Exemple #1
0
// Returns all (z, y, x0, x1) Spans in sorted order: z, then y, then x0.
func getSpans(ctx *datastore.VersionedCtx, minIndex, maxIndex indexRLE) ([]dvid.Span, error) {
	db, err := ctx.GetOrderedKeyValueDB()
	if err != nil {
		return nil, err
	}
	spans := []dvid.Span{}

	var f storage.ChunkFunc = func(chunk *storage.Chunk) error {
		ibytes, err := chunk.K.ClassBytes(keyROI)
		if err != nil {
			return err
		}
		index := new(indexRLE)
		if err = index.IndexFromBytes(ibytes); err != nil {
			return fmt.Errorf("Unable to get indexRLE out of []byte encoding: %v\n", err)
		}
		z := index.start.Value(2)
		y := index.start.Value(1)
		x0 := index.start.Value(0)
		x1 := x0 + int32(index.span) - 1
		spans = append(spans, dvid.Span{z, y, x0, x1})
		return nil
	}
	mintk := storage.NewTKey(keyROI, minIndex.Bytes())
	maxtk := storage.NewTKey(keyROI, maxIndex.Bytes())
	err = db.ProcessRange(ctx, mintk, maxtk, &storage.ChunkOp{}, f)
	return spans, err
}
Exemple #2
0
// 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)
}
Exemple #3
0
// 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)
}
Exemple #4
0
func putElements(ctx *datastore.VersionedCtx, tk storage.TKey, elems interface{}) error {
	val, err := json.Marshal(elems)
	if err != nil {
		return err
	}
	store, err := ctx.GetOrderedKeyValueDB()
	if err != nil {
		return err
	}
	if err := store.Put(ctx, tk, val); err != nil {
		return err
	}
	return nil
}
Exemple #5
0
func (d *Data) deleteElementInLabel(ctx *datastore.VersionedCtx, batch storage.Batch, pt dvid.Point3d) error {
	labelData := d.GetSyncedLabelblk()
	if labelData == nil {
		return nil // no synced labels
	}
	label, err := labelData.GetLabelAtPoint(ctx.VersionID(), pt)
	if err != nil {
		return err
	}
	tk := NewLabelTKey(label)
	elems, err := getElementsNR(ctx, tk)
	if err != nil {
		return fmt.Errorf("err getting elements for label %d: %v\n", label, err)
	}

	// Note all elements to be deleted.
	var delta DeltaModifyElements
	var toDel []int
	for i, elem := range elems {
		if pt.Equals(elem.Pos) {
			delta.Del = append(delta.Del, ElementPos{Label: label, Kind: elem.Kind, Pos: elem.Pos})
			toDel = append(toDel, i)
		}
	}
	if len(toDel) == 0 {
		return nil
	}

	// Delete them from high index to low index due while reusing slice.
	for i := len(toDel) - 1; i >= 0; i-- {
		d := toDel[i]
		elems[d] = elems[len(elems)-1]
		elems[len(elems)-1] = ElementNR{}
		elems = elems[:len(elems)-1]
	}

	// Put the modified list of elements
	if err := putBatchElements(batch, tk, elems); err != nil {
		return err
	}

	// Notify any subscribers of label annotation changes.
	evt := datastore.SyncEvent{Data: d.DataUUID(), Event: ModifyElementsEvent}
	msg := datastore.SyncMessage{Event: ModifyElementsEvent, Version: ctx.VersionID(), Delta: delta}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		return err
	}
	return nil
}
Exemple #6
0
// makes sure that no relationships are returned since they could be out of date.
func getElementsNR(ctx *datastore.VersionedCtx, tk storage.TKey) (ElementsNR, error) {
	store, err := ctx.GetOrderedKeyValueDB()
	if err != nil {
		return nil, err
	}
	val, err := store.Get(ctx, tk)
	if err != nil {
		return nil, err
	}
	if val == nil {
		return nil, nil
	}
	var elems ElementsNR
	if err := json.Unmarshal(val, &elems); err != nil {
		return nil, err
	}
	return elems, nil
}
Exemple #7
0
func (d *Data) moveElementInLabels(ctx *datastore.VersionedCtx, batch storage.Batch, from, to dvid.Point3d, moved ElementNR) error {
	labelData := d.GetSyncedLabelblk()
	if labelData == nil {
		return nil // no label denormalization possible
	}
	oldLabel, err := labelData.GetLabelAtPoint(ctx.VersionID(), from)
	if err != nil {
		return err
	}
	newLabel, err := labelData.GetLabelAtPoint(ctx.VersionID(), to)
	if err != nil {
		return err
	}
	if oldLabel == newLabel {
		return nil
	}

	var delta DeltaModifyElements
	if oldLabel != 0 {
		tk := NewLabelTKey(oldLabel)
		elems, err := getElementsNR(ctx, tk)
		if err != nil {
			return fmt.Errorf("err getting elements for label %d: %v", oldLabel, err)
		}
		if _, changed := elems.delete(from); changed {
			if err := putBatchElements(batch, tk, elems); err != nil {
				return fmt.Errorf("err putting deleted label %d element: %v", oldLabel, err)
			}
			delta.Del = append(delta.Del, ElementPos{Label: oldLabel, Kind: moved.Kind, Pos: from})
		}
	}
	if newLabel != 0 {
		tk := NewLabelTKey(newLabel)
		elems, err := getElementsNR(ctx, tk)
		if err != nil {
			return fmt.Errorf("err getting elements for label %d: %v", newLabel, err)
		}
		elems.add(ElementsNR{moved})
		if err := putBatchElements(batch, tk, elems); err != nil {
			return err
		}
		delta.Add = append(delta.Add, ElementPos{Label: newLabel, Kind: moved.Kind, Pos: to})
	}

	// Notify any subscribers of label annotation changes.
	if len(delta.Del) != 0 || len(delta.Add) != 0 {
		evt := datastore.SyncEvent{Data: d.DataUUID(), Event: ModifyElementsEvent}
		msg := datastore.SyncMessage{Event: ModifyElementsEvent, Version: ctx.VersionID(), Delta: delta}
		if err := datastore.NotifySubscribers(evt, msg); err != nil {
			return err
		}
	}

	return nil
}
Exemple #8
0
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()
}
Exemple #9
0
// ServeHTTP handles all incoming HTTP requests for this data.
func (d *Data) ServeHTTP(uuid dvid.UUID, ctx *datastore.VersionedCtx, w http.ResponseWriter, r *http.Request) {
	timedLog := dvid.NewTimeLog()

	// Get the action (GET, POST)
	action := strings.ToLower(r.Method)
	switch action {
	case "get":
	case "post":
	default:
		server.BadRequest(w, r, "Can only handle GET or POST HTTP verbs")
		return
	}

	// Break URL request into arguments
	url := r.URL.Path[len(server.WebAPIPath):]
	parts := strings.Split(url, "/")
	if len(parts[len(parts)-1]) == 0 {
		parts = parts[:len(parts)-1]
	}
	if len(parts) < 4 {
		server.BadRequest(w, r, "Incomplete API request")
		return
	}

	// Process help and info.
	switch parts[3] {
	case "help":
		w.Header().Set("Content-Type", "text/plain")
		fmt.Fprintln(w, d.Help())
		return
	case "info":
		jsonBytes, err := d.MarshalJSON()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/json")
		fmt.Fprintf(w, string(jsonBytes))
		return
	default:
	}

	// Get the data name and parse out the channel number or see if composite is required.
	var channelNum int32
	channumStr := strings.TrimPrefix(parts[2], string(d.DataName()))
	if len(channumStr) == 0 {
		channelNum = 0
	} else {
		n, err := strconv.ParseInt(channumStr, 10, 32)
		if err != nil {
			server.BadRequest(w, r, "Error parsing channel number from data name '%s': %v", parts[2], err)
			return
		}
		if int(n) > d.NumChannels {
			minChannelName := fmt.Sprintf("%s1", d.DataName())
			maxChannelName := fmt.Sprintf("%s%d", d.DataName(), d.NumChannels)
			server.BadRequest(w, r, "Data only has %d channels.  Use names '%s' -> '%s'", d.NumChannels,
				minChannelName, maxChannelName)
			return
		}
		channelNum = int32(n)
	}

	// Get the data shape.
	shapeStr := dvid.DataShapeString(parts[3])
	dataShape, err := shapeStr.DataShape()
	if err != nil {
		server.BadRequest(w, r, "Bad data shape given '%s'", shapeStr)
		return
	}

	switch dataShape.ShapeDimensions() {
	case 2:
		sizeStr, offsetStr := parts[4], parts[5]
		slice, err := dvid.NewSliceFromStrings(shapeStr, offsetStr, sizeStr, "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if action == "post" {
			server.BadRequest(w, r, "DVID does not yet support POST of slices into multichannel data")
			return
		} else {
			if d.NumChannels == 0 || d.Data.Values == nil {
				server.BadRequest(w, r, "Cannot retrieve absent data '%d'.  Please load data.", d.DataName())
				return
			}
			values := d.Data.Values
			if len(values) <= int(channelNum) {
				server.BadRequest(w, r, "Must choose channel from 0 to %d", len(values))
				return
			}
			stride := slice.Size().Value(0) * values.BytesPerElement()
			dataValues := dvid.DataValues{values[channelNum]}
			data := make([]uint8, int(slice.NumVoxels()))
			v := imageblk.NewVoxels(slice, dataValues, data, stride)
			channel := &Channel{
				Voxels:     v,
				channelNum: channelNum,
			}
			img, err := d.GetImage(ctx.VersionID(), channel.Voxels, nil)
			var formatStr string
			if len(parts) >= 7 {
				formatStr = parts[6]
			}
			//dvid.ElapsedTime(dvid.Normal, startTime, "%s %s upto image formatting", op, slice)
			err = dvid.WriteImageHttp(w, img.Get(), formatStr)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
		}
	case 3:
		sizeStr, offsetStr := parts[4], parts[5]
		_, err := dvid.NewSubvolumeFromStrings(offsetStr, sizeStr, "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if action == "get" {
			server.BadRequest(w, r, "DVID does not yet support GET of volume data")
			return
		} else {
			server.BadRequest(w, r, "DVID does not yet support POST of volume data")
			return
		}
	default:
		server.BadRequest(w, r, "DVID does not yet support nD volumes")
		return
	}
	timedLog.Infof("HTTP %s: %s", r.Method, dataShape)
}
Exemple #10
0
func (d *Data) mutateBlock(ctx *datastore.VersionedCtx, block imageblk.MutatedBlock, batcher storage.KeyValueBatcher) {
	// Iterate through previous and current labels, detecting set of previous labels and RLEs for current labels.
	blockBytes := len(block.Data)
	if blockBytes != int(d.BlockSize.Prod())*8 {
		dvid.Criticalf("Deserialized label block %d bytes, not uint64 size times %d block elements\n",
			blockBytes, d.BlockSize.Prod())
		return
	}
	labelRLEs := make(map[uint64]dvid.RLEs, 10)
	labelDiff := make(map[uint64]bool, 10)

	firstPt := block.Index.MinPoint(d.BlockSize)
	lastPt := block.Index.MaxPoint(d.BlockSize)

	var curStart dvid.Point3d
	var voxelLabel, curLabel, maxLabel uint64
	var z, y, x, curRun int32
	start := 0
	for z = firstPt.Value(2); z <= lastPt.Value(2); z++ {
		for y = firstPt.Value(1); y <= lastPt.Value(1); y++ {
			for x = firstPt.Value(0); x <= lastPt.Value(0); x++ {
				var pastLabel uint64
				if block.Prev == nil || len(block.Prev) == 0 {
					pastLabel = 0
				} else {
					pastLabel = binary.LittleEndian.Uint64(block.Prev[start : start+8])
				}
				voxelLabel = binary.LittleEndian.Uint64(block.Data[start : start+8])
				if maxLabel < voxelLabel {
					maxLabel = voxelLabel
				}
				if pastLabel != 0 {
					if pastLabel != voxelLabel {
						labelDiff[pastLabel] = true
					} else {
						_, found := labelDiff[pastLabel]
						if !found {
							labelDiff[pastLabel] = false
						}
					}
				}
				start += 8

				// If we hit background or have switched label, save old run and start new one.
				if voxelLabel == 0 || voxelLabel != curLabel {
					// Save old run
					if curRun > 0 {
						labelRLEs[curLabel] = append(labelRLEs[curLabel], dvid.NewRLE(curStart, curRun))
					}
					// Start new one if not zero label.
					if voxelLabel != 0 {
						curStart = dvid.Point3d{x, y, z}
						curRun = 1
					} else {
						curRun = 0
					}
					curLabel = voxelLabel
				} else {
					curRun++
				}
			}
			// Force break of any runs when we finish x scan.
			if curRun > 0 {
				labelRLEs[curLabel] = append(labelRLEs[curLabel], dvid.NewRLE(curStart, curRun))
				curLabel = 0
				curRun = 0
			}
		}
	}

	// If a previous label has no change with current label RLE, then delete the label RLE since no changes
	// are necessary.  Else if previous label is not present in current label RLEs, delete labelvol.
	var deletes []storage.TKey
	blockStr := block.Index.ToIZYXString()
	for label, diff := range labelDiff {
		_, found := labelRLEs[label]
		if diff && !found {
			// mark previous label's RLEs for deletion
			tk := NewTKey(label, blockStr)
			deletes = append(deletes, tk)
		} else if !diff && found {
			// delete current label's RLEs because there's no difference with past RLE
			delete(labelRLEs, label)
		}
	}
	if len(deletes) > 0 {
		batch := batcher.NewBatch(ctx)
		for _, tk := range deletes {
			batch.Delete(tk)
		}
		if err := batch.Commit(); err != nil {
			dvid.Errorf("batch commit on deleting previous labels' labelvols: %v\n", err)
		}
	}

	// Store the RLEs for each label in this block that are new or modified.
	if len(labelRLEs) > 0 {
		batch := batcher.NewBatch(ctx)
		for label, rles := range labelRLEs {
			tk := NewTKey(label, blockStr)
			rleBytes, err := rles.MarshalBinary()
			if err != nil {
				dvid.Errorf("Bad encoding labelvol keys for label %d: %v\n", label, err)
				return
			}
			batch.Put(tk, rleBytes)
		}
		// compare-and-set MaxLabel and batch commit
		d.casMaxLabel(batch, ctx.VersionID(), maxLabel)
	}
}
Exemple #11
0
// If a block of labels is deleted, the associated synapse elements should be changed to zero label elements.
func (d *Data) deleteBlock(ctx *datastore.VersionedCtx, block labels.DeleteBlock, batcher storage.KeyValueBatcher) {
	// Get the synaptic elements for this block
	chunkPt := dvid.ChunkPoint3d(*block.Index)
	tk := NewBlockTKey(chunkPt)
	elems, err := getElements(ctx, tk)
	if err != nil {
		dvid.Errorf("err getting elements for block %s: %v\n", chunkPt, err)
		return
	}
	if len(elems) == 0 {
		return
	}
	blockSize := d.blockSize()
	batch := batcher.NewBatch(ctx)

	// Compute the strides (in bytes)
	bX := blockSize[0] * 8
	bY := blockSize[1] * bX

	// Iterate through all element positions, finding corresponding label and storing elements.
	toDel := LabelPoints{}
	for _, elem := range elems {
		pt := elem.Pos.Point3dInChunk(blockSize)
		i := pt[2]*bY + pt[1]*bX + pt[0]*8
		label := binary.LittleEndian.Uint64(block.Data[i : i+8])
		toDel.add(label, elem.Pos)
	}

	// Delete any non-zero label elements from their respective label k/v.
	var delta DeltaModifyElements
	for label, pts := range toDel {
		tk := NewLabelTKey(label)
		elems, err := getElements(ctx, tk)
		if err != nil {
			dvid.Errorf("err getting elements for label %d: %v\n", label, err)
			return
		}
		save := false
		for _, pt := range pts {
			deleted, changed := elems.delete(pt)
			if changed {
				save = true
				delta.Del = append(delta.Del, ElementPos{Label: label, Kind: deleted.Kind, Pos: pt})
			}
		}
		if save {
			if len(elems) == 0 {
				batch.Delete(tk)
			} else {
				val, err := json.Marshal(elems)
				if err != nil {
					dvid.Errorf("couldn't serialize annotation elements in instance %q: %v\n", d.DataName(), err)
					return
				}
				batch.Put(tk, val)
			}
		}
	}

	if err := batch.Commit(); err != nil {
		dvid.Criticalf("bad commit in annotations %q after delete block: %v\n", d.DataName(), err)
		return
	}

	// Notify any subscribers of label annotation changes.
	evt := datastore.SyncEvent{Data: d.DataUUID(), Event: ModifyElementsEvent}
	msg := datastore.SyncMessage{Event: ModifyElementsEvent, Version: ctx.VersionID(), Delta: delta}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		dvid.Criticalf("unable to notify subscribers of event %s: %v\n", evt, err)
	}
}
Exemple #12
0
// Note that this does not delete any removed labels in the block since we only get the CURRENT block
// and not PAST blocks.  To allow mutation of label blocks, not just ingestion, we need another function.
func (d *Data) ingestBlock(ctx *datastore.VersionedCtx, block imageblk.Block, batcher storage.KeyValueBatcher) {

	// Iterate through this block of labels and create RLEs for each label.
	blockBytes := len(block.Data)
	if blockBytes != int(d.BlockSize.Prod())*8 {
		dvid.Criticalf("Deserialized label block %d bytes, not uint64 size times %d block elements\n",
			blockBytes, d.BlockSize.Prod())
		return
	}
	labelRLEs := make(map[uint64]dvid.RLEs, 10)
	firstPt := block.Index.MinPoint(d.BlockSize)
	lastPt := block.Index.MaxPoint(d.BlockSize)

	var curStart dvid.Point3d
	var voxelLabel, curLabel, maxLabel uint64
	var z, y, x, curRun int32
	start := 0
	for z = firstPt.Value(2); z <= lastPt.Value(2); z++ {
		for y = firstPt.Value(1); y <= lastPt.Value(1); y++ {
			for x = firstPt.Value(0); x <= lastPt.Value(0); x++ {
				voxelLabel = binary.LittleEndian.Uint64(block.Data[start : start+8])
				if maxLabel < voxelLabel {
					maxLabel = voxelLabel
				}
				start += 8

				// If we hit background or have switched label, save old run and start new one.
				if voxelLabel == 0 || voxelLabel != curLabel {
					// Save old run
					if curRun > 0 {
						labelRLEs[curLabel] = append(labelRLEs[curLabel], dvid.NewRLE(curStart, curRun))
					}
					// Start new one if not zero label.
					if voxelLabel != 0 {
						curStart = dvid.Point3d{x, y, z}
						curRun = 1
					} else {
						curRun = 0
					}
					curLabel = voxelLabel
				} else {
					curRun++
				}
			}
			// Force break of any runs when we finish x scan.
			if curRun > 0 {
				labelRLEs[curLabel] = append(labelRLEs[curLabel], dvid.NewRLE(curStart, curRun))
				curLabel = 0
				curRun = 0
			}
		}
	}

	// Store the RLEs for each label in this block.
	if maxLabel > 0 {
		batch := batcher.NewBatch(ctx)
		blockStr := block.Index.ToIZYXString()
		for label, rles := range labelRLEs {
			tk := NewTKey(label, blockStr)
			rleBytes, err := rles.MarshalBinary()
			if err != nil {
				dvid.Errorf("Bad encoding labelvol keys for label %d: %v\n", label, err)
				return
			}
			batch.Put(tk, rleBytes)
		}
		// compare-and-set MaxLabel and batch commit
		d.casMaxLabel(batch, ctx.VersionID(), maxLabel)
	}
}
Exemple #13
0
// If a block of labels is mutated, adjust any label that was either removed or added.
func (d *Data) mutateBlock(ctx *datastore.VersionedCtx, block imageblk.MutatedBlock, batcher storage.KeyValueBatcher) {
	// Get the synaptic elements for this block
	chunkPt := dvid.ChunkPoint3d(*block.Index)
	tk := NewBlockTKey(chunkPt)
	elems, err := getElementsNR(ctx, tk)
	if err != nil {
		dvid.Errorf("err getting elements for block %s: %v\n", chunkPt, err)
		return
	}
	if len(elems) == 0 {
		return
	}
	blockSize := d.blockSize()
	batch := batcher.NewBatch(ctx)

	// Compute the strides (in bytes)
	bX := blockSize[0] * 8
	bY := blockSize[1] * bX

	// Iterate through all element positions, finding corresponding label and storing elements.
	var delta DeltaModifyElements
	labels := make(map[uint64]struct{})
	toAdd := LabelElements{}
	toDel := LabelPoints{}
	for _, elem := range elems {
		pt := elem.Pos.Point3dInChunk(blockSize)
		i := pt[2]*bY + pt[1]*bX + pt[0]*8
		label := binary.LittleEndian.Uint64(block.Data[i : i+8])
		var prev uint64
		if len(block.Prev) != 0 {
			prev = binary.LittleEndian.Uint64(block.Prev[i : i+8])
		}
		if label == prev {
			continue
		}
		if label != 0 {
			toAdd.add(label, elem)
			labels[label] = struct{}{}
			delta.Add = append(delta.Add, ElementPos{Label: label, Kind: elem.Kind, Pos: elem.Pos})
		}
		if prev != 0 {
			toDel.add(prev, elem.Pos)
			labels[prev] = struct{}{}
			delta.Del = append(delta.Del, ElementPos{Label: prev, Kind: elem.Kind, Pos: elem.Pos})
		}
	}

	// Modify any modified label k/v.
	for label := range labels {
		tk := NewLabelTKey(label)
		elems, err := getElementsNR(ctx, tk)
		if err != nil {
			dvid.Errorf("err getting elements for label %d: %v\n", label, err)
			return
		}
		additions, found := toAdd[label]
		if found {
			elems.add(additions)
		}
		deletions, found := toDel[label]
		if found {
			for _, pt := range deletions {
				elems.delete(pt)
			}
		}
		val, err := json.Marshal(elems)
		if err != nil {
			dvid.Errorf("couldn't serialize annotation elements in instance %q: %v\n", d.DataName(), err)
			return
		}
		batch.Put(tk, val)
	}
	if err := batch.Commit(); err != nil {
		dvid.Criticalf("bad commit in annotations %q after delete block: %v\n", d.DataName(), err)
		return
	}

	// Notify any subscribers of label annotation changes.
	evt := datastore.SyncEvent{Data: d.DataUUID(), Event: ModifyElementsEvent}
	msg := datastore.SyncMessage{Event: ModifyElementsEvent, Version: ctx.VersionID(), Delta: delta}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		dvid.Criticalf("unable to notify subscribers of event %s: %v\n", evt, err)
	}
}
Exemple #14
0
// ServeHTTP handles all incoming HTTP requests for this data.
func (d *Data) ServeHTTP(uuid dvid.UUID, ctx *datastore.VersionedCtx, w http.ResponseWriter, r *http.Request) {
	timedLog := dvid.NewTimeLog()

	// Get the action (GET, POST)
	action := strings.ToLower(r.Method)
	switch action {
	case "get":
	case "post":
	default:
		server.BadRequest(w, r, "Can only handle GET or POST HTTP verbs")
		return
	}

	// Break URL request into arguments
	url := r.URL.Path[len(server.WebAPIPath):]
	parts := strings.Split(url, "/")
	if len(parts[len(parts)-1]) == 0 {
		parts = parts[:len(parts)-1]
	}

	// Get query strings and possible roi
	var roiptr *ROI
	queryValues := r.URL.Query()
	roiname := dvid.InstanceName(queryValues.Get("roi"))
	if len(roiname) != 0 {
		roiptr = new(ROI)
		attenuationStr := queryValues.Get("attenuation")
		if len(attenuationStr) != 0 {
			attenuation, err := strconv.Atoi(attenuationStr)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if attenuation < 1 || attenuation > 7 {
				server.BadRequest(w, r, "Attenuation should be from 1 to 7 (divides by 2^n)")
				return
			}
			roiptr.attenuation = uint8(attenuation)
		}
	}

	// Handle POST on data -> setting of configuration
	if len(parts) == 3 && action == "put" {
		fmt.Printf("Setting configuration of data '%s'\n", d.DataName())
		config, err := server.DecodeJSON(r)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if err := d.ModifyConfig(config); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if err := datastore.SaveDataByUUID(uuid, d); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		fmt.Fprintf(w, "Changed '%s' based on received configuration:\n%s\n", d.DataName(), config)
		return
	}

	if len(parts) < 4 {
		server.BadRequest(w, r, "Incomplete API request")
		return
	}

	// Process help and info.
	switch parts[3] {
	case "help":
		w.Header().Set("Content-Type", "text/plain")
		fmt.Fprintln(w, d.Help())
		return

	case "metadata":
		jsonStr, err := d.NdDataMetadata()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/vnd.dvid-nd-data+json")
		fmt.Fprintln(w, jsonStr)
		return

	case "info":
		jsonBytes, err := d.MarshalJSON()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/json")
		fmt.Fprintf(w, string(jsonBytes))
		return

	case "rawkey":
		// GET <api URL>/node/<UUID>/<data name>/rawkey?x=<block x>&y=<block y>&z=<block z>
		if len(parts) != 4 {
			server.BadRequest(w, r, "rawkey endpoint should be followed by query strings (x, y, and z) giving block coord")
			return
		}

	case "blocks":
		// GET  <api URL>/node/<UUID>/<data name>/blocks/<block coord>/<spanX>
		// POST <api URL>/node/<UUID>/<data name>/blocks/<block coord>/<spanX>
		if len(parts) < 6 {
			server.BadRequest(w, r, "%q must be followed by block-coord/span-x", parts[3])
			return
		}
		blockCoord, err := dvid.StringToChunkPoint3d(parts[4], "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		span, err := strconv.Atoi(parts[5])
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if action == "get" {
			data, err := d.GetBlocks(ctx.VersionID(), blockCoord, int32(span))
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			w.Header().Set("Content-type", "application/octet-stream")
			_, err = w.Write(data)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
		} else {
			if err := d.PutBlocks(ctx.VersionID(), blockCoord, span, r.Body); err != nil {
				server.BadRequest(w, r, err)
				return
			}
		}
		timedLog.Infof("HTTP %s: Blocks (%s)", r.Method, r.URL)

	case "arb":
		// GET  <api URL>/node/<UUID>/<data name>/arb/<top left>/<top right>/<bottom left>/<res>[/<format>]
		if len(parts) < 8 {
			server.BadRequest(w, r, "%q must be followed by top-left/top-right/bottom-left/res", parts[3])
			return
		}
		queryStrings := r.URL.Query()
		throttle := queryStrings.Get("throttle")
		if throttle == "true" || throttle == "on" {
			select {
			case <-server.Throttle:
				// Proceed with operation, returning throttle token to server at end.
				defer func() {
					server.Throttle <- 1
				}()
			default:
				throttleMsg := fmt.Sprintf("Server already running maximum of %d throttled operations",
					server.MaxThrottledOps)
				http.Error(w, throttleMsg, http.StatusServiceUnavailable)
				return
			}
		}
		img, err := d.GetArbitraryImage(ctx, parts[4], parts[5], parts[6], parts[7])
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		var formatStr string
		if len(parts) >= 9 {
			formatStr = parts[8]
		}
		err = dvid.WriteImageHttp(w, img.Get(), formatStr)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: Arbitrary image (%s)", r.Method, r.URL)

	case "raw", "isotropic":
		// GET  <api URL>/node/<UUID>/<data name>/isotropic/<dims>/<size>/<offset>[/<format>]
		if len(parts) < 7 {
			server.BadRequest(w, r, "%q must be followed by shape/size/offset", parts[3])
			return
		}
		var isotropic bool = (parts[3] == "isotropic")
		shapeStr, sizeStr, offsetStr := parts[4], parts[5], parts[6]
		planeStr := dvid.DataShapeString(shapeStr)
		plane, err := planeStr.DataShape()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		switch plane.ShapeDimensions() {
		case 2:
			slice, err := dvid.NewSliceFromStrings(planeStr, offsetStr, sizeStr, "_")
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if action != "get" {
				server.BadRequest(w, r, "DVID does not permit 2d mutations, only 3d block-aligned stores")
				return
			}
			rawSlice, err := dvid.Isotropy2D(d.Properties.VoxelSize, slice, isotropic)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			vox, err := d.NewVoxels(rawSlice, nil)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if roiptr != nil {
				roiptr.Iter, err = roi.NewIterator(roiname, ctx.VersionID(), vox)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
			}
			img, err := d.GetImage(ctx.VersionID(), vox, roiptr)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if isotropic {
				dstW := int(slice.Size().Value(0))
				dstH := int(slice.Size().Value(1))
				img, err = img.ScaleImage(dstW, dstH)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
			}
			var formatStr string
			if len(parts) >= 8 {
				formatStr = parts[7]
			}
			err = dvid.WriteImageHttp(w, img.Get(), formatStr)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			timedLog.Infof("HTTP %s: %s (%s)", r.Method, plane, r.URL)
		case 3:
			queryStrings := r.URL.Query()
			if queryStrings.Get("throttle") == "on" {
				select {
				case <-server.Throttle:
					// Proceed with operation, returning throttle token to server at end.
					defer func() {
						server.Throttle <- 1
					}()
				default:
					throttleMsg := fmt.Sprintf("Server already running maximum of %d throttled operations",
						server.MaxThrottledOps)
					http.Error(w, throttleMsg, http.StatusServiceUnavailable)
					return
				}
			}
			subvol, err := dvid.NewSubvolumeFromStrings(offsetStr, sizeStr, "_")
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if action == "get" {
				vox, err := d.NewVoxels(subvol, nil)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
				if roiptr != nil {
					roiptr.Iter, err = roi.NewIterator(roiname, ctx.VersionID(), vox)
					if err != nil {
						server.BadRequest(w, r, err)
						return
					}
				}
				data, err := d.GetVolume(ctx.VersionID(), vox, roiptr)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
				w.Header().Set("Content-type", "application/octet-stream")
				_, err = w.Write(data)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
			} else {
				if isotropic {
					err := fmt.Errorf("can only PUT 'raw' not 'isotropic' images")
					server.BadRequest(w, r, err)
					return
				}
				// Make sure vox is block-aligned
				if !dvid.BlockAligned(subvol, d.BlockSize()) {
					server.BadRequest(w, r, "cannot store voxels in non-block aligned geometry %s -> %s", subvol.StartPoint(), subvol.EndPoint())
					return
				}

				data, err := ioutil.ReadAll(r.Body)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
				vox, err := d.NewVoxels(subvol, data)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
				if roiptr != nil {
					roiptr.Iter, err = roi.NewIterator(roiname, ctx.VersionID(), vox)
					if err != nil {
						server.BadRequest(w, r, err)
						return
					}
				}
				if err = d.PutVoxels(ctx.VersionID(), vox, roiptr); err != nil {
					server.BadRequest(w, r, err)
					return
				}
			}
			timedLog.Infof("HTTP %s: %s (%s)", r.Method, subvol, r.URL)
		default:
			server.BadRequest(w, r, "DVID currently supports shapes of only 2 and 3 dimensions")
		}
	default:
		server.BadRequest(w, r, "Unrecognized API call for voxels %q.  See API help.", d.DataName())
	}
}
Exemple #15
0
// ServeHTTP handles all incoming HTTP requests for this data.
func (d *Data) ServeHTTP(uuid dvid.UUID, ctx *datastore.VersionedCtx, w http.ResponseWriter, r *http.Request) {
	timedLog := dvid.NewTimeLog()

	// Break URL request into arguments
	url := r.URL.Path[len(server.WebAPIPath):]
	parts := strings.Split(url, "/")
	if len(parts[len(parts)-1]) == 0 {
		parts = parts[:len(parts)-1]
	}

	if len(parts) < 4 {
		server.BadRequest(w, r, "incomplete API specification")
		return
	}

	// Process help and info.
	switch parts[3] {
	case "help":
		w.Header().Set("Content-Type", "text/plain")
		fmt.Fprintln(w, d.Help())
		return
	case "info":
		jsonBytes, err := d.MarshalJSON()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/json")
		fmt.Fprintf(w, string(jsonBytes))
		return
	default:
	}

	// Get the key and process request
	var comment string
	command := parts[3]
	method := strings.ToLower(r.Method)
	switch command {
	case "roi":
		switch method {
		case "get":
			if !d.Ready {
				w.WriteHeader(http.StatusPartialContent)
			}
			jsonBytes, err := Get(ctx)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			w.Header().Set("Content-Type", "application/json")
			fmt.Fprintf(w, string(jsonBytes))
			comment = fmt.Sprintf("HTTP GET ROI %q: %d bytes\n", d.DataName(), len(jsonBytes))
		case "post":
			data, err := ioutil.ReadAll(r.Body)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			err = d.PutJSON(ctx.VersionID(), data)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			comment = fmt.Sprintf("HTTP POST ROI %q: %d bytes\n", d.DataName(), len(data))
		case "delete":
			if err := d.Delete(ctx); err != nil {
				server.BadRequest(w, r, err)
				return
			}
			comment = fmt.Sprintf("HTTP DELETE ROI %q\n", d.DataName())
		}
	case "mask":
		if method != "get" {
			server.BadRequest(w, r, "ROI mask only supports GET")
			return
		}
		if len(parts) < 7 {
			server.BadRequest(w, r, "%q must be followed by shape/size/offset", command)
			return
		}
		shapeStr, sizeStr, offsetStr := parts[4], parts[5], parts[6]
		planeStr := dvid.DataShapeString(shapeStr)
		plane, err := planeStr.DataShape()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		switch plane.ShapeDimensions() {
		case 3:
			subvol, err := dvid.NewSubvolumeFromStrings(offsetStr, sizeStr, "_")
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			data, err := d.GetMask(ctx, subvol)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			w.Header().Set("Content-type", "application/octet-stream")
			_, err = w.Write(data)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
		default:
			server.BadRequest(w, r, "Currently only 3d masks ('0_1_2' shape) is supported")
			return
		}
	case "ptquery":
		switch method {
		case "get":
			server.BadRequest(w, r, "ptquery requires POST with list of points")
			return
		case "post":
			data, err := ioutil.ReadAll(r.Body)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			jsonBytes, err := d.PointQuery(ctx, data)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			w.Header().Set("Content-Type", "application/json")
			fmt.Fprintf(w, string(jsonBytes))
			comment = fmt.Sprintf("HTTP POST ptquery '%s'\n", d.DataName())
		}
	case "partition":
		if method != "get" {
			server.BadRequest(w, r, "partition only supports GET request")
			return
		}
		queryValues := r.URL.Query()
		batchsizeStr := queryValues.Get("batchsize")
		batchsize, err := strconv.Atoi(batchsizeStr)
		if err != nil {
			server.BadRequest(w, r, fmt.Sprintf("Error reading batchsize query string: %v", err))
			return
		}

		var jsonBytes []byte
		optimizedStr := queryValues.Get("optimized")
		dvid.Infof("queryvalues = %v\n", queryValues)
		if optimizedStr == "true" || optimizedStr == "on" {
			dvid.Infof("Perform optimized partitioning into subvolumes using batchsize %d\n", batchsize)
			jsonBytes, err = d.Partition(ctx, int32(batchsize))
		} else {
			dvid.Infof("Performing simple partitioning into subvolumes using batchsize %d\n", batchsize)
			jsonBytes, err = d.SimplePartition(ctx, int32(batchsize))
		}
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/json")
		fmt.Fprintf(w, string(jsonBytes))
		comment = fmt.Sprintf("HTTP partition '%s' with batch size %d\n",
			d.DataName(), batchsize)
	default:
		w.Header().Set("Content-Type", "text/plain")
		server.BadRequest(w, r, "Can only handle GET or POST HTTP verbs")
		return
	}

	timedLog.Infof(comment)
}
Exemple #16
0
// stores synaptic elements arranged by label, replacing any
// elements at same position.
func (d *Data) storeLabelElements(ctx *datastore.VersionedCtx, batch storage.Batch, be blockElements) error {
	labelData := d.GetSyncedLabelblk()
	if labelData == nil {
		dvid.Infof("No synced labels for annotation %q, skipping label-aware denormalization.\n", d.DataName())
		return nil // no synced labels
	}

	// Compute the strides (in bytes)
	blockSize := d.blockSize()
	bX := blockSize[0] * 8
	bY := blockSize[1] * bX
	blockBytes := int(blockSize[0] * blockSize[1] * blockSize[2] * 8)

	toAdd := LabelElements{}
	for izyxStr, elems := range be {
		blockCoord, err := izyxStr.ToChunkPoint3d()
		if err != nil {
			return err
		}

		// Get the labels for this block
		labels, err := labelData.GetLabelBlock(ctx.VersionID(), blockCoord)
		if err != nil {
			return err
		}
		if len(labels) == 0 {
			continue
		}
		if len(labels) != blockBytes {
			return fmt.Errorf("Expected %d bytes in %q label block, got %d instead.  Aborting.", blockBytes, d.DataName(), len(labels))
		}

		// Group annotations by label
		for _, elem := range elems {
			pt := elem.Pos.Point3dInChunk(blockSize)
			i := pt[2]*bY + pt[1]*bX + pt[0]*8
			label := binary.LittleEndian.Uint64(labels[i : i+8])
			if label != 0 {
				toAdd.add(label, elem.ElementNR)
			}
		}
	}

	// Store all the added annotations to the appropriate labels.
	var delta DeltaModifyElements
	for label, additions := range toAdd {
		tk := NewLabelTKey(label)
		elems, err := getElementsNR(ctx, tk)
		if err != nil {
			return fmt.Errorf("err getting elements for label %d: %v\n", label, err)
		}

		// Check if these annotations already exist.
		emap := make(map[string]int)
		for i, elem := range elems {
			emap[elem.Pos.MapKey()] = i
		}
		for _, elem := range additions {
			i, found := emap[elem.Pos.MapKey()]
			if !found {
				elems = append(elems, elem)
				delta.Add = append(delta.Add, ElementPos{Label: label, Kind: elem.Kind, Pos: elem.Pos})
			} else {
				elems[i] = elem // replace properties if same position
			}
		}
		if err := putBatchElements(batch, tk, elems); err != nil {
			return fmt.Errorf("couldn't serialize label %d annotations in instance %q: %v\n", label, d.DataName(), err)
		}
	}

	// Notify any subscribers of label annotation changes.
	evt := datastore.SyncEvent{Data: d.DataUUID(), Event: ModifyElementsEvent}
	msg := datastore.SyncMessage{Event: ModifyElementsEvent, Version: ctx.VersionID(), Delta: delta}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		return err
	}

	return nil
}
Exemple #17
0
// ServeHTTP handles all incoming HTTP requests for this data.
func (d *Data) ServeHTTP(uuid dvid.UUID, ctx *datastore.VersionedCtx, w http.ResponseWriter, r *http.Request) {
	timedLog := dvid.NewTimeLog()

	// Check the action
	action := strings.ToLower(r.Method)
	if action != "get" {
		server.BadRequest(w, r, "labelsz data can only accept GET HTTP requests")
		return
	}

	// Break URL request into arguments
	url := r.URL.Path[len(server.WebAPIPath):]
	parts := strings.Split(url, "/")
	if len(parts[len(parts)-1]) == 0 {
		parts = parts[:len(parts)-1]
	}

	if len(parts) < 4 {
		server.BadRequest(w, r, "Incomplete API request")
		return
	}

	// Process help and info.
	switch parts[3] {
	case "help":
		w.Header().Set("Content-Type", "text/plain")
		fmt.Fprintln(w, dtype.Help())

	case "info":
		jsonBytes, err := d.MarshalJSON()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/json")
		fmt.Fprintf(w, string(jsonBytes))

	case "size":
		// GET <api URL>/node/<UUID>/<data name>/size/<label>
		if len(parts) < 5 {
			server.BadRequest(w, r, "ERROR: DVID requires label ID to follow 'size' command")
			return
		}
		label, err := strconv.ParseUint(parts[4], 10, 64)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		size, err := d.GetSize(ctx.VersionID(), label)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-type", "application/json")
		fmt.Fprintf(w, "{%q: %d, %q: %d}", "Label", label, "Voxels", size)
		timedLog.Infof("HTTP %s: get label %d size", r.Method, label)

	case "sizerange":
		// GET <api URL>/node/<UUID>/<data name>/sizerange/<min size>/<optional max size>
		if len(parts) < 5 {
			server.BadRequest(w, r, "ERROR: DVID requires at least the minimum size to follow 'sizerange' command")
			return
		}
		minSize, err := strconv.ParseUint(parts[4], 10, 64)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		var maxSize uint64
		if len(parts) >= 6 {
			maxSize, err = strconv.ParseUint(parts[5], 10, 64)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
		}
		jsonStr, err := d.GetSizeRange(ctx.VersionID(), minSize, maxSize)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-type", "application/json")
		fmt.Fprintf(w, jsonStr)
		timedLog.Infof("HTTP %s: get labels with volume > %d and < %d (%s)", r.Method, minSize, maxSize, r.URL)

	default:
		server.BadRequest(w, r, "Unrecognized API call '%s' for labelsz data '%s'.  See API help.",
			parts[3], d.DataName())
	}
}
Exemple #18
0
// ServeHTTP handles all incoming HTTP requests for this data.
func (d *Data) ServeHTTP(uuid dvid.UUID, ctx *datastore.VersionedCtx, w http.ResponseWriter, r *http.Request) {
	// TODO -- Refactor this method to break it up and make it simpler.  Use the web routing for the endpoints.

	timedLog := dvid.NewTimeLog()

	// Get the action (GET, POST)
	action := strings.ToLower(r.Method)
	switch action {
	case "get":
	case "post":
	case "delete":
	default:
		server.BadRequest(w, r, "labelblk only handles GET, POST, and DELETE HTTP verbs")
		return
	}

	// Break URL request into arguments
	url := r.URL.Path[len(server.WebAPIPath):]
	parts := strings.Split(url, "/")
	if len(parts[len(parts)-1]) == 0 {
		parts = parts[:len(parts)-1]
	}

	// Get query strings and possible roi
	var roiptr *imageblk.ROI
	queryValues := r.URL.Query()
	roiname := dvid.InstanceName(queryValues.Get("roi"))
	if len(roiname) != 0 {
		roiptr = new(imageblk.ROI)
	}

	// Handle POST on data -> setting of configuration
	if len(parts) == 3 && action == "post" {
		config, err := server.DecodeJSON(r)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if err := d.ModifyConfig(config); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if err := datastore.SaveDataByUUID(uuid, d); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		fmt.Fprintf(w, "Changed '%s' based on received configuration:\n%s\n", d.DataName(), config)
		return
	}

	if len(parts) < 4 {
		server.BadRequest(w, r, "Incomplete API request")
		return
	}

	// Process help and info.
	switch parts[3] {
	case "help":
		w.Header().Set("Content-Type", "text/plain")
		fmt.Fprintln(w, dtype.Help())

	case "metadata":
		jsonStr, err := d.NdDataMetadata()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/vnd.dvid-nd-data+json")
		fmt.Fprintln(w, jsonStr)

	case "info":
		jsonBytes, err := d.MarshalJSON()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/json")
		fmt.Fprintf(w, string(jsonBytes))

	case "label":
		// GET <api URL>/node/<UUID>/<data name>/label/<coord>
		if len(parts) < 5 {
			server.BadRequest(w, r, "DVID requires coord to follow 'label' command")
			return
		}
		coord, err := dvid.StringToPoint(parts[4], "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		label, err := d.GetLabelAtPoint(ctx.VersionID(), coord)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-type", "application/json")
		jsonStr := fmt.Sprintf(`{"Label": %d}`, label)
		fmt.Fprintf(w, jsonStr)
		timedLog.Infof("HTTP %s: label at %s (%s)", r.Method, coord, r.URL)

	case "labels":
		// POST <api URL>/node/<UUID>/<data name>/labels
		if action != "post" {
			server.BadRequest(w, r, "Batch labels query must be a POST request")
			return
		}
		data, err := ioutil.ReadAll(r.Body)
		if err != nil {
			server.BadRequest(w, r, "Bad POSTed data for batch reverse query.  Should be JSON.")
			return
		}
		var coords []dvid.Point3d
		if err := json.Unmarshal(data, &coords); err != nil {
			server.BadRequest(w, r, fmt.Sprintf("Bad labels request JSON: %v", err))
			return
		}
		w.Header().Set("Content-type", "application/json")
		fmt.Fprintf(w, "[")
		sep := false
		for _, coord := range coords {
			label, err := d.GetLabelAtPoint(ctx.VersionID(), coord)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if sep {
				fmt.Fprintf(w, ",")
			}
			fmt.Fprintf(w, "%d", label)
			sep = true
		}
		fmt.Fprintf(w, "]")
		timedLog.Infof("HTTP batch label-at-point query (%d coordinates)", len(coords))

	case "blocks":
		// DELETE <api URL>/node/<UUID>/<data name>/blocks/<block coord>/<spanX>
		if len(parts) < 6 {
			server.BadRequest(w, r, "DVID requires starting block coord and # of blocks along X to follow 'blocks' endpoint.")
			return
		}
		blockCoord, err := dvid.StringToChunkPoint3d(parts[4], "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		span, err := strconv.Atoi(parts[5])
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if action != "delete" {
			server.BadRequest(w, r, "DVID currently accepts only DELETE on the 'blocks' endpoint")
			return
		}
		if err := d.DeleteBlocks(ctx, blockCoord, span); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: delete %d blocks from %s (%s)", r.Method, span, blockCoord, r.URL)

	case "pseudocolor":
		if len(parts) < 7 {
			server.BadRequest(w, r, "'%s' must be followed by shape/size/offset", parts[3])
			return
		}
		shapeStr, sizeStr, offsetStr := parts[4], parts[5], parts[6]
		planeStr := dvid.DataShapeString(shapeStr)
		plane, err := planeStr.DataShape()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		switch plane.ShapeDimensions() {
		case 2:
			slice, err := dvid.NewSliceFromStrings(planeStr, offsetStr, sizeStr, "_")
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if action != "get" {
				server.BadRequest(w, r, "DVID does not permit 2d mutations, only 3d block-aligned stores")
				return
			}
			lbl, err := d.NewLabels(slice, nil)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if roiptr != nil {
				roiptr.Iter, err = roi.NewIterator(roiname, ctx.VersionID(), lbl)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
			}
			img, err := d.GetImage(ctx.VersionID(), lbl, roiptr)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}

			// Convert to pseudocolor
			pseudoColor, err := colorImage(img)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}

			//dvid.ElapsedTime(dvid.Normal, startTime, "%s %s upto image formatting", op, slice)
			var formatStr string
			if len(parts) >= 8 {
				formatStr = parts[7]
			}
			err = dvid.WriteImageHttp(w, pseudoColor, formatStr)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			timedLog.Infof("HTTP %s: %s (%s)", r.Method, plane, r.URL)
		default:
			server.BadRequest(w, r, "DVID currently supports only 2d pseudocolor image requests")
			return
		}

	case "raw", "isotropic":
		if len(parts) < 7 {
			server.BadRequest(w, r, "'%s' must be followed by shape/size/offset", parts[3])
			return
		}
		var isotropic bool = (parts[3] == "isotropic")
		shapeStr, sizeStr, offsetStr := parts[4], parts[5], parts[6]
		planeStr := dvid.DataShapeString(shapeStr)
		plane, err := planeStr.DataShape()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		switch plane.ShapeDimensions() {
		case 2:
			slice, err := dvid.NewSliceFromStrings(planeStr, offsetStr, sizeStr, "_")
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if action != "get" {
				server.BadRequest(w, r, "DVID does not permit 2d mutations, only 3d block-aligned stores")
				return
			}
			rawSlice, err := dvid.Isotropy2D(d.Properties.VoxelSize, slice, isotropic)
			lbl, err := d.NewLabels(rawSlice, nil)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if roiptr != nil {
				roiptr.Iter, err = roi.NewIterator(roiname, ctx.VersionID(), lbl)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
			}
			img, err := d.GetImage(ctx.VersionID(), lbl, roiptr)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if isotropic {
				dstW := int(slice.Size().Value(0))
				dstH := int(slice.Size().Value(1))
				img, err = img.ScaleImage(dstW, dstH)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
			}
			var formatStr string
			if len(parts) >= 8 {
				formatStr = parts[7]
			}
			//dvid.ElapsedTime(dvid.Normal, startTime, "%s %s upto image formatting", op, slice)
			err = dvid.WriteImageHttp(w, img.Get(), formatStr)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			timedLog.Infof("HTTP %s: %s (%s)", r.Method, plane, r.URL)
		case 3:
			queryStrings := r.URL.Query()
			throttle := queryStrings.Get("throttle")
			if throttle == "true" || throttle == "on" {
				select {
				case <-server.Throttle:
					// Proceed with operation, returning throttle token to server at end.
					defer func() {
						server.Throttle <- 1
					}()
				default:
					throttleMsg := fmt.Sprintf("Server already running maximum of %d throttled operations",
						server.MaxThrottledOps)
					http.Error(w, throttleMsg, http.StatusServiceUnavailable)
					return
				}
			}
			compression := queryValues.Get("compression")
			subvol, err := dvid.NewSubvolumeFromStrings(offsetStr, sizeStr, "_")
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if action == "get" {
				lbl, err := d.NewLabels(subvol, nil)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
				if roiptr != nil {
					roiptr.Iter, err = roi.NewIterator(roiname, ctx.VersionID(), lbl)
					if err != nil {
						server.BadRequest(w, r, err)
						return
					}
				}
				data, err := d.GetVolume(ctx.VersionID(), lbl, roiptr)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
				w.Header().Set("Content-type", "application/octet-stream")
				switch compression {
				case "":
					_, err = w.Write(data)
					if err != nil {
						server.BadRequest(w, r, err)
						return
					}
				case "lz4":
					compressed := make([]byte, lz4.CompressBound(data))
					var n, outSize int
					if outSize, err = lz4.Compress(data, compressed); err != nil {
						server.BadRequest(w, r, err)
						return
					}
					compressed = compressed[:outSize]
					if n, err = w.Write(compressed); err != nil {
						server.BadRequest(w, r, err)
						return
					}
					if n != outSize {
						errmsg := fmt.Sprintf("Only able to write %d of %d lz4 compressed bytes\n", n, outSize)
						dvid.Errorf(errmsg)
						server.BadRequest(w, r, errmsg)
						return
					}
				case "gzip":
					gw := gzip.NewWriter(w)
					if _, err = gw.Write(data); err != nil {
						server.BadRequest(w, r, err)
						return
					}
					if err = gw.Close(); err != nil {
						server.BadRequest(w, r, err)
						return
					}
				default:
					server.BadRequest(w, r, "unknown compression type %q", compression)
					return
				}
			} else {
				if isotropic {
					server.BadRequest(w, r, "can only POST 'raw' not 'isotropic' images")
					return
				}
				// Make sure vox is block-aligned
				if !dvid.BlockAligned(subvol, d.BlockSize()) {
					server.BadRequest(w, r, "cannot store labels in non-block aligned geometry %s -> %s", subvol.StartPoint(), subvol.EndPoint())
					return
				}

				var data []byte
				switch compression {
				case "":
					tlog := dvid.NewTimeLog()
					data, err = ioutil.ReadAll(r.Body)
					if err != nil {
						server.BadRequest(w, r, err)
						return
					}
					tlog.Debugf("read 3d uncompressed POST")
				case "lz4":
					tlog := dvid.NewTimeLog()
					data, err = ioutil.ReadAll(r.Body)
					if err != nil {
						server.BadRequest(w, r, err)
						return
					}
					if len(data) == 0 {
						server.BadRequest(w, r, "received 0 LZ4 compressed bytes")
						return
					}
					tlog.Debugf("read 3d lz4 POST")
					tlog = dvid.NewTimeLog()
					uncompressed := make([]byte, subvol.NumVoxels()*8)
					err = lz4.Uncompress(data, uncompressed)
					if err != nil {
						server.BadRequest(w, r, err)
						return
					}
					data = uncompressed
					tlog.Debugf("uncompressed 3d lz4 POST")
				case "gzip":
					tlog := dvid.NewTimeLog()
					gr, err := gzip.NewReader(r.Body)
					if err != nil {
						server.BadRequest(w, r, err)
						return
					}
					data, err = ioutil.ReadAll(gr)
					if err != nil {
						server.BadRequest(w, r, err)
						return
					}
					if err = gr.Close(); err != nil {
						server.BadRequest(w, r, err)
						return
					}
					tlog.Debugf("read and uncompress 3d gzip POST")
				default:
					server.BadRequest(w, r, "unknown compression type %q", compression)
					return
				}
				lbl, err := d.NewLabels(subvol, data)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
				if roiptr != nil {
					roiptr.Iter, err = roi.NewIterator(roiname, ctx.VersionID(), lbl)
					if err != nil {
						server.BadRequest(w, r, err)
						return
					}
				}
				if err = d.PutVoxels(ctx.VersionID(), lbl.Voxels, roiptr); err != nil {
					server.BadRequest(w, r, err)
					return
				}
			}
			timedLog.Infof("HTTP %s: %s (%s)", r.Method, subvol, r.URL)
		default:
			server.BadRequest(w, r, "DVID currently supports shapes of only 2 and 3 dimensions")
			return
		}

	default:
		server.BadRequest(w, r, "Unrecognized API call %q for labelblk data %q.  See API help.",
			parts[3], d.DataName())
	}
}
Exemple #19
0
// If a block of labels is ingested, adjust each label's synaptic element list.
func (d *Data) ingestBlock(ctx *datastore.VersionedCtx, block imageblk.Block, batcher storage.KeyValueBatcher) {
	// Get the synaptic elements for this block
	chunkPt := dvid.ChunkPoint3d(*block.Index)
	tk := NewBlockTKey(chunkPt)
	elems, err := getElementsNR(ctx, tk)
	if err != nil {
		dvid.Errorf("err getting elements for block %s: %v\n", chunkPt, err)
		return
	}
	if len(elems) == 0 {
		return
	}
	blockSize := d.blockSize()
	batch := batcher.NewBatch(ctx)

	// Compute the strides (in bytes)
	bX := blockSize[0] * 8
	bY := blockSize[1] * bX

	// Iterate through all element positions, finding corresponding label and storing elements.
	added := 0
	toAdd := LabelElements{}
	for _, elem := range elems {
		pt := elem.Pos.Point3dInChunk(blockSize)
		i := (pt[2]*bY+pt[1])*bX + pt[0]*8
		label := binary.LittleEndian.Uint64(block.Data[i : i+8])
		if label != 0 {
			toAdd.add(label, elem)
			added++
		}
	}

	// Add any non-zero label elements to their respective label k/v.
	var delta DeltaModifyElements
	delta.Add = make([]ElementPos, added)
	i := 0
	for label, addElems := range toAdd {
		tk := NewLabelTKey(label)
		elems, err := getElementsNR(ctx, tk)
		if err != nil {
			dvid.Errorf("err getting elements for label %d: %v\n", label, err)
			return
		}
		elems.add(addElems)
		val, err := json.Marshal(elems)
		if err != nil {
			dvid.Errorf("couldn't serialize annotation elements in instance %q: %v\n", d.DataName(), err)
			return
		}
		batch.Put(tk, val)

		for _, addElem := range addElems {
			delta.Add[i] = ElementPos{Label: label, Kind: addElem.Kind, Pos: addElem.Pos}
			i++
		}
	}

	if err := batch.Commit(); err != nil {
		dvid.Criticalf("bad commit in annotations %q after delete block: %v\n", d.DataName(), err)
		return
	}

	// Notify any subscribers of label annotation changes.
	evt := datastore.SyncEvent{Data: d.DataUUID(), Event: ModifyElementsEvent}
	msg := datastore.SyncMessage{Event: ModifyElementsEvent, Version: ctx.VersionID(), Delta: delta}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		dvid.Criticalf("unable to notify subscribers of event %s: %v\n", evt, err)
	}
}
Exemple #20
0
// ServeHTTP handles all incoming HTTP requests for this data.
func (d *Data) ServeHTTP(uuid dvid.UUID, ctx *datastore.VersionedCtx, w http.ResponseWriter, r *http.Request) {
	timedLog := dvid.NewTimeLog()

	// Check the action
	action := strings.ToLower(r.Method)
	if action != "get" {
		server.BadRequest(w, r, "labelsurf data can only accept GET HTTP requests")
		return
	}

	// Break URL request into arguments
	url := r.URL.Path[len(server.WebAPIPath):]
	parts := strings.Split(url, "/")
	if len(parts[len(parts)-1]) == 0 {
		parts = parts[:len(parts)-1]
	}

	if len(parts) < 4 {
		server.BadRequest(w, r, "Incomplete API request")
		return
	}

	// Process help and info.
	switch parts[3] {
	case "help":
		w.Header().Set("Content-Type", "text/plain")
		fmt.Fprintln(w, dtype.Help())

	case "info":
		jsonBytes, err := d.MarshalJSON()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/json")
		fmt.Fprintf(w, string(jsonBytes))

	case "surface":
		// GET <api URL>/node/<UUID>/<data name>/surface/<label>
		if len(parts) < 5 {
			server.BadRequest(w, r, "ERROR: DVID requires label ID to follow 'surface' command")
			return
		}
		label, err := strconv.ParseUint(parts[4], 10, 64)
		fmt.Printf("Getting surface for label %d\n", label)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		gzipData, found, err := GetSurface(ctx, label)
		if err != nil {
			server.BadRequest(w, r, "Error on getting surface for label %d: %v", label, err)
			return
		}
		if !found {
			http.Error(w, fmt.Sprintf("Surface for label '%d' not found", label), http.StatusNotFound)
			return
		}
		w.Header().Set("Content-type", "application/octet-stream")
		if err := dvid.WriteGzip(gzipData, w, r); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: surface on label %d (%s)", r.Method, label, r.URL)

	case "surface-by-point":
		// GET <api URL>/node/<UUID>/<data name>/surface-by-point/<coord>
		if len(parts) < 5 {
			server.BadRequest(w, r, "ERROR: DVID requires coord to follow 'surface-by-point' command")
			return
		}
		coord, err := dvid.StringToPoint(parts[4], "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		label, err := d.GetLabelAtPoint(ctx.VersionID(), coord)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		gzipData, found, err := GetSurface(ctx, label)
		if err != nil {
			server.BadRequest(w, r, "Error on getting surface for label %d: %v", label, err)
			return
		}
		if !found {
			http.Error(w, fmt.Sprintf("Surface for label '%d' not found", label), http.StatusNotFound)
			return
		}
		fmt.Printf("Found surface for label %d: %d bytes (gzip payload)\n", label, len(gzipData))
		w.Header().Set("Content-type", "application/octet-stream")
		if err := dvid.WriteGzip(gzipData, w, r); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: surface-by-point at %s (%s)", r.Method, coord, r.URL)

	default:
		server.BadRequest(w, r, "Unrecognized API call '%s' for labelsurf data '%s'.  See API help.",
			parts[3], d.DataName())
	}
}
Exemple #21
0
// ServeHTTP handles all incoming HTTP requests for this data.
func (d *Data) ServeHTTP(uuid dvid.UUID, ctx *datastore.VersionedCtx, w http.ResponseWriter, r *http.Request) {
	timedLog := dvid.NewTimeLog()
	versionID := ctx.VersionID()

	// Get the action (GET, POST)
	action := strings.ToLower(r.Method)

	// Break URL request into arguments
	url := r.URL.Path[len(server.WebAPIPath):]
	parts := strings.Split(url, "/")
	if len(parts[len(parts)-1]) == 0 {
		parts = parts[:len(parts)-1]
	}

	// Handle POST on data -> setting of configuration
	if len(parts) == 3 && action == "put" {
		config, err := server.DecodeJSON(r)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if err := d.ModifyConfig(config); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if err := datastore.SaveDataByUUID(uuid, d); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		fmt.Fprintf(w, "Changed '%s' based on received configuration:\n%s\n", d.DataName(), config)
		return
	}

	if len(parts) < 4 {
		server.BadRequest(w, r, "Incomplete API request")
		return
	}

	// Process help and info.
	switch parts[3] {
	case "help":
		w.Header().Set("Content-Type", "text/plain")
		fmt.Fprintln(w, dtype.Help())

	case "info":
		jsonBytes, err := d.MarshalJSON()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/json")
		fmt.Fprintf(w, string(jsonBytes))

	case "sparsevol":
		// GET <api URL>/node/<UUID>/<data name>/sparsevol/<label>
		// POST <api URL>/node/<UUID>/<data name>/sparsevol/<label>
		if len(parts) < 5 {
			server.BadRequest(w, r, "ERROR: DVID requires label ID to follow 'sparsevol' command")
			return
		}
		label, err := strconv.ParseUint(parts[4], 10, 64)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		switch action {
		case "get":
			queryValues := r.URL.Query()
			var b Bounds
			b.VoxelBounds, err = dvid.BoundsFromQueryString(r)
			if err != nil {
				server.BadRequest(w, r, "Error parsing bounds from query string: %v\n", err)
				return
			}
			b.BlockBounds = b.VoxelBounds.Divide(d.BlockSize)
			b.Exact = queryValues.Get("exact") == "true"
			data, err := GetSparseVol(ctx, label, b)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			w.Header().Set("Content-type", "application/octet-stream")
			_, err = w.Write(data)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
		case "post":
			server.BadRequest(w, r, "POST of sparsevol not currently implemented\n")
			return
			// if err := d.PutSparseVol(versionID, label, r.Body); err != nil {
			// 	server.BadRequest(w, r, err)
			// 	return
			// }
		default:
			server.BadRequest(w, r, "Unable to handle HTTP action %s on sparsevol endpoint", action)
			return
		}
		timedLog.Infof("HTTP %s: sparsevol on label %d (%s)", r.Method, label, r.URL)

	case "sparsevol-by-point":
		// GET <api URL>/node/<UUID>/<data name>/sparsevol-by-point/<coord>
		if len(parts) < 5 {
			server.BadRequest(w, r, "ERROR: DVID requires coord to follow 'sparsevol-by-point' command")
			return
		}
		coord, err := dvid.StringToPoint(parts[4], "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		source, err := d.GetSyncedLabelblk(versionID)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		label, err := source.GetLabelAtPoint(ctx.VersionID(), coord)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		data, err := GetSparseVol(ctx, label, Bounds{})
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-type", "application/octet-stream")
		_, err = w.Write(data)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: sparsevol-by-point at %s (%s)", r.Method, coord, r.URL)

	case "sparsevol-coarse":
		// GET <api URL>/node/<UUID>/<data name>/sparsevol-coarse/<label>
		if len(parts) < 5 {
			server.BadRequest(w, r, "ERROR: DVID requires label ID to follow 'sparsevol-coarse' command")
			return
		}
		label, err := strconv.ParseUint(parts[4], 10, 64)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		data, err := GetSparseCoarseVol(ctx, label)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-type", "application/octet-stream")
		_, err = w.Write(data)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: sparsevol-coarse on label %d (%s)", r.Method, label, r.URL)

	case "maxlabel":
		// GET <api URL>/node/<UUID>/<data name>/maxlabel
		w.Header().Set("Content-Type", "application/json")
		switch action {
		case "get":
			maxlabel, ok := d.MaxLabel[versionID]
			if !ok {
				server.BadRequest(w, r, "No maximum label found for %s version %d\n", d.DataName(), versionID)
				return
			}
			fmt.Fprintf(w, "{%q: %d}", "maxlabel", maxlabel)
		default:
			server.BadRequest(w, r, "Unknown action %q requested: %s\n", action, r.URL)
			return
		}
		timedLog.Infof("HTTP maxlabel request (%s)", r.URL)

	case "nextlabel":
		// GET <api URL>/node/<UUID>/<data name>/nextlabel
		// POST <api URL>/node/<UUID>/<data name>/nextlabel
		w.Header().Set("Content-Type", "application/json")
		switch action {
		case "get":
			fmt.Fprintf(w, "{%q: %d}", "nextlabel", d.MaxRepoLabel+1)
		case "post":
			server.BadRequest(w, r, "POST on maxlabel is not supported yet.\n")
			return
		default:
			server.BadRequest(w, r, "Unknown action %q requested: %s\n", action, r.URL)
			return
		}
		timedLog.Infof("HTTP maxlabel request (%s)", r.URL)

	case "split":
		// POST <api URL>/node/<UUID>/<data name>/split/<label>
		if action != "post" {
			server.BadRequest(w, r, "Split requests must be POST actions.")
			return
		}
		if len(parts) < 5 {
			server.BadRequest(w, r, "ERROR: DVID requires label ID to follow 'split' command")
			return
		}
		fromLabel, err := strconv.ParseUint(parts[4], 10, 64)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		toLabel, err := d.SplitLabels(ctx.VersionID(), fromLabel, r.Body)
		if err != nil {
			server.BadRequest(w, r, fmt.Sprintf("Error on split: %v", err))
			return
		}
		w.Header().Set("Content-Type", "application/json")
		fmt.Fprintf(w, "{%q: %d}", "label", toLabel)
		timedLog.Infof("HTTP split request (%s)", r.URL)

	case "merge":
		// POST <api URL>/node/<UUID>/<data name>/merge
		if action != "post" {
			server.BadRequest(w, r, "Merge requests must be POST actions.")
			return
		}
		data, err := ioutil.ReadAll(r.Body)
		if err != nil {
			server.BadRequest(w, r, "Bad POSTed data for merge.  Should be JSON.")
			return
		}
		var tuple labels.MergeTuple
		if err := json.Unmarshal(data, &tuple); err != nil {
			server.BadRequest(w, r, fmt.Sprintf("Bad merge op JSON: %v", err))
			return
		}
		mergeOp, err := tuple.Op()
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if err := d.MergeLabels(ctx.VersionID(), mergeOp); err != nil {
			server.BadRequest(w, r, fmt.Sprintf("Error on merge: %v", err))
			return
		}
		timedLog.Infof("HTTP merge request (%s)", r.URL)

	default:
		server.BadRequest(w, r, "Unrecognized API call %q for labelvol data %q.  See API help.",
			parts[3], d.DataName())
	}
}