rleResult struct {
runs uint32
serialization []byte
}
// goroutine to process retrieved label data and generate RLEs, could be sharded by block coordinate
func (d *Data) processBlocksToRLEs(lbls labels.Set, bounds dvid.Bounds, in chan labelBlock, out chan rleResult) {
for {
lb, more := <-in
if !more {
return
}
var result rleResult
data, _, err := dvid.DeserializeData(lb.data, true)
if err != nil {
dvid.Errorf("could not deserialize %d bytes in block %s: %v\n", len(lb.data), lb.index, err)
out <- result
continue
}