// deserializeVertex deserializes a dvid.GraphVertex (compression turned off for now)
func (db *GraphKeyValueDB) deserializeVertex(vertexdata []byte) (dvid.GraphVertex, error) {
// create vertex to be returned
vert := dvid.GraphVertex{GraphElement: &dvid.GraphElement{}}
// if vertexdata is empty return an error
if vertexdata == nil || len(vertexdata) == 0 {
return vert, fmt.Errorf("Vertex data empty")
}
// boilerplate deserialization from DVID
data, _, err := dvid.DeserializeData(vertexdata, true)
if err != nil {
return vert, err
}
// load data from vertex (vertex id, vertex weight, num vertices,
// vertex array, num properties, property array
// load vertex id
start := 0
vert.Id = dvid.VertexID(binary.LittleEndian.Uint64(data[start:]))
start += 8
// load vertex weight
floatbits := binary.LittleEndian.Uint64(data[start:])
vert.Weight = math.Float64frombits(floatbits)
start += 8
// number of vertices
count := binary.LittleEndian.Uint64(data[start:])
start += 8
vert.Vertices = make([]dvid.VertexID, count, count)
// load vertices
for i := uint64(0); i < count; i++ {
vert.Vertices[i] = dvid.VertexID(binary.LittleEndian.Uint64(data[start:]))
start += 8
}
// number of properties
vert.Properties = make(dvid.ElementProperties)
count = binary.LittleEndian.Uint64(data[start:])
start += 8
// create property strings
for i := uint64(0); i < count; i++ {
propertyname := string("")
// null separated strings
for data[start] != byte(0) {
propertyname += string(data[start])
start += 1
}
vert.Properties[propertyname] = struct{}{}
// increment beyond null
start += 1
}
return vert, nil
}
// Loads blocks with old data if they exist.
func (d *Data) loadOldBlocks(v dvid.VersionID, vox *Voxels, blocks storage.TKeyValues) error {
store, err := storage.MutableStore()
if err != nil {
return fmt.Errorf("Data type imageblk had error initializing store: %v\n", err)
}
ctx := datastore.NewVersionedCtx(d, v)
// Create a map of old blocks indexed by the index
oldBlocks := map[dvid.IZYXString]([]byte){}
// Iterate through index space for this data using ZYX ordering.
blockSize := d.BlockSize()
blockNum := 0
for it, err := vox.IndexIterator(blockSize); err == nil && it.Valid(); it.NextSpan() {
indexBeg, indexEnd, err := it.IndexSpan()
if err != nil {
return err
}
begTKey := NewTKey(indexBeg)
endTKey := NewTKey(indexEnd)
// Get previous data.
keyvalues, err := store.GetRange(ctx, begTKey, endTKey)
if err != nil {
return err
}
for _, kv := range keyvalues {
indexZYX, err := DecodeTKey(kv.K)
if err != nil {
return err
}
block, _, err := dvid.DeserializeData(kv.V, true)
if err != nil {
return fmt.Errorf("Unable to deserialize block, %s: %v", ctx, err)
}
oldBlocks[indexZYX.ToIZYXString()] = block
}
// Load previous data into blocks
ptBeg := indexBeg.Duplicate().(dvid.ChunkIndexer)
ptEnd := indexEnd.Duplicate().(dvid.ChunkIndexer)
begX := ptBeg.Value(0)
endX := ptEnd.Value(0)
c := dvid.ChunkPoint3d{begX, ptBeg.Value(1), ptBeg.Value(2)}
for x := begX; x <= endX; x++ {
c[0] = x
curIndex := dvid.IndexZYX(c)
curTKey := NewTKey(&curIndex)
blocks[blockNum].K = curTKey
block, ok := oldBlocks[curIndex.ToIZYXString()]
if ok {
copy(blocks[blockNum].V, block)
}
blockNum++
}
}
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)
}
// GetBlocks returns a slice of bytes corresponding to all the blocks along a span in X
func (d *Data) GetBlocks(v dvid.VersionID, start dvid.ChunkPoint3d, span int) ([]byte, error) {
store, err := storage.MutableStore()
if err != nil {
return nil, fmt.Errorf("Data type imageblk had error initializing store: %v\n", err)
}
indexBeg := dvid.IndexZYX(start)
end := start
end[0] += int32(span - 1)
indexEnd := dvid.IndexZYX(end)
begTKey := NewTKey(&indexBeg)
endTKey := NewTKey(&indexEnd)
ctx := datastore.NewVersionedCtx(d, v)
iv := dvid.InstanceVersion{d.DataName(), v}
mapping := labels.MergeCache.LabelMap(iv)
keyvalues, err := store.GetRange(ctx, begTKey, endTKey)
if err != nil {
return nil, err
}
var buf bytes.Buffer
// Save the # of keyvalues actually obtained.
numkv := len(keyvalues)
binary.Write(&buf, binary.LittleEndian, int32(numkv))
// Write the block indices in XYZ little-endian format + the size of each block
uncompress := true
for _, kv := range keyvalues {
block, _, err := dvid.DeserializeData(kv.V, uncompress)
if err != nil {
return nil, fmt.Errorf("Unable to deserialize block, %s (%v): %v", ctx, kv.K, err)
}
if mapping != nil {
n := len(block) / 8
for i := 0; i < n; i++ {
orig := binary.LittleEndian.Uint64(block[i*8 : i*8+8])
mapped, found := mapping.FinalLabel(orig)
if !found {
mapped = orig
}
binary.LittleEndian.PutUint64(block[i*8:i*8+8], mapped)
}
}
_, err = buf.Write(block)
if err != nil {
return nil, err
}
}
return buf.Bytes(), nil
}
// 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()
}
}
// deserializeEdge deserializes a dvid.GraphEdge (compression turned off for now)
func (db *GraphKeyValueDB) deserializeEdge(edgedata []byte) (dvid.GraphEdge, error) {
// create edge to be returned
edge := dvid.GraphEdge{GraphElement: &dvid.GraphElement{}}
// if edgedata is empty return an error
if edgedata == nil || len(edgedata) == 0 {
return edge, fmt.Errorf("Edge data empty")
}
// boilerplate deserialization from DVID
data, _, err := dvid.DeserializeData(edgedata, true)
if err != nil {
return edge, err
}
// load data from edge (vertex1 id, vertex2 id, edge weight,
// num properties, property array
// load vertex1 id
start := 0
edge.Vertexpair.Vertex1 = dvid.VertexID(binary.LittleEndian.Uint64(data[start:]))
start += 8
// load vertex2 id
edge.Vertexpair.Vertex2 = dvid.VertexID(binary.LittleEndian.Uint64(data[start:]))
start += 8
// load edge weight
floatbits := binary.LittleEndian.Uint64(data[start:])
edge.Weight = math.Float64frombits(floatbits)
start += 8
// number of properties
count := binary.LittleEndian.Uint64(data[start:])
start += 8
// create property strings
edge.Properties = make(dvid.ElementProperties)
for i := uint64(0); i < count; i++ {
propertyname := string("")
// null separated strings
for data[start] != 0 {
propertyname += string(data[start])
start += 1
}
edge.Properties[propertyname] = struct{}{}
// increment beyond null
start += 1
}
return edge, nil
}
// 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)
}
func xferBlock(buf []byte, chunk *storage.Chunk, wg *sync.WaitGroup) {
defer wg.Done()
kv := chunk.TKeyValue
uncompress := true
block, _, err := dvid.DeserializeData(kv.V, uncompress)
if err != nil {
dvid.Errorf("Unable to deserialize block (%v): %v", kv.K, err)
return
}
if len(block) != len(buf) {
dvid.Errorf("Deserialized block length (%d) != allocated block length (%d)", len(block), len(buf))
return
}
copy(buf, block)
}
// load block of data from storage
func (d *Data) loadOldBlock(v dvid.VersionID, k storage.TKey) ([]byte, error) {
store, err := d.GetOrderedKeyValueDB()
if err != nil {
return nil, fmt.Errorf("Data type imageblk had error initializing store: %v\n", err)
}
ctx := datastore.NewVersionedCtx(d, v)
serialization, err := store.Get(ctx, k)
if err != nil {
return nil, err
}
data, _, err := dvid.DeserializeData(serialization, true)
if err != nil {
return nil, fmt.Errorf("Unable to deserialize block, %s: %v", ctx, err)
}
return data, err
}
// GetSurface returns a gzipped byte array with # voxels and float32 arrays for vertices and
// normals.
func GetSurface(ctx storage.Context, label uint64) ([]byte, bool, error) {
bigdata, err := storage.BigDataStore()
if err != nil {
return nil, false, fmt.Errorf("Cannot get datastore that handles big data: %v\n", err)
}
// Retrieve the precomputed surface or that it's not available.
data, err := bigdata.Get(ctx, NewLabelSurfaceIndex(label))
if err != nil {
return nil, false, fmt.Errorf("Error in retrieving surface for label %d: %v", label, err)
}
if data == nil {
return []byte{}, false, nil
}
uncompress := false
surfaceBytes, _, err := dvid.DeserializeData(data, uncompress)
if err != nil {
return nil, false, fmt.Errorf("Unable to deserialize surface for label %d: %v\n", label, err)
}
return surfaceBytes, true, nil
}
// GetData gets a value using a key
func (d *Data) GetData(ctx storage.Context, keyStr string) ([]byte, bool, error) {
db, err := storage.MutableStore()
if err != nil {
return nil, false, err
}
tk, err := NewTKey(keyStr)
if err != nil {
return nil, false, err
}
data, err := db.Get(ctx, tk)
if err != nil {
return nil, false, fmt.Errorf("Error in retrieving key '%s': %v", keyStr, err)
}
if data == nil {
return nil, false, nil
}
uncompress := true
value, _, err := dvid.DeserializeData(data, uncompress)
if err != nil {
return nil, false, fmt.Errorf("Unable to deserialize data for key '%s': %v\n", keyStr, err)
}
return value, true, nil
}
// GetLabelBytesAtPoint returns the 8 byte slice corresponding to a 64-bit label at a point.
func (d *Data) GetLabelBytesAtPoint(v dvid.VersionID, pt dvid.Point) ([]byte, error) {
store, err := storage.MutableStore()
if err != nil {
return nil, err
}
// Compute the block key that contains the given point.
coord, ok := pt.(dvid.Chunkable)
if !ok {
return nil, fmt.Errorf("Can't determine block of point %s", pt)
}
blockSize := d.BlockSize()
blockCoord := coord.Chunk(blockSize).(dvid.ChunkPoint3d)
index := dvid.IndexZYX(blockCoord)
// Retrieve the block of labels
ctx := datastore.NewVersionedCtx(d, v)
serialization, err := store.Get(ctx, NewTKey(&index))
if err != nil {
return nil, fmt.Errorf("Error getting '%s' block for index %s\n", d.DataName(), blockCoord)
}
if serialization == nil {
return zeroLabelBytes, nil
}
labelData, _, err := dvid.DeserializeData(serialization, true)
if err != nil {
return nil, fmt.Errorf("Unable to deserialize block %s in '%s': %v\n", blockCoord, d.DataName(), err)
}
// Retrieve the particular label within the block.
ptInBlock := coord.PointInChunk(blockSize)
nx := int64(blockSize.Value(0))
nxy := nx * int64(blockSize.Value(1))
i := (int64(ptInBlock.Value(0)) + int64(ptInBlock.Value(1))*nx + int64(ptInBlock.Value(2))*nxy) * 8
return labelData[i : i+8], nil
}
// 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)
}
}
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
}
}
// Calculates value of a 3d real world point in space defined by underlying data resolution.
func (d *Data) computeValue(pt dvid.Vector3d, ctx storage.Context, keyF KeyFunc, cache *ValueCache) ([]byte, error) {
db, err := storage.BigDataStore()
if err != nil {
return nil, err
}
valuesPerElement := d.Properties.Values.ValuesPerElement()
bytesPerValue, err := d.Properties.Values.BytesPerValue()
if err != nil {
return nil, err
}
bytesPerVoxel := valuesPerElement * bytesPerValue
// Allocate an empty block.
blockSize, ok := d.BlockSize().(dvid.Point3d)
if !ok {
return nil, fmt.Errorf("Data %q does not have a 3d block size", d.DataName())
}
nx := blockSize[0]
nxy := nx * blockSize[1]
emptyBlock := d.BackgroundBlock()
populateF := func(key []byte) ([]byte, error) {
serializedData, err := db.Get(ctx, key)
if err != nil {
return nil, err
}
var deserializedData []byte
if serializedData == nil || len(serializedData) == 0 {
deserializedData = emptyBlock
} else {
deserializedData, _, err = dvid.DeserializeData(serializedData, true)
if err != nil {
return nil, fmt.Errorf("Unable to deserialize block: %v", err)
}
}
return deserializedData, nil
}
// For the given point, compute surrounding lattice points and retrieve values.
neighbors := d.neighborhood(pt)
var valuesI int32
for _, voxelCoord := range neighbors.coords {
deserializedData, _, err := cache.Get(keyF(voxelCoord), populateF)
if err != nil {
return nil, err
}
blockPt := voxelCoord.PointInChunk(blockSize).(dvid.Point3d)
blockI := blockPt[2]*nxy + blockPt[1]*nx + blockPt[0]
//fmt.Printf("Block %s (%d) len %d -> Neighbor %s (buffer %d, len %d)\n",
// blockPt, blockI, len(blockData), voxelCoord, valuesI, len(neighbors.values))
copy(neighbors.values[valuesI:valuesI+bytesPerVoxel], deserializedData[blockI:blockI+bytesPerVoxel])
valuesI += bytesPerVoxel
}
// Perform trilinear interpolation on the underlying data values.
unsupported := func() error {
return fmt.Errorf("DVID cannot retrieve images with arbitrary orientation using %d channels and %d bytes/channel",
valuesPerElement, bytesPerValue)
}
var value []byte
switch valuesPerElement {
case 1:
switch bytesPerValue {
case 1:
if d.Interpolable {
interpValue := trilinearInterpUint8(neighbors.xd, neighbors.yd, neighbors.zd, []uint8(neighbors.values))
value = []byte{byte(interpValue)}
} else {
value = []byte{nearestNeighborUint8(neighbors.xd, neighbors.yd, neighbors.zd, []uint8(neighbors.values))}
}
case 2:
fallthrough
case 4:
fallthrough
case 8:
fallthrough
default:
return nil, unsupported()
}
case 4:
switch bytesPerValue {
case 1:
value = make([]byte, 4, 4)
for c := 0; c < 4; c++ {
channelValues := make([]uint8, 8, 8)
for i := 0; i < 8; i++ {
channelValues[i] = uint8(neighbors.values[i*4+c])
}
if d.Interpolable {
interpValue := trilinearInterpUint8(neighbors.xd, neighbors.yd, neighbors.zd, channelValues)
value[c] = byte(interpValue)
} else {
value[c] = byte(nearestNeighborUint8(neighbors.xd, neighbors.yd, neighbors.zd, channelValues))
}
}
case 2:
fallthrough
default:
return nil, unsupported()
}
default:
}
return value, nil
}
func (d *Data) readChunk(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.(*getOperation)
if !ok {
log.Fatalf("Illegal operation passed to readChunk() for data %s\n", d.DataName())
}
// Make sure our received chunk is valid.
if chunk == nil {
dvid.Errorf("Received nil chunk in readChunk. Ignoring chunk.\n")
return
}
if chunk.K == nil {
dvid.Errorf("Received nil chunk key in readChunk. Ignoring chunk.\n")
return
}
// If there's an ROI, if outside ROI, use blank buffer or allow scaling via attenuation.
var zeroOut bool
var attenuation uint8
indexZYX, err := DecodeTKey(chunk.K)
if err != nil {
dvid.Errorf("Error processing voxel block: %v\n", err)
return
}
if op.blocksInROI != nil {
indexString := string(indexZYX.Bytes())
_, insideROI := op.blocksInROI[indexString]
if !insideROI {
if op.attenuation == 0 {
zeroOut = true
}
attenuation = op.attenuation
}
}
// Initialize the block buffer using the chunk of data. For voxels, this chunk of
// data needs to be uncompressed and deserialized.
var blockData []byte
if zeroOut || 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{chunk.K, blockData}
if err = op.voxels.ReadBlock(block, d.BlockSize(), attenuation); err != nil {
dvid.Errorf("Unable to ReadFromBlock() in %q: %v\n", d.DataName(), err)
return
}
}
func (d *Data) foregroundROI(v dvid.VersionID, dest *roi.Data, background dvid.PointNd) {
dest.Ready = false
store, err := storage.MutableStore()
if err != nil {
dvid.Criticalf("Data type imageblk had error initializing store: %v\n", err)
return
}
timedLog := dvid.NewTimeLog()
timedLog.Infof("Starting foreground ROI %q for %s", dest.DataName(), d.DataName())
// Iterate through all voxel blocks, loading and then checking blocks
// for any foreground voxels.
ctx := datastore.NewVersionedCtx(d, v)
backgroundBytes := make([]byte, len(background))
for i, b := range background {
backgroundBytes[i] = byte(b)
}
const BATCH_SIZE = 1000
var numBatches int
var span *dvid.Span
spans := []dvid.Span{}
var f storage.ChunkFunc = func(chunk *storage.Chunk) error {
if chunk == nil || chunk.V == nil {
return nil
}
data, _, err := dvid.DeserializeData(chunk.V, true)
if err != nil {
return fmt.Errorf("Error decoding block: %v\n", err)
}
numVoxels := d.BlockSize().Prod()
var foreground bool
for i := int64(0); i < numVoxels; i++ {
isBackground := false
for _, b := range backgroundBytes {
if data[i] == b {
isBackground = true
break
}
}
if !isBackground {
foreground = true
break
}
}
if foreground {
indexZYX, err := DecodeTKey(chunk.K)
if err != nil {
return fmt.Errorf("Error decoding voxel block key: %v\n", err)
}
x, y, z := indexZYX.Unpack()
if span == nil {
span = &dvid.Span{z, y, x, x}
} else if !span.Extends(x, y, z) {
spans = append(spans, *span)
if len(spans) >= BATCH_SIZE {
init := (numBatches == 0)
numBatches++
go func(spans []dvid.Span) {
if err := dest.PutSpans(v, spans, init); err != nil {
dvid.Errorf("Error in storing ROI: %v\n", err)
} else {
timedLog.Debugf("-- Wrote batch %d of spans for foreground ROI %q", numBatches, dest.DataName())
}
}(spans)
spans = []dvid.Span{}
}
span = &dvid.Span{z, y, x, x}
}
}
server.BlockOnInteractiveRequests("voxels [compute foreground ROI]")
return nil
}
minTKey := storage.MinTKey(keyImageBlock)
maxTKey := storage.MaxTKey(keyImageBlock)
err = store.ProcessRange(ctx, minTKey, maxTKey, &storage.ChunkOp{}, f)
if err != nil {
dvid.Errorf("Error in processing chunks in ROI: %v\n", err)
return
}
if span != nil {
spans = append(spans, *span)
}
// Save new ROI
if len(spans) > 0 {
if err := dest.PutSpans(v, spans, numBatches == 0); err != nil {
dvid.Errorf("Error in storing ROI: %v\n", err)
return
}
}
timedLog.Infof("Created foreground ROI %q for %s", dest.DataName(), d.DataName())
dest.Ready = true
}
func (d *Data) DeleteBlocks(ctx *datastore.VersionedCtx, start dvid.ChunkPoint3d, span int) error {
store, err := storage.MutableStore()
if err != nil {
return fmt.Errorf("Data type labelblk had error initializing store: %v\n", err)
}
batcher, ok := store.(storage.KeyValueBatcher)
if !ok {
return fmt.Errorf("Data type labelblk requires batch-enabled store, which %q is not\n", store)
}
indexBeg := dvid.IndexZYX(start)
end := start
end[0] += int32(span - 1)
indexEnd := dvid.IndexZYX(end)
begTKey := NewTKey(&indexBeg)
endTKey := NewTKey(&indexEnd)
iv := dvid.InstanceVersion{d.DataName(), ctx.VersionID()}
mapping := labels.MergeCache.LabelMap(iv)
kvs, err := store.GetRange(ctx, begTKey, endTKey)
if err != nil {
return err
}
batch := batcher.NewBatch(ctx)
uncompress := true
for _, kv := range kvs {
izyx, err := DecodeTKey(kv.K)
if err != nil {
return err
}
// Delete the labelblk (really tombstones it)
batch.Delete(kv.K)
// Send data to delete associated labelvol for labels in this block
block, _, err := dvid.DeserializeData(kv.V, uncompress)
if err != nil {
return fmt.Errorf("Unable to deserialize block, %s (%v): %v", ctx, kv.K, err)
}
if mapping != nil {
n := len(block) / 8
for i := 0; i < n; i++ {
orig := binary.LittleEndian.Uint64(block[i*8 : i*8+8])
mapped, found := mapping.FinalLabel(orig)
if !found {
mapped = orig
}
binary.LittleEndian.PutUint64(block[i*8:i*8+8], mapped)
}
}
// Notify any subscribers that we've deleted this block.
evt := datastore.SyncEvent{d.DataName(), labels.DeleteBlockEvent}
msg := datastore.SyncMessage{ctx.VersionID(), labels.DeleteBlock{izyx, block}}
if err := datastore.NotifySubscribers(evt, msg); err != nil {
return err
}
}
return batch.Commit()
}
// Deserialize returns a type key-value pair where the value has been deserialized.
func (kv TKeyValue) Deserialize(uncompress bool) (TKeyValue, error) {
value, _, err := dvid.DeserializeData(kv.V, uncompress)
return TKeyValue{kv.K, value}, err
}
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())
}
}
// 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()
}
}
// Store the cache then relay changes to any downstream instance.
// If we are getting these events, this particular data instance's goroutines
// should only be occupied processing the downsize events.
func (d *Data) downsizeCommit(v dvid.VersionID, mutID uint64) {
// block until we have all of the operation completed.
d.MutWait(mutID)
d.MutDelete(mutID)
d.vcache_mu.RLock()
defer d.vcache_mu.RUnlock()
bc, err := d.getReadOnlyBlockCache(v)
if err != nil {
dvid.Criticalf("downsize commit for %q: %v\n", d.DataName(), err)
}
// Allocate block buffer for writing so that it gets reused instead of reallocated over loop.
blockSize := d.BlockSize()
blockBytes := blockSize.Prod() * 8
// Do GET/PUT for each block, unless we have all 8 octants and can just do a PUT.
// For each block, send to downstream if any.
store, err := d.GetKeyValueDB()
if err != nil {
dvid.Errorf("Data type labelblk had error initializing store: %v\n", err)
return
}
ctx := datastore.NewVersionedCtx(d, v)
for downresBlock, oct := range bc {
blockData := make([]byte, blockBytes)
tk := NewTKeyByCoord(downresBlock)
// Are all 8 octants set?
partial := false
for _, data := range oct {
if data == nil {
partial = true
break
}
}
// If not, GET the previous block data for reintegration and insert into nil octants.
if partial {
serialization, err := store.Get(ctx, tk)
if err != nil {
dvid.Errorf("unable to get data for %q, block %s: %v\n", d.DataName(), downresBlock, err)
continue
}
uncompress := true
deserialized, _, err := dvid.DeserializeData(serialization, uncompress)
if err != nil {
dvid.Criticalf("Unable to deserialize data for %q, block %s: %v", d.DataName(), downresBlock, err)
continue
}
copy(blockData, deserialized)
}
// Write the data.
serialization, err := d.serializeOctants(oct, blockData)
if err != nil {
dvid.Errorf("unable to serialize octant data in %q, block %s: %v\n", d.DataName(), downresBlock, err)
continue
}
if err := store.Put(ctx, tk, serialization); err != nil {
dvid.Errorf("unable to write downsized data in %q, block %s: %v\n", d.DataName(), downresBlock, err)
continue
}
// Notify any downstream downres that we've just modified a block at this level.
d.publishBlockChange(v, mutID, downresBlock, blockData)
}
// Notify and downstream downres that we're done and can commit.
d.publishDownresCommit(v, mutID)
}
