// GetVoxels copies voxels from the storage engine to Voxels, a requested subvolume or 2d image.
func (d *Data) GetVoxels(v dvid.VersionID, vox *Voxels, r *ROI) error {
timedLog := dvid.NewTimeLog()
defer timedLog.Infof("GetVoxels %s", vox)
store, err := storage.MutableStore()
if err != nil {
return fmt.Errorf("Data type imageblk had error initializing store: %v\n", err)
}
// Only do one request at a time, although each request can start many goroutines.
server.SpawnGoroutineMutex.Lock()
defer server.SpawnGoroutineMutex.Unlock()
ctx := datastore.NewVersionedCtx(d, v)
wg := new(sync.WaitGroup)
for it, err := vox.IndexIterator(d.BlockSize()); err == nil && it.Valid(); it.NextSpan() {
indexBeg, indexEnd, err := it.IndexSpan()
if err != nil {
return err
}
begTKey := NewTKey(indexBeg)
endTKey := NewTKey(indexEnd)
// Get set of blocks in ROI if ROI provided
var chunkOp *storage.ChunkOp
if r != nil && r.Iter != nil {
ptBeg := indexBeg.Duplicate().(dvid.ChunkIndexer)
ptEnd := indexEnd.Duplicate().(dvid.ChunkIndexer)
begX := ptBeg.Value(0)
endX := ptEnd.Value(0)
blocksInROI := make(map[string]bool, (endX - begX + 1))
c := dvid.ChunkPoint3d{begX, ptBeg.Value(1), ptBeg.Value(2)}
for x := begX; x <= endX; x++ {
c[0] = x
curIndex := dvid.IndexZYX(c)
if r.Iter.InsideFast(curIndex) {
indexString := string(curIndex.Bytes())
blocksInROI[indexString] = true
}
}
chunkOp = &storage.ChunkOp{&getOperation{vox, blocksInROI, r.attenuation}, wg}
} else {
chunkOp = &storage.ChunkOp{&getOperation{vox, nil, 0}, wg}
}
// Send the entire range of key-value pairs to chunk processor
err = store.ProcessRange(ctx, begTKey, endTKey, chunkOp, storage.ChunkFunc(d.ReadChunk))
if err != nil {
return fmt.Errorf("Unable to GET data %s: %v", ctx, err)
}
}
if err != nil {
return err
}
wg.Wait()
return nil
}
// CreateComposite creates a new rgba8 image by combining hash of labels + the grayscale
func (d *Data) CreateComposite(request datastore.Request, reply *datastore.Response) error {
timedLog := dvid.NewTimeLog()
// Parse the request
var uuidStr, dataName, cmdStr, grayscaleName, destName string
request.CommandArgs(1, &uuidStr, &dataName, &cmdStr, &grayscaleName, &destName)
// Get the version
uuid, v, err := datastore.MatchingUUID(uuidStr)
if err != nil {
return err
}
// Log request
if err = datastore.AddToNodeLog(uuid, []string{request.Command.String()}); err != nil {
return err
}
// Get the grayscale data.
dataservice, err := datastore.GetDataByUUIDName(uuid, dvid.InstanceName(grayscaleName))
if err != nil {
return err
}
grayscale, ok := dataservice.(*imageblk.Data)
if !ok {
return fmt.Errorf("%s is not the name of uint8 data", grayscaleName)
}
// Create a new rgba8blk data.
var compservice datastore.DataService
compservice, err = datastore.GetDataByUUIDName(uuid, dvid.InstanceName(destName))
if err == nil {
return fmt.Errorf("Data instance with name %q already exists", destName)
}
typeService, err := datastore.TypeServiceByName("rgba8blk")
if err != nil {
return fmt.Errorf("Could not get rgba8 type service from DVID")
}
config := dvid.NewConfig()
compservice, err = datastore.NewData(uuid, typeService, dvid.InstanceName(destName), config)
if err != nil {
return err
}
composite, ok := compservice.(*imageblk.Data)
if !ok {
return fmt.Errorf("Error: %s was unable to be set to rgba8 data", destName)
}
// Iterate through all labels and grayscale chunks incrementally in Z, a layer at a time.
wg := new(sync.WaitGroup)
op := &compositeOp{grayscale, composite, v}
chunkOp := &storage.ChunkOp{op, wg}
store, err := d.GetOrderedKeyValueDB()
if err != nil {
return err
}
ctx := datastore.NewVersionedCtx(d, v)
extents := d.Extents()
blockBeg := imageblk.NewTKey(extents.MinIndex)
blockEnd := imageblk.NewTKey(extents.MaxIndex)
err = store.ProcessRange(ctx, blockBeg, blockEnd, chunkOp, storage.ChunkFunc(d.CreateCompositeChunk))
wg.Wait()
// Set new mapped data to same extents.
composite.Properties.Extents = grayscale.Properties.Extents
if err := datastore.SaveDataByUUID(uuid, composite); err != nil {
dvid.Infof("Could not save new data '%s': %v\n", destName, err)
}
timedLog.Infof("Created composite of %s and %s", grayscaleName, destName)
return nil
}
// GetLabels copies labels from the storage engine to Labels, a requested subvolume or 2d image.
func (d *Data) GetLabels(v dvid.VersionID, vox *Labels, r *imageblk.ROI) error {
store, err := d.GetOrderedKeyValueDB()
if err != nil {
return fmt.Errorf("Data type imageblk had error initializing store: %v\n", err)
}
// Only do one request at a time, although each request can start many goroutines.
server.SpawnGoroutineMutex.Lock()
defer server.SpawnGoroutineMutex.Unlock()
ctx := datastore.NewVersionedCtx(d, v)
iv := dvid.InstanceVersion{d.DataUUID(), v}
mapping := labels.LabelMap(iv)
wg := new(sync.WaitGroup)
okv := store.(storage.BufferableOps)
// extract buffer interface
req, hasbuffer := okv.(storage.KeyValueRequester)
if hasbuffer {
okv = req.NewBuffer(ctx)
}
for it, err := vox.IndexIterator(d.BlockSize()); err == nil && it.Valid(); it.NextSpan() {
indexBeg, indexEnd, err := it.IndexSpan()
if err != nil {
return err
}
begTKey := NewTKey(indexBeg)
endTKey := NewTKey(indexEnd)
// Get set of blocks in ROI if ROI provided
var chunkOp *storage.ChunkOp
if r != nil && r.Iter != nil {
ptBeg := indexBeg.Duplicate().(dvid.ChunkIndexer)
ptEnd := indexEnd.Duplicate().(dvid.ChunkIndexer)
begX := ptBeg.Value(0)
endX := ptEnd.Value(0)
blocksInROI := make(map[string]bool, (endX - begX + 1))
c := dvid.ChunkPoint3d{begX, ptBeg.Value(1), ptBeg.Value(2)}
for x := begX; x <= endX; x++ {
c[0] = x
curIndex := dvid.IndexZYX(c)
if r.Iter.InsideFast(curIndex) {
indexString := string(curIndex.Bytes())
blocksInROI[indexString] = true
}
}
chunkOp = &storage.ChunkOp{&getOperation{vox, blocksInROI, mapping}, wg}
} else {
chunkOp = &storage.ChunkOp{&getOperation{vox, nil, mapping}, wg}
}
// Send the entire range of key-value pairs to chunk processor
err = okv.ProcessRange(ctx, begTKey, endTKey, chunkOp, storage.ChunkFunc(d.ReadChunk))
if err != nil {
return fmt.Errorf("Unable to GET data %s: %v", ctx, err)
}
}
if hasbuffer {
// submit the entire buffer to the DB
err = okv.(storage.RequestBuffer).Flush()
if err != nil {
return fmt.Errorf("Unable to GET data %s: %v", ctx, err)
}
}
if err != nil {
return err
}
wg.Wait()
return nil
}