// TODO -- Clean up all the writing and simplify now that we have block-aligned writes.
// writeBlocks ingests blocks of voxel data asynchronously using batch writes.
func (d *Data) writeBlocks(v dvid.VersionID, b storage.TKeyValues, wg1, wg2 *sync.WaitGroup) error {
batcher, err := d.GetKeyValueBatcher()
if err != nil {
return err
}
preCompress, postCompress := 0, 0
ctx := datastore.NewVersionedCtx(d, v)
evt := datastore.SyncEvent{d.DataUUID(), IngestBlockEvent}
<-server.HandlerToken
go func() {
defer func() {
wg1.Done()
wg2.Done()
dvid.Debugf("Wrote voxel blocks. Before %s: %d bytes. After: %d bytes\n", d.Compression(), preCompress, postCompress)
server.HandlerToken <- 1
}()
mutID := d.NewMutationID()
batch := batcher.NewBatch(ctx)
for i, block := range b {
serialization, err := dvid.SerializeData(block.V, d.Compression(), d.Checksum())
preCompress += len(block.V)
postCompress += len(serialization)
if err != nil {
dvid.Errorf("Unable to serialize block: %v\n", err)
return
}
batch.Put(block.K, serialization)
indexZYX, err := DecodeTKey(block.K)
if err != nil {
dvid.Errorf("Unable to recover index from block key: %v\n", block.K)
return
}
msg := datastore.SyncMessage{IngestBlockEvent, v, Block{indexZYX, block.V, mutID}}
if err := datastore.NotifySubscribers(evt, msg); err != nil {
dvid.Errorf("Unable to notify subscribers of ChangeBlockEvent in %s\n", d.DataName())
return
}
// Check if we should commit
if i%KVWriteSize == KVWriteSize-1 {
if err := batch.Commit(); err != nil {
dvid.Errorf("Error on trying to write batch: %v\n", err)
return
}
batch = batcher.NewBatch(ctx)
}
}
if err := batch.Commit(); err != nil {
dvid.Errorf("Error on trying to write batch: %v\n", err)
return
}
}()
return nil
}
// Goroutine that handles splits across a lot of blocks for one label.
func (d *Data) splitBlock(ctx *datastore.VersionedCtx, op splitOp) {
defer d.MutDone(op.mutID)
store, err := d.GetOrderedKeyValueDB()
if err != nil {
dvid.Errorf("Data type labelblk had error initializing store: %v\n", err)
return
}
// Read the block.
tk := NewTKeyByCoord(op.block)
data, err := store.Get(ctx, tk)
if err != nil {
dvid.Errorf("Error on GET of labelblk with coord string %v\n", []byte(op.block))
return
}
if data == nil {
dvid.Errorf("nil label block where split was done, coord %v\n", []byte(op.block))
return
}
blockData, _, err := dvid.DeserializeData(data, true)
if err != nil {
dvid.Criticalf("unable to deserialize label block in '%s' key %v: %v\n", d.DataName(), []byte(op.block), err)
return
}
blockBytes := int(d.BlockSize().Prod() * 8)
if len(blockData) != blockBytes {
dvid.Criticalf("splitBlock: coord %v got back %d bytes, expected %d bytes\n", []byte(op.block), len(blockData), blockBytes)
return
}
// Modify the block using either voxel-level changes or coarser block-level mods.
if op.rles != nil {
if err := d.storeRLEs(blockData, op.newLabel, op.block, op.rles); err != nil {
dvid.Errorf("can't store label %d RLEs into block %s: %v\n", op.newLabel, op.block, err)
return
}
} else {
// We are doing coarse split and will replace all
if err := d.replaceLabel(blockData, op.oldLabel, op.newLabel); err != nil {
dvid.Errorf("can't replace label %d with %d in block %s: %v\n", op.oldLabel, op.newLabel, op.block, err)
return
}
}
// Write the modified block.
serialization, err := dvid.SerializeData(blockData, d.Compression(), d.Checksum())
if err != nil {
dvid.Criticalf("Unable to serialize block %s in %q: %v\n", op.block, d.DataName(), err)
return
}
if err := store.Put(ctx, tk, serialization); err != nil {
dvid.Errorf("Error in putting key %v: %v\n", tk, err)
}
// Notify any downstream downres instance.
d.publishBlockChange(ctx.VersionID(), op.mutID, op.block, blockData)
}
// Goroutine that handles relabeling of blocks during a merge operation.
// Since the same block coordinate always gets mapped to the same goroutine, we handle
// concurrency by serializing GET/PUT for a particular block coordinate.
func (d *Data) mergeBlock(in <-chan mergeOp) {
store, err := storage.MutableStore()
if err != nil {
dvid.Errorf("Data type labelblk had error initializing store: %v\n", err)
return
}
blockBytes := int(d.BlockSize().Prod() * 8)
for op := range in {
tk := NewTKeyByCoord(op.izyx)
data, err := store.Get(op.ctx, tk)
if err != nil {
dvid.Errorf("Error on GET of labelblk with coord string %q\n", op.izyx)
op.wg.Done()
continue
}
if data == nil {
dvid.Errorf("nil label block where merge was done!\n")
op.wg.Done()
continue
}
blockData, _, err := dvid.DeserializeData(data, true)
if err != nil {
dvid.Criticalf("unable to deserialize label block in '%s': %v\n", d.DataName(), err)
op.wg.Done()
continue
}
if len(blockData) != blockBytes {
dvid.Criticalf("After labelblk deserialization got back %d bytes, expected %d bytes\n", len(blockData), blockBytes)
op.wg.Done()
continue
}
// Iterate through this block of labels and relabel if label in merge.
for i := 0; i < blockBytes; i += 8 {
label := binary.LittleEndian.Uint64(blockData[i : i+8])
if _, merged := op.Merged[label]; merged {
binary.LittleEndian.PutUint64(blockData[i:i+8], op.Target)
}
}
// Store this block.
serialization, err := dvid.SerializeData(blockData, d.Compression(), d.Checksum())
if err != nil {
dvid.Criticalf("Unable to serialize block in %q: %v\n", d.DataName(), err)
op.wg.Done()
continue
}
if err := store.Put(op.ctx, tk, serialization); err != nil {
dvid.Errorf("Error in putting key %v: %v\n", tk, err)
}
op.wg.Done()
}
}
// serializeVertex serializes a dvid.GraphVertex (compression turned off for now)
func (db *GraphKeyValueDB) serializeVertex(vert dvid.GraphVertex) []byte {
// encode: vertex id, vertex weight, num vertices, vertex array,
// num properties, property array
total_size := 24 + 8*len(vert.Vertices) + 8
// find size for property strings (account for null character)
for propname, _ := range vert.Properties {
total_size += len(propname) + 1
}
// create byte buffer
buf := make([]byte, total_size, total_size)
// encode vertex id
start := 0
binary.LittleEndian.PutUint64(buf[start:], uint64(vert.Id))
start += 8
// encode vertex weight
floatbits := math.Float64bits(vert.Weight)
binary.LittleEndian.PutUint64(buf[start:], floatbits)
start += 8
// encode number of vertices
binary.LittleEndian.PutUint64(buf[start:], uint64(len(vert.Vertices)))
start += 8
// encode vertex partners
for _, vertpartner := range vert.Vertices {
binary.LittleEndian.PutUint64(buf[start:], uint64(vertpartner))
start += 8
}
// encode number of properties
binary.LittleEndian.PutUint64(buf[start:], uint64(len(vert.Properties)))
start += 8
// encode property strings
for propname, _ := range vert.Properties {
for _, propchar := range propname {
buf[start] = byte(propchar)
start += 1
}
buf[start] = byte(0)
start += 1
}
// encode DVID related info (currenlty compression is disabled)
compression, _ := dvid.NewCompression(dvid.Uncompressed, dvid.DefaultCompression)
finalbuf, _ := dvid.SerializeData(buf, compression, dvid.NoChecksum)
return finalbuf
}
// handles relabeling of blocks during a merge operation.
func (d *Data) mergeBlock(ctx *datastore.VersionedCtx, op mergeOp) {
defer d.MutDone(op.mutID)
store, err := d.GetKeyValueDB()
if err != nil {
dvid.Errorf("Data type labelblk had error initializing store: %v\n", err)
return
}
tk := NewTKeyByCoord(op.block)
data, err := store.Get(ctx, tk)
if err != nil {
dvid.Errorf("Error on GET of labelblk with coord string %q\n", op.block)
return
}
if data == nil {
dvid.Errorf("nil label block where merge was done!\n")
return
}
blockData, _, err := dvid.DeserializeData(data, true)
if err != nil {
dvid.Criticalf("unable to deserialize label block in '%s': %v\n", d.DataName(), err)
return
}
blockBytes := int(d.BlockSize().Prod() * 8)
if len(blockData) != blockBytes {
dvid.Criticalf("After labelblk deserialization got back %d bytes, expected %d bytes\n", len(blockData), blockBytes)
return
}
// Iterate through this block of labels and relabel if label in merge.
for i := 0; i < blockBytes; i += 8 {
label := binary.LittleEndian.Uint64(blockData[i : i+8])
if _, merged := op.Merged[label]; merged {
binary.LittleEndian.PutUint64(blockData[i:i+8], op.Target)
}
}
// Store this block.
serialization, err := dvid.SerializeData(blockData, d.Compression(), d.Checksum())
if err != nil {
dvid.Criticalf("Unable to serialize block in %q: %v\n", d.DataName(), err)
return
}
if err := store.Put(ctx, tk, serialization); err != nil {
dvid.Errorf("Error in putting key %v: %v\n", tk, err)
}
// Notify any downstream downres instance.
d.publishBlockChange(ctx.VersionID(), op.mutID, op.block, blockData)
}
// PutData puts a key-value at a given uuid
func (d *Data) PutData(ctx storage.Context, keyStr string, value []byte) error {
db, err := storage.MutableStore()
if err != nil {
return err
}
serialization, err := dvid.SerializeData(value, d.Compression(), d.Checksum())
if err != nil {
return fmt.Errorf("Unable to serialize data: %v\n", err)
}
tk, err := NewTKey(keyStr)
if err != nil {
return err
}
return db.Put(ctx, tk, serialization)
}
// serializeEdge serializes a dvid.GraphEdge (compression turned off for now)
func (db *GraphKeyValueDB) serializeEdge(edge dvid.GraphEdge) []byte {
// encode: vertex1 id, vertex2 id, weight,
// num properties, property array
total_size := 32
// find size for property strings (account for null character)
for propname, _ := range edge.Properties {
total_size += len(propname) + 1
}
// create byte buffer
buf := make([]byte, total_size, total_size)
// encode vertex 1
start := 0
binary.LittleEndian.PutUint64(buf[start:], uint64(edge.Vertexpair.Vertex1))
start += 8
// encode vertex 2
binary.LittleEndian.PutUint64(buf[start:], uint64(edge.Vertexpair.Vertex2))
start += 8
// encode weight
floatbits := math.Float64bits(edge.Weight)
binary.LittleEndian.PutUint64(buf[start:], floatbits)
start += 8
// encode number of properties
binary.LittleEndian.PutUint64(buf[start:], uint64(len(edge.Properties)))
start += 8
// encode property strings
for propname, _ := range edge.Properties {
for _, propchar := range propname {
buf[start] = byte(propchar)
start += 1
}
buf[start] = byte(0)
start += 1
}
// encode DVID related info (currenlty compression is disabled)
compression, _ := dvid.NewCompression(dvid.Uncompressed, dvid.DefaultCompression)
finalbuf, _ := dvid.SerializeData(buf, compression, dvid.NoChecksum)
return finalbuf
}
// serializes octant contents. Writes octants into preallocated block buffer that may have old data,
// and then returns a serialized data slice suitable for storage.
func (d *Data) serializeOctants(oct octant, blockBuf []byte) ([]byte, error) {
blockSize := d.BlockSize()
nx := blockSize.Value(0)
nxy := blockSize.Value(1) * nx
halfx := blockSize.Value(0) >> 1
halfy := blockSize.Value(1) >> 1
halfz := blockSize.Value(2) >> 1
sectorbytes := int(halfx * halfy * halfz * 8)
xbytes := halfx * 8
for sector, data := range oct {
if len(data) > 0 {
if len(data) != sectorbytes {
dvid.Criticalf("Expected %d bytes in octant for %d, instead got %d bytes.\n", sectorbytes, d.DataName(), len(data))
}
// Get the corner voxel (in block coordinates) for this sector.
iz := sector >> 2
sector -= iz * 4
iy := sector >> 1
ix := sector % 2
ox := int32(ix) * halfx
oy := int32(iy) * halfy
oz := int32(iz) * halfz
// Copy data from octant into larger block buffer.
var oi int32
for z := oz; z < oz+halfz; z++ {
for y := oy; y < oy+halfy; y++ {
di := (z*nxy + y*nx + ox) * 8
copy(blockBuf[di:di+xbytes], data[oi:oi+xbytes])
oi += xbytes
}
}
}
}
return dvid.SerializeData(blockBuf, d.Compression(), d.Checksum())
}
// handelPropertyTransaction allows gets/posts (really puts) of edge or vertex properties.
func (d *Data) handlePropertyTransaction(ctx *datastore.VersionedCtx, db storage.GraphDB, w http.ResponseWriter, r *http.Request, path []string, method string) error {
if len(path) < 2 {
return fmt.Errorf("Must specify edges or vertices in URI and property name")
}
if method == "delete" {
return fmt.Errorf("Transactional delete not supported")
}
edgemode := false
if path[0] == "edges" {
edgemode = true
} else if path[0] != "vertices" {
return fmt.Errorf("Must specify edges or vertices in URI")
}
propertyname := path[1]
readonly := false
if method == "get" {
readonly = true
}
data, err := ioutil.ReadAll(r.Body)
// only allow 1000 vertices to be locked
transactions, start, err := d.transaction_log.createTransactionGroupBinary(data, readonly)
defer transactions.closeTransaction()
if err != nil {
return fmt.Errorf("Failed to create property transaction: %v", err)
}
returned_data := transactions.exportTransactionsBinary()
if method == "post" {
// deserialize transaction (vertex or edge) -- use URI?
num_properties := binary.LittleEndian.Uint64(data[start:])
start += 8
for i := uint64(0); i < num_properties; i++ {
temp := binary.LittleEndian.Uint64(data[start:])
id := dvid.VertexID(temp)
var id2 dvid.VertexID
start += 8
if edgemode {
temp = binary.LittleEndian.Uint64(data[start:])
id2 = dvid.VertexID(temp)
start += 8
}
data_size := binary.LittleEndian.Uint64(data[start:])
start += 8
data_begin := start
start += int(data_size)
data_end := start
if data_begin == data_end {
continue
}
// check if post is possible
if _, ok := transactions.locked_ids[id]; !ok {
continue
}
if edgemode {
if _, ok := transactions.locked_ids[id2]; !ok {
continue
}
}
// execute post
serialization, err := dvid.SerializeData(data[data_begin:data_end], d.Compression(), d.Checksum())
if err != nil {
return fmt.Errorf("Unable to serialize data: %v\n", err)
}
if edgemode {
err = db.SetEdgeProperty(ctx, id, id2, propertyname, serialization)
} else {
err = db.SetVertexProperty(ctx, id, propertyname, serialization)
}
if err != nil {
return fmt.Errorf("Failed to add property %s: %v\n", propertyname, err)
}
}
} else {
num_properties := binary.LittleEndian.Uint64(data[start:])
start += 8
num_properties_loc := len(returned_data)
longbuf := make([]byte, 8, 8)
binary.LittleEndian.PutUint64(longbuf, 0)
returned_data = append(returned_data, longbuf...)
num_executed_transactions := uint64(0)
// read the vertex or edge properties desired
for i := uint64(0); i < num_properties; i++ {
temp := binary.LittleEndian.Uint64(data[start:])
id := dvid.VertexID(temp)
var id2 dvid.VertexID
start += 8
if edgemode {
temp := binary.LittleEndian.Uint64(data[start:])
id2 = dvid.VertexID(temp)
start += 8
}
// check if post is possible
if _, ok := transactions.locked_ids[id]; !ok {
continue
}
if edgemode {
if _, ok := transactions.locked_ids[id2]; !ok {
continue
}
}
// execute get command
var dataout []byte
if edgemode {
dataout, err = db.GetEdgeProperty(ctx, id, id2, propertyname)
} else {
dataout, err = db.GetVertexProperty(ctx, id, propertyname)
}
// serialize return data only if there is return data and no error;
// otherwise return just return the id and size of 0
var data_serialized []byte
if (err == nil) && len(dataout) > 0 {
uncompress := true
data_serialized, _, err = dvid.DeserializeData(dataout, uncompress)
if err != nil {
return fmt.Errorf("Unable to deserialize data for property '%s': %v\n", propertyname, err)
}
}
// save transaction
num_executed_transactions += 1
binary.LittleEndian.PutUint64(longbuf, uint64(id))
returned_data = append(returned_data, longbuf...)
if edgemode {
binary.LittleEndian.PutUint64(longbuf, uint64(id2))
returned_data = append(returned_data, longbuf...)
}
binary.LittleEndian.PutUint64(longbuf, uint64(len(data_serialized)))
returned_data = append(returned_data, longbuf...)
returned_data = append(returned_data, data_serialized...)
}
// update the number of transactions
binary.LittleEndian.PutUint64(returned_data[num_properties_loc:], num_executed_transactions)
}
w.Header().Set("Content-Type", "application/octet-stream")
_, err = w.Write(returned_data)
return err
}
// Goroutine that handles splits across a lot of blocks for one label.
func (d *Data) splitBlock(in <-chan splitOp) {
store, err := storage.MutableStore()
if err != nil {
dvid.Errorf("Data type labelblk had error initializing store: %v\n", err)
return
}
batcher, ok := store.(storage.KeyValueBatcher)
if !ok {
err = fmt.Errorf("Data type labelblk requires batch-enabled store, which %q is not\n", store)
return
}
blockBytes := int(d.BlockSize().Prod() * 8)
for op := range in {
// Iterate through all the modified blocks, inserting the new label using the RLEs for that block.
timedLog := dvid.NewTimeLog()
splitCache.Incr(op.ctx.InstanceVersion(), op.OldLabel)
batch := batcher.NewBatch(&op.ctx)
for _, zyxStr := range op.SortedBlocks {
// Read the block.
tk := NewTKeyByCoord(zyxStr)
data, err := store.Get(&op.ctx, tk)
if err != nil {
dvid.Errorf("Error on GET of labelblk with coord string %v\n", []byte(zyxStr))
continue
}
if data == nil {
dvid.Errorf("nil label block where split was done, coord %v\n", []byte(zyxStr))
continue
}
bdata, _, err := dvid.DeserializeData(data, true)
if err != nil {
dvid.Criticalf("unable to deserialize label block in '%s' key %v: %v\n", d.DataName(), []byte(zyxStr), err)
continue
}
if len(bdata) != blockBytes {
dvid.Criticalf("splitBlock: coord %v got back %d bytes, expected %d bytes\n", []byte(zyxStr), len(bdata), blockBytes)
continue
}
// Modify the block using either voxel-level changes or coarser block-level mods.
if op.Split != nil {
rles, found := op.Split[zyxStr]
if !found {
dvid.Errorf("split block %s not present in block RLEs\n", zyxStr.Print())
continue
}
if err := d.storeRLEs(bdata, op.NewLabel, zyxStr, rles); err != nil {
dvid.Errorf("can't store label %d RLEs into block %s: %v\n", op.NewLabel, zyxStr.Print(), err)
continue
}
} else {
// We are doing coarse split and will replace all
if err := d.replaceLabel(bdata, op.OldLabel, op.NewLabel); err != nil {
dvid.Errorf("can't replace label %d with %d in block %s: %v\n", op.OldLabel, op.NewLabel, zyxStr.Print(), err)
continue
}
}
// Write the modified block.
serialization, err := dvid.SerializeData(bdata, d.Compression(), d.Checksum())
if err != nil {
dvid.Criticalf("Unable to serialize block %s in %q: %v\n", zyxStr.Print(), d.DataName(), err)
continue
}
batch.Put(tk, serialization)
}
if err := batch.Commit(); err != nil {
dvid.Errorf("Batch PUT during %q block split of %d: %v\n", d.DataName(), op.OldLabel, err)
}
splitCache.Decr(op.ctx.InstanceVersion(), op.OldLabel)
timedLog.Debugf("labelblk sync complete for split of %d -> %d", op.OldLabel, op.NewLabel)
}
}
// TODO -- Clean up all the writing and simplify now that we have block-aligned writes.
// writeBlocks persists blocks of voxel data asynchronously using batch writes.
func (d *Data) writeBlocks(v dvid.VersionID, b storage.TKeyValues, wg1, wg2 *sync.WaitGroup) error {
store, err := storage.BigDataStore()
if err != nil {
return fmt.Errorf("Data type imageblk had error initializing store: %v\n", err)
}
batcher, ok := store.(storage.KeyValueBatcher)
if !ok {
return fmt.Errorf("Data type imageblk requires batch-enabled store, which %q is not\n", store)
}
preCompress, postCompress := 0, 0
ctx := datastore.NewVersionedCtx(d, v)
evt := datastore.SyncEvent{d.DataName(), ChangeBlockEvent}
<-server.HandlerToken
go func() {
defer func() {
wg1.Done()
wg2.Done()
dvid.Debugf("Wrote voxel blocks. Before %s: %d bytes. After: %d bytes\n", d.Compression(), preCompress, postCompress)
server.HandlerToken <- 1
}()
batch := batcher.NewBatch(ctx)
for i, block := range b {
serialization, err := dvid.SerializeData(block.V, d.Compression(), d.Checksum())
preCompress += len(block.V)
postCompress += len(serialization)
if err != nil {
dvid.Errorf("Unable to serialize block: %v\n", err)
return
}
batch.Put(block.K, serialization)
indexZYX, err := DecodeTKey(block.K)
if err != nil {
dvid.Errorf("Unable to recover index from block key: %v\n", block.K)
return
}
msg := datastore.SyncMessage{v, Block{indexZYX, block.V}}
if err := datastore.NotifySubscribers(evt, msg); err != nil {
dvid.Errorf("Unable to notify subscribers of ChangeBlockEvent in %s\n", d.DataName())
return
}
// Check if we should commit
if i%KVWriteSize == KVWriteSize-1 {
if err := batch.Commit(); err != nil {
dvid.Errorf("Error on trying to write batch: %v\n", err)
return
}
batch = batcher.NewBatch(ctx)
}
}
if err := batch.Commit(); err != nil {
dvid.Errorf("Error on trying to write batch: %v\n", err)
return
}
}()
return nil
}
func (d *Data) putChunk(chunk *storage.Chunk) {
defer func() {
// After processing a chunk, return the token.
server.HandlerToken <- 1
// Notify the requestor that this chunk is done.
if chunk.Wg != nil {
chunk.Wg.Done()
}
}()
op, ok := chunk.Op.(*putOperation)
if !ok {
log.Fatalf("Illegal operation passed to ProcessChunk() for data %s\n", d.DataName())
}
// Make sure our received chunk is valid.
if chunk == nil {
dvid.Errorf("Received nil chunk in ProcessChunk. Ignoring chunk.\n")
return
}
if chunk.K == nil {
dvid.Errorf("Received nil chunk key in ProcessChunk. Ignoring chunk.\n")
return
}
// Initialize the block buffer using the chunk of data. For voxels, this chunk of
// data needs to be uncompressed and deserialized.
var blockData []byte
var err error
if chunk.V == nil {
blockData = d.BackgroundBlock()
} else {
blockData, _, err = dvid.DeserializeData(chunk.V, true)
if err != nil {
dvid.Errorf("Unable to deserialize block in '%s': %v\n", d.DataName(), err)
return
}
}
// Perform the operation.
block := &storage.TKeyValue{K: chunk.K, V: blockData}
if err = op.voxels.WriteBlock(block, d.BlockSize()); err != nil {
dvid.Errorf("Unable to WriteBlock() in %q: %v\n", d.DataName(), err)
return
}
serialization, err := dvid.SerializeData(blockData, d.Compression(), d.Checksum())
if err != nil {
dvid.Errorf("Unable to serialize block in %q: %v\n", d.DataName(), err)
return
}
store, err := storage.BigDataStore()
if err != nil {
dvid.Errorf("Data type imageblk had error initializing store: %v\n", err)
return
}
ctx := datastore.NewVersionedCtx(d, op.version)
if err := store.Put(ctx, chunk.K, serialization); err != nil {
dvid.Errorf("Unable to PUT voxel data for key %v: %v\n", chunk.K, err)
return
}
// Notify any subscribers that you've changed block.
evt := datastore.SyncEvent{d.DataName(), ChangeBlockEvent}
msg := datastore.SyncMessage{op.version, Block{&op.indexZYX, block.V}}
if err := datastore.NotifySubscribers(evt, msg); err != nil {
dvid.Errorf("Unable to notify subscribers of ChangeBlockEvent in %s\n", d.DataName())
}
}
// PutBlocks stores blocks of data in a span along X
func (d *Data) PutBlocks(v dvid.VersionID, start dvid.ChunkPoint3d, span int, data io.ReadCloser) error {
store, err := storage.BigDataStore()
if err != nil {
return fmt.Errorf("Data type imageblk had error initializing store: %v\n", err)
}
batcher, ok := store.(storage.KeyValueBatcher)
if !ok {
return fmt.Errorf("Data type imageblk requires batch-enabled store, which %q is not\n", store)
}
ctx := datastore.NewVersionedCtx(d, v)
batch := batcher.NewBatch(ctx)
// Read blocks from the stream until we can output a batch put.
const BatchSize = 1000
var readBlocks int
numBlockBytes := d.BlockSize().Prod()
chunkPt := start
buf := make([]byte, numBlockBytes)
for {
// Read a block's worth of data
readBytes := int64(0)
for {
n, err := data.Read(buf[readBytes:])
readBytes += int64(n)
if readBytes == numBlockBytes {
break
}
if err == io.EOF {
return fmt.Errorf("Block data ceased before all block data read")
}
if err != nil {
return fmt.Errorf("Error reading blocks: %v\n", err)
}
}
if readBytes != numBlockBytes {
return fmt.Errorf("Expected %d bytes in block read, got %d instead! Aborting.", numBlockBytes, readBytes)
}
serialization, err := dvid.SerializeData(buf, d.Compression(), d.Checksum())
if err != nil {
return err
}
zyx := dvid.IndexZYX(chunkPt)
batch.Put(NewTKey(&zyx), serialization)
// Notify any subscribers that you've changed block.
evt := datastore.SyncEvent{d.DataName(), ChangeBlockEvent}
msg := datastore.SyncMessage{v, Block{&zyx, buf}}
if err := datastore.NotifySubscribers(evt, msg); err != nil {
return err
}
// Advance to next block
chunkPt[0]++
readBlocks++
finish := (readBlocks == span)
if finish || readBlocks%BatchSize == 0 {
if err := batch.Commit(); err != nil {
return fmt.Errorf("Error on batch commit, block %d: %v\n", readBlocks, err)
}
batch = batcher.NewBatch(ctx)
}
if finish {
break
}
}
return nil
}
func (d *Data) createCompositeChunk(chunk *storage.Chunk) {
defer func() {
// After processing a chunk, return the token.
server.HandlerToken <- 1
// Notify the requestor that this chunk is done.
if chunk.Wg != nil {
chunk.Wg.Done()
}
}()
op := chunk.Op.(*compositeOp)
// Get the spatial index associated with this chunk.
zyx, err := imageblk.DecodeTKey(chunk.K)
if err != nil {
dvid.Errorf("Error in %s.ChunkApplyMap(): %v", d.Data.DataName(), err)
return
}
// Initialize the label buffers. For voxels, this data needs to be uncompressed and deserialized.
curZMutex.Lock()
if zyx[2] > curZ {
curZ = zyx[2]
minZ := zyx.MinPoint(d.BlockSize()).Value(2)
maxZ := zyx.MaxPoint(d.BlockSize()).Value(2)
dvid.Debugf("Now creating composite blocks for Z %d to %d\n", minZ, maxZ)
}
curZMutex.Unlock()
labelData, _, err := dvid.DeserializeData(chunk.V, true)
if err != nil {
dvid.Infof("Unable to deserialize block in '%s': %v\n", d.DataName(), err)
return
}
blockBytes := len(labelData)
if blockBytes%8 != 0 {
dvid.Infof("Retrieved, deserialized block is wrong size: %d bytes\n", blockBytes)
return
}
// Get the corresponding grayscale block.
store, err := op.grayscale.GetOrderedKeyValueDB()
if err != nil {
dvid.Errorf("Unable to retrieve store for %q: %v\n", op.grayscale.DataName(), err)
return
}
grayscaleCtx := datastore.NewVersionedCtx(op.grayscale, op.versionID)
blockData, err := store.Get(grayscaleCtx, chunk.K)
if err != nil {
dvid.Errorf("Error getting grayscale block for index %s\n", zyx)
return
}
grayscaleData, _, err := dvid.DeserializeData(blockData, true)
if err != nil {
dvid.Errorf("Unable to deserialize block in '%s': %v\n", op.grayscale.DataName(), err)
return
}
// Compute the composite block.
// TODO -- Exploit run lengths, use cache of hash?
compositeBytes := blockBytes / 2
compositeData := make([]byte, compositeBytes, compositeBytes)
compositeI := 0
labelI := 0
hashBuf := make([]byte, 4, 4)
for _, grayscale := range grayscaleData {
//murmurhash3(labelData[labelI:labelI+8], hashBuf)
//hashBuf[3] = grayscale
writePseudoColor(grayscale, labelData[labelI:labelI+8], hashBuf)
copy(compositeData[compositeI:compositeI+4], hashBuf)
compositeI += 4
labelI += 8
}
// Store the composite block into the rgba8 data.
serialization, err := dvid.SerializeData(compositeData, d.Compression(), d.Checksum())
if err != nil {
dvid.Errorf("Unable to serialize composite block %s: %v\n", zyx, err)
return
}
compositeCtx := datastore.NewVersionedCtx(op.composite, op.versionID)
err = store.Put(compositeCtx, chunk.K, serialization)
if err != nil {
dvid.Errorf("Unable to PUT composite block %s: %v\n", zyx, err)
return
}
}
// PutBlocks stores blocks of data in a span along X
func (d *Data) PutBlocks(v dvid.VersionID, mutID uint64, start dvid.ChunkPoint3d, span int, data io.ReadCloser, mutate bool) error {
batcher, err := d.GetKeyValueBatcher()
if err != nil {
return err
}
ctx := datastore.NewVersionedCtx(d, v)
batch := batcher.NewBatch(ctx)
// Read blocks from the stream until we can output a batch put.
const BatchSize = 1000
var readBlocks int
numBlockBytes := d.BlockSize().Prod()
chunkPt := start
buf := make([]byte, numBlockBytes)
for {
// Read a block's worth of data
readBytes := int64(0)
for {
n, err := data.Read(buf[readBytes:])
readBytes += int64(n)
if readBytes == numBlockBytes {
break
}
if err == io.EOF {
return fmt.Errorf("Block data ceased before all block data read")
}
if err != nil {
return fmt.Errorf("Error reading blocks: %v\n", err)
}
}
if readBytes != numBlockBytes {
return fmt.Errorf("Expected %d bytes in block read, got %d instead! Aborting.", numBlockBytes, readBytes)
}
serialization, err := dvid.SerializeData(buf, d.Compression(), d.Checksum())
if err != nil {
return err
}
zyx := dvid.IndexZYX(chunkPt)
tk := NewTKey(&zyx)
// If we are mutating, get the previous block of data.
var oldBlock []byte
if mutate {
oldBlock, err = d.loadOldBlock(v, tk)
if err != nil {
return fmt.Errorf("Unable to load previous block in %q, key %v: %v\n", d.DataName(), tk, err)
}
}
// Write the new block
batch.Put(tk, serialization)
// Notify any subscribers that you've changed block.
var event string
var delta interface{}
if mutate {
event = MutateBlockEvent
delta = MutatedBlock{&zyx, oldBlock, buf, mutID}
} else {
event = IngestBlockEvent
delta = Block{&zyx, buf, mutID}
}
evt := datastore.SyncEvent{d.DataUUID(), event}
msg := datastore.SyncMessage{event, v, delta}
if err := datastore.NotifySubscribers(evt, msg); err != nil {
return err
}
// Advance to next block
chunkPt[0]++
readBlocks++
finish := (readBlocks == span)
if finish || readBlocks%BatchSize == 0 {
if err := batch.Commit(); err != nil {
return fmt.Errorf("Error on batch commit, block %d: %v\n", readBlocks, err)
}
batch = batcher.NewBatch(ctx)
}
if finish {
break
}
}
return nil
}
// handleProperty retrieves or deletes properties that can be added to a vertex or edge -- data posted
// or retrieved uses default compression
func (d *Data) handleProperty(ctx *datastore.VersionedCtx, db storage.GraphDB, w http.ResponseWriter, r *http.Request, path []string, method string) error {
edgemode := false
var propertyname string
if len(path) == 3 {
edgemode = true
propertyname = path[2]
} else if len(path) != 2 {
return fmt.Errorf("Incorrect number of parameters specified for handling properties")
} else {
propertyname = path[1]
}
temp, err := strconv.Atoi(path[0])
if err != nil {
return fmt.Errorf("Vertex number not provided")
}
id1 := dvid.VertexID(temp)
id2 := dvid.VertexID(0)
if edgemode {
temp, err := strconv.Atoi(path[1])
if err != nil {
return fmt.Errorf("Vertex number not provided")
}
id2 = dvid.VertexID(temp)
}
// remove a property from a vertex or edge
if method == "delete" {
if edgemode {
db.RemoveEdgeProperty(ctx, id1, id2, propertyname)
if err != nil {
return fmt.Errorf("Failed to remove edge property %d-%d %s: %v\n", id1, id2, propertyname, err)
}
} else {
db.RemoveVertexProperty(ctx, id1, propertyname)
if err != nil {
return fmt.Errorf("Failed to remove vertex property %d %s: %v\n", id1, propertyname, err)
}
}
} else if method == "get" {
var data []byte
if edgemode {
data, err = db.GetEdgeProperty(ctx, id1, id2, propertyname)
} else {
data, err = db.GetVertexProperty(ctx, id1, propertyname)
}
if err != nil {
return fmt.Errorf("Failed to get property %s: %v\n", propertyname, err)
}
uncompress := true
value, _, e := dvid.DeserializeData(data, uncompress)
if e != nil {
err = fmt.Errorf("Unable to deserialize data for property '%s': %v\n", propertyname, e.Error())
return err
}
w.Header().Set("Content-Type", "application/octet-stream")
_, err = w.Write(value)
if err != nil {
return err
}
} else if method == "post" {
// read as binary and load into propertyname
data, err := ioutil.ReadAll(r.Body)
if err != nil {
return err
}
serialization, err := dvid.SerializeData(data, d.Compression(), d.Checksum())
if err != nil {
return fmt.Errorf("Unable to serialize data: %v\n", err)
}
if edgemode {
err = db.SetEdgeProperty(ctx, id1, id2, propertyname, serialization)
} else {
err = db.SetVertexProperty(ctx, id1, propertyname, serialization)
}
if err != nil {
return fmt.Errorf("Failed to add property %s: %v\n", propertyname, err)
}
}
return err
}
func (d *Data) putChunk(chunk *storage.Chunk, putbuffer storage.RequestBuffer) {
defer func() {
// After processing a chunk, return the token.
server.HandlerToken <- 1
// Notify the requestor that this chunk is done.
if chunk.Wg != nil {
chunk.Wg.Done()
}
}()
op, ok := chunk.Op.(*putOperation)
if !ok {
log.Fatalf("Illegal operation passed to ProcessChunk() for data %s\n", d.DataName())
}
// Make sure our received chunk is valid.
if chunk == nil {
dvid.Errorf("Received nil chunk in ProcessChunk. Ignoring chunk.\n")
return
}
if chunk.K == nil {
dvid.Errorf("Received nil chunk key in ProcessChunk. Ignoring chunk.\n")
return
}
// Initialize the block buffer using the chunk of data. For voxels, this chunk of
// data needs to be uncompressed and deserialized.
var blockData []byte
var err error
if chunk.V == nil {
blockData = d.BackgroundBlock()
} else {
blockData, _, err = dvid.DeserializeData(chunk.V, true)
if err != nil {
dvid.Errorf("Unable to deserialize block in %q: %v\n", d.DataName(), err)
return
}
}
// If we are mutating, get the previous block of data.
var oldBlock []byte
if op.mutate {
oldBlock, err = d.loadOldBlock(op.version, chunk.K)
if err != nil {
dvid.Errorf("Unable to load previous block in %q, key %v: %v\n", d.DataName(), chunk.K, err)
return
}
}
// Perform the operation.
block := &storage.TKeyValue{K: chunk.K, V: blockData}
if err = op.voxels.WriteBlock(block, d.BlockSize()); err != nil {
dvid.Errorf("Unable to WriteBlock() in %q: %v\n", d.DataName(), err)
return
}
serialization, err := dvid.SerializeData(blockData, d.Compression(), d.Checksum())
if err != nil {
dvid.Errorf("Unable to serialize block in %q: %v\n", d.DataName(), err)
return
}
store, err := d.GetOrderedKeyValueDB()
if err != nil {
dvid.Errorf("Data type imageblk had error initializing store: %v\n", err)
return
}
ready := make(chan error, 1)
callback := func() {
// Notify any subscribers that you've changed block.
resperr := <-ready
if resperr != nil {
dvid.Errorf("Unable to PUT voxel data for key %v: %v\n", chunk.K, resperr)
return
}
var event string
var delta interface{}
if op.mutate {
event = MutateBlockEvent
delta = MutatedBlock{&op.indexZYX, oldBlock, block.V, op.mutID}
} else {
event = IngestBlockEvent
delta = Block{&op.indexZYX, block.V, op.mutID}
}
evt := datastore.SyncEvent{d.DataUUID(), event}
msg := datastore.SyncMessage{event, op.version, delta}
if err := datastore.NotifySubscribers(evt, msg); err != nil {
dvid.Errorf("Unable to notify subscribers of event %s in %s\n", event, d.DataName())
}
}
// put data -- use buffer if available
ctx := datastore.NewVersionedCtx(d, op.version)
if putbuffer != nil {
go callback()
putbuffer.PutCallback(ctx, chunk.K, serialization, ready)
} else {
if err := store.Put(ctx, chunk.K, serialization); err != nil {
dvid.Errorf("Unable to PUT voxel data for key %v: %v\n", chunk.K, err)
return
}
ready <- nil
callback()
}
}