Example #1
0
// call KVAutobus key_range API
func (db *KVAutobus) getKeyRange(kStart, kEnd storage.Key) (Ks, error) {
	b64key1 := encodeKey(kStart)
	b64key2 := encodeKey(kEnd)
	url := fmt.Sprintf("%s/kvautobus/api/key_range/%s/%s/%s/", db.host, db.collection, b64key1, b64key2)

	timedLog := dvid.NewTimeLog()
	resp, err := db.client.Get(url)
	if err != nil {
		return nil, err
	}
	defer resp.Body.Close()
	if resp.StatusCode == http.StatusNotFound {
		return nil, nil // Handle no keys found.
	}

	r := msgp.NewReader(bufio.NewReader(resp.Body))
	var mks Ks
	if err := mks.DecodeMsg(r); err != nil {
		return nil, err
	}
	for _, mk := range mks {
		storage.StoreKeyBytesRead <- len(mk)
	}
	timedLog.Infof("PROXY key_range to %s returned %d (%d keys)\n", db.host, resp.StatusCode, len(mks))
	return mks, nil
}
Example #2
0
// check if any metadata has been written into this store.
func (db *KVAutobus) metadataExists() (bool, error) {
	var ctx storage.MetadataContext
	kStart, kEnd := ctx.KeyRange()
	b64key1 := encodeKey(kStart)
	b64key2 := encodeKey(kEnd)
	url := fmt.Sprintf("%s/kvautobus/api/key_range/%s/%s/%s/", db.host, db.collection, b64key1, b64key2)
	dvid.Infof("metdataExists: doing GET on %s\n", url)

	timedLog := dvid.NewTimeLog()
	resp, err := db.client.Get(url)
	if err != nil {
		return false, err
	}
	defer resp.Body.Close()
	if resp.StatusCode == http.StatusNotFound {
		return true, nil // Handle no keys found.
	}

	r := msgp.NewReader(bufio.NewReader(resp.Body))
	var mks Ks
	if err := mks.DecodeMsg(r); err != nil {
		return false, err
	}
	timedLog.Infof("PROXY key_range metadata to %s returned %d (%d keys)\n", db.host, resp.StatusCode, len(mks))
	if len(mks) == 0 {
		return false, nil
	}
	return true, nil
}
Example #3
0
// call KVAutobus keyvalue_range API
func (db *KVAutobus) getKVRange(kStart, kEnd storage.Key) (KVs, error) {
	b64key1 := encodeKey(kStart)
	b64key2 := encodeKey(kEnd)
	url := fmt.Sprintf("%s/kvautobus/api/keyvalue_range/%s/%s/", db.host, b64key1, b64key2)

	timedLog := dvid.NewTimeLog()
	resp, err := http.Get(url)
	if err != nil {
		return nil, err
	}
	defer resp.Body.Close()
	if resp.StatusCode == http.StatusNotFound {
		return nil, nil // Handle no keys found.
	}

	r := msgp.NewReader(bufio.NewReader(resp.Body))
	var mkvs KVs
	if err := mkvs.DecodeMsg(r); err != nil {
		dvid.Errorf("Couldn't decode getKVRange return\n")
		return nil, err
	}

	timedLog.Infof("PROXY keyvalue_range to %s returned %d (%d kv pairs)\n", db.host, resp.StatusCode, len(mkvs))
	return mkvs, nil
}
Example #4
0
// 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
}
Example #5
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()

	action := strings.ToLower(r.Method)
	switch action {
	case "get":
		// Acceptable
	default:
		server.BadRequest(w, r, "googlevoxels can only handle GET HTTP verbs at this time")
		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
	}

	switch parts[3] {
	case "help":
		w.Header().Set("Content-Type", "text/plain")
		fmt.Fprintln(w, d.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 "tile":
		if err := d.ServeTile(w, r, parts); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: tile (%s)", r.Method, r.URL)

	case "raw":
		if err := d.ServeImage(w, r, parts); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: image (%s)", r.Method, r.URL)
	default:
		server.BadRequest(w, r, "Illegal request for googlevoxels data.  See 'help' for REST API")
	}
}
Example #6
0
func (d *Data) processSplit(v dvid.VersionID, delta labels.DeltaSplit) {
	timedLog := dvid.NewTimeLog()

	mutID := d.NewMutationID()
	splitOpStart := labels.DeltaSplitStart{delta.OldLabel, delta.NewLabel}
	splitOpEnd := labels.DeltaSplitEnd{delta.OldLabel, delta.NewLabel}
	iv := dvid.InstanceVersion{d.DataUUID(), v}
	labels.SplitStart(iv, splitOpStart)

	d.StartUpdate()
	if delta.Split == nil {
		// Coarse Split
		for _, izyxStr := range delta.SortedBlocks {
			n := izyxStr.Hash(numBlockHandlers)
			d.MutAdd(mutID)
			op := splitOp{
				mutID:    mutID,
				oldLabel: delta.OldLabel,
				newLabel: delta.NewLabel,
				block:    izyxStr,
			}
			d.procCh[n] <- procMsg{op: op, v: v}
		}
	} else {
		// Fine Split
		for izyxStr, blockRLEs := range delta.Split {
			n := izyxStr.Hash(numBlockHandlers)
			d.MutAdd(mutID)
			op := splitOp{
				mutID:    mutID,
				oldLabel: delta.OldLabel,
				newLabel: delta.NewLabel,
				rles:     blockRLEs,
				block:    izyxStr,
			}
			d.procCh[n] <- procMsg{op: op, v: v}
		}
	}
	// Wait for all blocks to be split then mark end of split op.
	go func() {
		d.MutWait(mutID)
		d.MutDelete(mutID)
		labels.SplitStop(iv, splitOpEnd)
		timedLog.Debugf("labelblk sync complete for split of %d -> %d", delta.OldLabel, delta.NewLabel)
		d.StopUpdate()
		d.publishDownresCommit(v, mutID)
	}()
}
Example #7
0
func (db *KVAutobus) deleteRange(kStart, kEnd storage.Key) error {
	b64key1 := encodeKey(kStart)
	b64key2 := encodeKey(kEnd)
	url := fmt.Sprintf("%s/kvautobus/api/keyvalue_range/%s/%s/%s/", db.host, db.collection, b64key1, b64key2)

	timedLog := dvid.NewTimeLog()
	req, err := http.NewRequest("DELETE", url, nil)
	if err != nil {
		return err
	}
	defer resp.Body.Close()
	resp, err := db.client.Do(req)
	if err != nil {
		return err
	}
	timedLog.Infof("PROXY delete keyvalue_range to %s returned %d\n", db.host, resp.StatusCode)
	return nil
}
Example #8
0
// LoadImages bulk loads images using different techniques if it is a multidimensional
// file like HDF5 or a sequence of PNG/JPG/TIF images.
func (d *Data) LoadImages(v dvid.VersionID, offset dvid.Point, filenames []string) error {
	if len(filenames) == 0 {
		return nil
	}
	timedLog := dvid.NewTimeLog()

	// We only want one PUT on given version for given data to prevent interleaved
	// chunk PUTs that could potentially overwrite slice modifications.
	ctx := storage.NewDataContext(d, v)
	loadMutex := ctx.Mutex()
	loadMutex.Lock()

	// Handle cleanup given multiple goroutines still writing data.
	load := &bulkLoadInfo{filenames: filenames, versionID: v, offset: offset}
	defer func() {
		loadMutex.Unlock()

		if load.extentChanged.Value() {
			err := datastore.SaveDataByVersion(v, d)
			if err != nil {
				dvid.Errorf("Error in trying to save repo for voxel extent change: %v\n", err)
			}
		}
	}()

	// Use different loading techniques if we have a potentially multidimensional HDF5 file
	// or many 2d images.
	var err error
	if dvid.Filename(filenames[0]).HasExtensionPrefix("hdf", "h5") {
		err = d.loadHDF(load)
	} else {
		err = d.loadXYImages(load)
	}

	if err != nil {
		timedLog.Infof("RPC load of %d files had error: %v\n", err)
	} else {
		timedLog.Infof("RPC load of %d files completed.\n", len(filenames))
	}
	return err
}
Example #9
0
func (d *Data) processMerge(v dvid.VersionID, delta labels.DeltaMerge) {
	timedLog := dvid.NewTimeLog()
	d.StartUpdate()

	mutID := d.NewMutationID()
	for izyxStr := range delta.Blocks {
		n := izyxStr.Hash(numBlockHandlers)
		d.MutAdd(mutID)
		op := mergeOp{mutID: mutID, MergeOp: delta.MergeOp, block: izyxStr}
		d.procCh[n] <- procMsg{op: op, v: v}
	}
	// When we've processed all the delta blocks, we can remove this merge op
	// from the merge cache since all labels will have completed.
	go func() {
		d.MutWait(mutID)
		d.MutDelete(mutID)
		timedLog.Debugf("labelblk sync complete for merge (%d blocks) of %s -> %d", len(delta.Blocks), delta.MergeOp.Merged, delta.MergeOp.Target)
		d.StopUpdate()
		d.publishDownresCommit(v, mutID)
	}()
}
Example #10
0
// call KVAutobus keyvalue_range API
func (db *KVAutobus) getKVRange(ctx storage.Context, kStart, kEnd storage.Key) (KVs, error) {
	// Get any request context and pass to kvautobus for tracking.
	reqctx, ok := ctx.(storage.RequestCtx)
	var reqID string
	if ok {
		parts := strings.Split(reqctx.GetRequestID(), "/")
		if len(parts) > 0 {
			reqID = parts[len(parts)-1]
		}
	}

	// Construct the KVAutobus URL
	b64key1 := encodeKey(kStart)
	b64key2 := encodeKey(kEnd)
	url := fmt.Sprintf("%s/kvautobus/api/keyvalue_range/%s/%s/%s/?=%s", db.host, db.collection, b64key1, b64key2, reqID)

	timedLog := dvid.NewTimeLog()
	resp, err := db.client.Get(url)
	if err != nil {
		return nil, err
	}
	defer resp.Body.Close()
	if resp.StatusCode == http.StatusNotFound {
		return nil, nil // Handle no keys found.
	}

	r := msgp.NewReader(bufio.NewReader(resp.Body))
	var mkvs KVs
	if err := mkvs.DecodeMsg(r); err != nil {
		dvid.Errorf("Couldn't decode getKVRange return\n")
		return nil, err
	}
	for _, mkv := range mkvs {
		storage.StoreKeyBytesRead <- len(mkv[0])
		storage.StoreValueBytesRead <- len(mkv[1])
	}

	timedLog.Infof("[%s] PROXY keyvalue_range to %s returned %d (%d kv pairs)\n", reqID, db.host, resp.StatusCode, len(mkvs))
	return mkvs, nil
}
Example #11
0
func (db *KVAutobus) RawGet(key storage.Key) ([]byte, error) {
	b64key := encodeKey(key)
	url := fmt.Sprintf("%s/kvautobus/api/value/%s/", db.host, b64key)

	timedLog := dvid.NewTimeLog()
	resp, err := http.Get(url)
	if err != nil {
		return nil, err
	}
	timedLog.Infof("PROXY get to %s returned %d\n", db.host, resp.StatusCode)
	defer resp.Body.Close()
	if resp.StatusCode == http.StatusNotFound {
		return nil, nil // Handle no key found.
	}

	r := msgp.NewReader(bufio.NewReader(resp.Body))
	var bin Binary
	if err := bin.DecodeMsg(r); err != nil {
		return nil, err
	}
	return []byte(bin), nil
}
Example #12
0
func (d *Data) serveVolume(w http.ResponseWriter, r *http.Request, geom *GoogleSubvolGeom, noblanks bool) error {
	// If it's outside, write blank tile unless user wants no blanks.
	if geom.outside {
		if noblanks {
			http.NotFound(w, r)
			return fmt.Errorf("Requested subvolume is outside of available volume.")
		}
		return nil
	}

	// If we are within volume, get data from Google.
	url, err := geom.GetURL(d.VolumeID, "")
	if err != nil {
		return err
	}

	timedLog := dvid.NewTimeLog()
	client, err := d.GetClient()
	if err != nil {
		dvid.Errorf("Can't get OAuth2 connection to Google: %v\n", err)
		return err
	}
	resp, err := client.Get(url)
	if err != nil {
		return err
	}
	timedLog.Infof("PROXY HTTP to Google: %s, returned response %d", url, resp.StatusCode)
	defer resp.Body.Close()

	// If it's on edge, we need to pad the subvolume to the requested size.
	if geom.edge {
		return fmt.Errorf("Googlevoxels subvolume GET does not pad data on edge at this time")
	}

	// If we aren't on edge or outside, our return status should be OK.
	if resp.StatusCode != http.StatusOK {
		return fmt.Errorf("Unexpected status code %d on volume request (%q, volume id %q)", resp.StatusCode, d.DataName(), d.VolumeID)
	}

	w.Header().Set("Content-type", "application/octet-stream")

	queryStrings := r.URL.Query()
	compression := queryStrings.Get("compression")

	switch compression {
	case "lz4":
		// Decompress snappy
		sdata, err := ioutil.ReadAll(resp.Body)
		timedLog.Infof("Got snappy-encoded subvolume from Google, %d bytes\n", len(sdata))
		if err != nil {
			return err
		}
		data, err := snappy.Decode(nil, sdata)
		if err != nil {
			return err
		}
		// Recompress and transmit as lz4
		lz4data := make([]byte, lz4.CompressBound(data))
		outSize, err := lz4.Compress(data, lz4data)
		if err != nil {
			return err
		}
		if _, err := w.Write(lz4data[:outSize]); err != nil {
			return err
		}
		timedLog.Infof("Sent lz4-encoded subvolume from DVID, %d bytes\n", outSize)

	default: // "snappy"
		// Just stream data from Google
		respBytes := 0
		const BufferSize = 32 * 1024
		buf := make([]byte, BufferSize)
		for {
			n, err := resp.Body.Read(buf)
			respBytes += n
			eof := (err == io.EOF)
			if err != nil && !eof {
				return err
			}
			if _, err = w.Write(buf[:n]); err != nil {
				return err
			}
			if f, ok := w.(http.Flusher); ok {
				f.Flush()
			}
			if eof {
				break
			}
		}
		timedLog.Infof("Proxied snappy-encoded subvolume from Google, %d bytes\n", respBytes)
	}

	return nil
}
Example #13
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()

	action := strings.ToLower(r.Method)
	switch action {
	case "get", "post":
		// Acceptable
	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
	}

	switch parts[3] {
	case "help":
		w.Header().Set("Content-Type", "text/plain")
		fmt.Fprintln(w, d.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 "tile":
		if action == "post" {
			server.BadRequest(w, r, "DVID does not yet support POST of imagetile")
			return
		}
		if err := d.ServeTile(uuid, ctx, w, r, parts); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: tile (%s)", r.Method, r.URL)

	case "raw", "isotropic":
		if action == "post" {
			server.BadRequest(w, r, "imagetile '%s' can only PUT tiles not images", d.DataName())
			return
		}
		if len(parts) < 7 {
			server.BadRequest(w, r, "%q 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
		}
		if plane.ShapeDimensions() != 2 {
			server.BadRequest(w, r, "Quadtrees can only return 2d images not %s", plane)
			return
		}
		slice, err := dvid.NewSliceFromStrings(planeStr, offsetStr, sizeStr, "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		source, err := datastore.GetDataByUUID(uuid, d.Source)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		src, ok := source.(*imageblk.Data)
		if !ok {
			server.BadRequest(w, r, "Cannot construct imagetile for non-voxels data: %s", d.Source)
			return
		}
		img, err := d.GetImage(ctx, src, slice, parts[3] == "isotropic")
		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: tile-accelerated %s %s (%s)", r.Method, planeStr, parts[3], r.URL)
	default:
		server.BadRequest(w, r, "Illegal request for imagetile data.  See 'help' for REST API")
	}
}
Example #14
0
func (d *Data) ConstructTiles(uuidStr string, tileSpec TileSpec, request datastore.Request) error {
	config := request.Settings()
	uuid, versionID, err := datastore.MatchingUUID(uuidStr)
	if err != nil {
		return err
	}
	if err = datastore.AddToNodeLog(uuid, []string{request.Command.String()}); err != nil {
		return err
	}

	source, err := datastore.GetDataByUUID(uuid, d.Source)
	if err != nil {
		return err
	}
	src, ok := source.(*imageblk.Data)
	if !ok {
		return fmt.Errorf("Cannot construct imagetile for non-voxels data: %s", d.Source)
	}

	// Save the current tile specification
	d.Levels = tileSpec
	if err := datastore.SaveDataByUUID(uuid, d); err != nil {
		return err
	}

	// Get size of tile at lowest resolution.
	lastLevel := Scaling(len(tileSpec) - 1)
	loresSpec, found := tileSpec[lastLevel]
	if !found {
		return fmt.Errorf("Illegal tile spec.  Should have levels 0 to absent %d.", lastLevel)
	}
	var loresSize [3]float64
	for i := 0; i < 3; i++ {
		loresSize[i] = float64(loresSpec.Resolution[i]) * float64(DefaultTileSize[i])
	}
	loresMag := dvid.Point3d{1, 1, 1}
	for i := Scaling(0); i < lastLevel; i++ {
		levelMag := tileSpec[i].levelMag
		loresMag[0] *= levelMag[0]
		loresMag[1] *= levelMag[1]
		loresMag[2] *= levelMag[2]
	}

	// Get min and max points in terms of distance.
	var minPtDist, maxPtDist [3]float64
	for i := uint8(0); i < 3; i++ {
		minPtDist[i] = float64(src.MinPoint.Value(i)) * float64(src.VoxelSize[i])
		maxPtDist[i] = float64(src.MaxPoint.Value(i)) * float64(src.VoxelSize[i])
	}

	// Adjust min and max points for the tileable surface at lowest resolution.
	var minTiledPt, maxTiledPt dvid.Point3d
	for i := 0; i < 3; i++ {
		minInt, _ := math.Modf(minPtDist[i] / loresSize[i])
		maxInt, _ := math.Modf(maxPtDist[i] / loresSize[i])
		minTileCoord := int32(minInt)
		maxTileCoord := int32(maxInt)
		minTiledPt[i] = minTileCoord * DefaultTileSize[i] * loresMag[i]
		maxTiledPt[i] = (maxTileCoord+1)*DefaultTileSize[i]*loresMag[i] - 1
	}
	sizeVolume := maxTiledPt.Sub(minTiledPt).AddScalar(1)

	// Setup swappable ExtData buffers (the stitched slices) so we can be generating tiles
	// at same time we are reading and stitching them.
	var bufferLock [2]sync.Mutex
	var sliceBuffers [2]*imageblk.Voxels
	var bufferNum int

	// Get the planes we should tile.
	planes, err := config.GetShapes("planes", ";")
	if planes == nil {
		// If no planes are specified, construct imagetile for 3 orthogonal planes.
		planes = []dvid.DataShape{dvid.XY, dvid.XZ, dvid.YZ}
	}

	outF, err := d.putTileFunc(versionID)

	// sort the tile spec keys to iterate from highest to lowest resolution
	var sortedKeys []int
	for scaling, _ := range tileSpec {
		sortedKeys = append(sortedKeys, int(scaling))
	}
	sort.Ints(sortedKeys)

	for _, plane := range planes {
		timedLog := dvid.NewTimeLog()
		offset := minTiledPt.Duplicate()

		switch {

		case plane.Equals(dvid.XY):
			width, height, err := plane.GetSize2D(sizeVolume)
			if err != nil {
				return err
			}
			dvid.Debugf("Tiling XY image %d x %d pixels\n", width, height)
			for z := src.MinPoint.Value(2); z <= src.MaxPoint.Value(2); z++ {
				server.BlockOnInteractiveRequests("imagetile.ConstructTiles [xy]")

				sliceLog := dvid.NewTimeLog()
				offset = offset.Modify(map[uint8]int32{2: z})
				slice, err := dvid.NewOrthogSlice(dvid.XY, offset, dvid.Point2d{width, height})
				if err != nil {
					return err
				}
				bufferLock[bufferNum].Lock()
				sliceBuffers[bufferNum], err = src.NewVoxels(slice, nil)
				if err != nil {
					return err
				}
				if err = src.GetVoxels(versionID, sliceBuffers[bufferNum], nil); err != nil {
					return err
				}
				// Iterate through the different scales, extracting tiles at each resolution.
				go func(bufferNum int, offset dvid.Point) {
					defer bufferLock[bufferNum].Unlock()
					timedLog := dvid.NewTimeLog()
					for _, key := range sortedKeys {
						scaling := Scaling(key)
						levelSpec := tileSpec[scaling]
						if err != nil {
							dvid.Errorf("Error in tiling: %v\n", err)
							return
						}
						if err := d.extractTiles(sliceBuffers[bufferNum], offset, scaling, outF); err != nil {
							dvid.Errorf("Error in tiling: %v\n", err)
							return
						}
						if int(scaling) < len(tileSpec)-1 {
							if err := sliceBuffers[bufferNum].DownRes(levelSpec.levelMag); err != nil {
								dvid.Errorf("Error in tiling: %v\n", err)
								return
							}
						}
					}
					timedLog.Debugf("Tiled XY Tile using buffer %d", bufferNum)
				}(bufferNum, offset)

				sliceLog.Infof("Read XY Tile @ Z = %d, now tiling...", z)
				bufferNum = (bufferNum + 1) % 2
			}
			timedLog.Infof("Total time to generate XY Tiles")

		case plane.Equals(dvid.XZ):
			width, height, err := plane.GetSize2D(sizeVolume)
			if err != nil {
				return err
			}
			dvid.Debugf("Tiling XZ image %d x %d pixels\n", width, height)
			for y := src.MinPoint.Value(1); y <= src.MaxPoint.Value(1); y++ {
				server.BlockOnInteractiveRequests("imagetile.ConstructTiles [xz]")

				sliceLog := dvid.NewTimeLog()
				offset = offset.Modify(map[uint8]int32{1: y})
				slice, err := dvid.NewOrthogSlice(dvid.XZ, offset, dvid.Point2d{width, height})
				if err != nil {
					return err
				}
				bufferLock[bufferNum].Lock()
				sliceBuffers[bufferNum], err = src.NewVoxels(slice, nil)
				if err != nil {
					return err
				}
				if err = src.GetVoxels(versionID, sliceBuffers[bufferNum], nil); err != nil {
					return err
				}
				// Iterate through the different scales, extracting tiles at each resolution.
				go func(bufferNum int, offset dvid.Point) {
					defer bufferLock[bufferNum].Unlock()
					timedLog := dvid.NewTimeLog()
					for _, key := range sortedKeys {
						scaling := Scaling(key)
						levelSpec := tileSpec[scaling]
						if err != nil {
							dvid.Errorf("Error in tiling: %v\n", err)
							return
						}
						if err := d.extractTiles(sliceBuffers[bufferNum], offset, scaling, outF); err != nil {
							dvid.Errorf("Error in tiling: %v\n", err)
							return
						}
						if int(scaling) < len(tileSpec)-1 {
							if err := sliceBuffers[bufferNum].DownRes(levelSpec.levelMag); err != nil {
								dvid.Errorf("Error in tiling: %v\n", err)
								return
							}
						}
					}
					timedLog.Debugf("Tiled XZ Tile using buffer %d", bufferNum)
				}(bufferNum, offset)

				sliceLog.Infof("Read XZ Tile @ Y = %d, now tiling...", y)
				bufferNum = (bufferNum + 1) % 2
			}
			timedLog.Infof("Total time to generate XZ Tiles")

		case plane.Equals(dvid.YZ):
			width, height, err := plane.GetSize2D(sizeVolume)
			if err != nil {
				return err
			}
			dvid.Debugf("Tiling YZ image %d x %d pixels\n", width, height)
			for x := src.MinPoint.Value(0); x <= src.MaxPoint.Value(0); x++ {
				server.BlockOnInteractiveRequests("imagetile.ConstructTiles [yz]")

				sliceLog := dvid.NewTimeLog()
				offset = offset.Modify(map[uint8]int32{0: x})
				slice, err := dvid.NewOrthogSlice(dvid.YZ, offset, dvid.Point2d{width, height})
				if err != nil {
					return err
				}
				bufferLock[bufferNum].Lock()
				sliceBuffers[bufferNum], err = src.NewVoxels(slice, nil)
				if err != nil {
					return err
				}
				if err = src.GetVoxels(versionID, sliceBuffers[bufferNum], nil); err != nil {
					return err
				}
				// Iterate through the different scales, extracting tiles at each resolution.
				go func(bufferNum int, offset dvid.Point) {
					defer bufferLock[bufferNum].Unlock()
					timedLog := dvid.NewTimeLog()
					for _, key := range sortedKeys {
						scaling := Scaling(key)
						levelSpec := tileSpec[scaling]
						outF, err := d.putTileFunc(versionID)
						if err != nil {
							dvid.Errorf("Error in tiling: %v\n", err)
							return
						}
						if err := d.extractTiles(sliceBuffers[bufferNum], offset, scaling, outF); err != nil {
							dvid.Errorf("Error in tiling: %v\n", err)
							return
						}
						if int(scaling) < len(tileSpec)-1 {
							if err := sliceBuffers[bufferNum].DownRes(levelSpec.levelMag); err != nil {
								dvid.Errorf("Error in tiling: %v\n", err)
								return
							}
						}
					}
					timedLog.Debugf("Tiled YZ Tile using buffer %d", bufferNum)
				}(bufferNum, offset)

				sliceLog.Debugf("Read YZ Tile @ X = %d, now tiling...", x)
				bufferNum = (bufferNum + 1) % 2
			}
			timedLog.Infof("Total time to generate YZ Tiles")

		default:
			dvid.Infof("Skipping request to tile '%s'.  Unsupported.", plane)
		}
	}
	return nil
}
Example #15
0
// 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 int32) ([]byte, error) {
	timedLog := dvid.NewTimeLog()
	defer timedLog.Infof("GetBlocks %s, span %d", start, span)

	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)
	sx, sy, sz := indexBeg.Unpack()

	end := start
	end[0] += int32(span - 1)
	indexEnd := dvid.IndexZYX(end)
	keyBeg := NewTKey(&indexBeg)
	keyEnd := NewTKey(&indexEnd)

	// Allocate one uncompressed-sized slice with background values.
	blockBytes := int32(d.BlockSize().Prod()) * d.Values.BytesPerElement()
	numBytes := blockBytes * span

	buf := make([]byte, numBytes, numBytes)
	if d.Background != 0 {
		for i := range buf {
			buf[i] = byte(d.Background)
		}
	}

	// Write the blocks that we can get concurrently on this byte slice.
	ctx := datastore.NewVersionedCtx(d, v)

	var wg sync.WaitGroup
	err = store.ProcessRange(ctx, keyBeg, keyEnd, &storage.ChunkOp{}, func(c *storage.Chunk) error {
		if c == nil || c.TKeyValue == nil {
			return nil
		}
		kv := c.TKeyValue
		if kv.V == nil {
			return nil
		}

		// Determine which block this is.
		indexZYX, err := DecodeTKey(kv.K)
		if err != nil {
			return err
		}
		x, y, z := indexZYX.Unpack()
		if z != sz || y != sy || x < sx || x >= sx+int32(span) {
			return fmt.Errorf("Received key-value for %s, not supposed to be within span range %s, length %d", *indexZYX, start, span)
		}
		n := x - sx
		i := n * blockBytes
		j := i + blockBytes

		// Spawn goroutine to transfer data
		wg.Add(1)
		go xferBlock(buf[i:j], c, &wg)
		return nil
	})
	if err != nil {
		return nil, err
	}
	wg.Wait()
	return buf, nil
}
Example #16
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()

	action := strings.ToLower(r.Method)
	switch action {
	case "get", "post":
		// Acceptable
	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
	}

	switch parts[3] {
	case "help":
		w.Header().Set("Content-Type", "text/plain")
		fmt.Fprintln(w, d.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 "metadata":
		switch action {
		case "post":
			jsonBytes, err := ioutil.ReadAll(r.Body)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if err := d.SetMetadata(uuid, jsonBytes); err != nil {
				server.BadRequest(w, r, err)
				return
			}

		case "get":
			if d.Levels == nil || len(d.Levels) == 0 {
				server.BadRequest(w, r, "tile metadata for imagetile %q was not set\n", d.DataName())
				return
			}
			metadata := struct {
				MinTileCoord dvid.Point3d
				MaxTileCoord dvid.Point3d
				Levels       TileSpec
			}{
				d.MinTileCoord,
				d.MaxTileCoord,
				d.Levels,
			}
			jsonBytes, err := json.Marshal(metadata)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			w.Header().Set("Content-Type", "application/json")
			fmt.Fprintf(w, string(jsonBytes))
		}
		timedLog.Infof("HTTP %s: metadata (%s)", r.Method, r.URL)

	case "tile":
		switch action {
		case "post":
			err := d.PostTile(ctx, w, r, parts)
			if err != nil {
				server.BadRequest(w, r, "Error in posting tile with URL %q: %v\n", url, err)
				return
			}
		case "get":
			if err := d.ServeTile(ctx, w, r, parts); err != nil {
				server.BadRequest(w, r, err)
				return
			}
		}
		timedLog.Infof("HTTP %s: tile (%s)", r.Method, r.URL)

	case "tilekey":
		switch action {
		case "get":
			var err error
			var hexkey string
			if hexkey, err = d.GetTileKey(ctx, w, r, parts); err != nil {
				server.BadRequest(w, r, err)
				return
			}
			w.Header().Set("Content-Type", "application/json")
			fmt.Fprintf(w, `{"key": "%s"}`, hexkey)
			timedLog.Infof("HTTP %s: tilekey (%s) returns %s", r.Method, r.URL, hexkey)
		default:
			server.BadRequest(w, r, fmt.Errorf("Cannot use HTTP %s for tilekey endpoint", action))
			return
		}

	case "raw", "isotropic":
		if action == "post" {
			server.BadRequest(w, r, "imagetile '%s' can only PUT tiles not images", d.DataName())
			return
		}
		if len(parts) < 7 {
			server.BadRequest(w, r, "%q 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
		}
		if plane.ShapeDimensions() != 2 {
			server.BadRequest(w, r, "Quadtrees can only return 2d images not %s", plane)
			return
		}
		slice, err := dvid.NewSliceFromStrings(planeStr, offsetStr, sizeStr, "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		source, err := datastore.GetDataByUUIDName(uuid, d.Source)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		src, ok := source.(*imageblk.Data)
		if !ok {
			server.BadRequest(w, r, "Cannot construct imagetile for non-voxels data: %s", d.Source)
			return
		}
		img, err := d.GetImage(ctx, src, slice, parts[3] == "isotropic")
		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: tile-accelerated %s %s (%s)", r.Method, planeStr, parts[3], r.URL)
	default:
		server.BadAPIRequest(w, r, d)
	}
}
Example #17
0
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
}
Example #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) {
	timedLog := dvid.NewTimeLog()

	// 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 "sync":
		if action != "post" {
			server.BadRequest(w, r, "Only POST allowed to sync endpoint")
			return
		}
		replace := r.URL.Query().Get("replace") == "true"
		if err := datastore.SetSyncByJSON(d, uuid, replace, r.Body); err != nil {
			server.BadRequest(w, r, err)
			return
		}

	case "count":
		if action != "get" {
			server.BadRequest(w, r, "Only GET action is available on 'count' endpoint.")
			return
		}
		if len(parts) < 6 {
			server.BadRequest(w, r, "Must include label and element type after 'count' endpoint.")
			return
		}
		label, err := strconv.ParseUint(parts[4], 10, 64)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		i := StringToIndexType(parts[5])
		if i == UnknownIndex {
			server.BadRequest(w, r, fmt.Errorf("unknown index type specified (%q)", parts[5]))
			return
		}
		count, err := d.GetCountElementType(ctx, label, i)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-type", "application/json")
		jsonStr := fmt.Sprintf(`{"Label":%d,%q:%d}`, label, i, count)
		if _, err := io.WriteString(w, jsonStr); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: get count for label %d, index type %s: %s", r.Method, label, i, r.URL)

	case "top":
		if action != "get" {
			server.BadRequest(w, r, "Only GET action is available on 'top' endpoint.")
			return
		}
		if len(parts) < 6 {
			server.BadRequest(w, r, "Must include N and element type after 'top' endpoint.")
			return
		}
		n, err := strconv.ParseUint(parts[4], 10, 32)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		i := StringToIndexType(parts[5])
		if i == UnknownIndex {
			server.BadRequest(w, r, fmt.Errorf("unknown index type specified (%q)", parts[5]))
			return
		}
		labelSizes, err := d.GetTopElementType(ctx, int(n), i)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-type", "application/json")
		jsonBytes, err := json.Marshal(labelSizes)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if _, err := w.Write(jsonBytes); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: get top %d labels for index type %s: %s", r.Method, n, i, r.URL)

	case "threshold":
		if action != "get" {
			server.BadRequest(w, r, "Only GET action is available on 'threshold' endpoint.")
			return
		}
		if len(parts) < 6 {
			server.BadRequest(w, r, "Must include threshold # and element type after 'threshold' endpoint.")
			return
		}
		t, err := strconv.ParseUint(parts[4], 10, 32)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		minSize := uint32(t)
		i := StringToIndexType(parts[5])
		if i == UnknownIndex {
			server.BadRequest(w, r, fmt.Errorf("unknown index type specified (%q)", parts[5]))
			return
		}

		queryStrings := r.URL.Query()
		var num, offset int
		offsetStr := queryStrings.Get("offset")
		if offsetStr != "" {
			offset, err = strconv.Atoi(offsetStr)
			if err != nil {
				server.BadRequest(w, r, fmt.Errorf("bad offset specified in query string (%q)", offsetStr))
				return
			}
		}
		numStr := queryStrings.Get("n")
		if numStr != "" {
			num, err = strconv.Atoi(numStr)
			if err != nil {
				server.BadRequest(w, r, fmt.Errorf("bad num specified in query string (%q)", numStr))
				return
			}
		}

		labels, err := d.GetLabelsByThreshold(ctx, i, minSize, offset, num)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-type", "application/json")
		jsonBytes, err := json.Marshal(labels)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if _, err := w.Write(jsonBytes); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: get %d labels for index type %s with threshold %d: %s", r.Method, num, i, t, r.URL)

	default:
		server.BadAPIRequest(w, r, d)
	}
}
Example #19
0
// Optimized bulk loading of XY images by loading all slices for a block before processing.
// Trades off memory for speed.
func (d *Data) loadXYImages(load *bulkLoadInfo) error {
	// Load first slice, get dimensions, allocate blocks for whole slice.
	// Note: We don't need to lock the block slices because goroutines do NOT
	// access the same elements of a slice.
	const numLayers = 2
	var numBlocks int
	var blocks [numLayers]storage.TKeyValues
	var layerTransferred, layerWritten [numLayers]sync.WaitGroup
	var waitForWrites sync.WaitGroup

	curBlocks := 0
	blockSize := d.BlockSize()
	blockBytes := blockSize.Prod() * int64(d.Values.BytesPerElement())

	// Iterate through XY slices batched into the Z length of blocks.
	fileNum := 1
	for _, filename := range load.filenames {
		server.BlockOnInteractiveRequests("imageblk.loadXYImages")

		timedLog := dvid.NewTimeLog()

		zInBlock := load.offset.Value(2) % blockSize.Value(2)
		firstSlice := fileNum == 1
		lastSlice := fileNum == len(load.filenames)
		firstSliceInBlock := firstSlice || zInBlock == 0
		lastSliceInBlock := lastSlice || zInBlock == blockSize.Value(2)-1
		lastBlocks := fileNum+int(blockSize.Value(2)) > len(load.filenames)

		// Load images synchronously
		vox, err := d.loadXYImage(filename, load.offset)
		if err != nil {
			return err
		}

		// Allocate blocks and/or load old block data if first/last XY blocks.
		// Note: Slices are only zeroed out on first and last slice with assumption
		// that ExtData is packed in XY footprint (values cover full extent).
		// If that is NOT the case, we need to zero out blocks for each block layer.
		if fileNum == 1 || (lastBlocks && firstSliceInBlock) {
			numBlocks = dvid.GetNumBlocks(vox, blockSize)
			if fileNum == 1 {
				for layer := 0; layer < numLayers; layer++ {
					blocks[layer] = make(storage.TKeyValues, numBlocks, numBlocks)
					for b := 0; b < numBlocks; b++ {
						blocks[layer][b].V = d.BackgroundBlock()
					}
				}
				var bufSize uint64 = uint64(blockBytes) * uint64(numBlocks) * uint64(numLayers) / 1000000
				dvid.Debugf("Allocated %d MB for buffers.\n", bufSize)
			} else {
				blocks[curBlocks] = make(storage.TKeyValues, numBlocks, numBlocks)
				for b := 0; b < numBlocks; b++ {
					blocks[curBlocks][b].V = d.BackgroundBlock()
				}
			}
			err = d.loadOldBlocks(load.versionID, vox, blocks[curBlocks])
			if err != nil {
				return err
			}
		}

		// Transfer data between external<->internal blocks asynchronously
		layerTransferred[curBlocks].Add(1)
		go func(vox *Voxels, curBlocks int) {
			// Track point extents
			if d.Extents().AdjustPoints(vox.StartPoint(), vox.EndPoint()) {
				load.extentChanged.SetTrue()
			}

			// Process an XY image (slice).
			changed, err := d.writeXYImage(load.versionID, vox, blocks[curBlocks])
			if err != nil {
				dvid.Infof("Error writing XY image: %v\n", err)
			}
			if changed {
				load.extentChanged.SetTrue()
			}
			layerTransferred[curBlocks].Done()
		}(vox, curBlocks)

		// If this is the end of a block (or filenames), wait until all goroutines complete,
		// then asynchronously write blocks.
		if lastSliceInBlock {
			waitForWrites.Add(1)
			layerWritten[curBlocks].Add(1)
			go func(curBlocks int) {
				layerTransferred[curBlocks].Wait()
				dvid.Debugf("Writing block buffer %d using %s and %s...\n",
					curBlocks, d.Compression(), d.Checksum())
				err := d.writeBlocks(load.versionID, blocks[curBlocks], &layerWritten[curBlocks], &waitForWrites)
				if err != nil {
					dvid.Errorf("Error in async write of voxel blocks: %v", err)
				}
			}(curBlocks)
			// We can't move to buffer X until all blocks from buffer X have already been written.
			curBlocks = (curBlocks + 1) % numLayers
			dvid.Debugf("Waiting for layer %d to be written before reusing layer %d blocks\n",
				curBlocks, curBlocks)
			layerWritten[curBlocks].Wait()
			dvid.Debugf("Using layer %d...\n", curBlocks)
		}

		fileNum++
		load.offset = load.offset.Add(dvid.Point3d{0, 0, 1})
		timedLog.Infof("Loaded %s slice %s", d.DataName(), vox)
	}
	waitForWrites.Wait()
	return nil
}
Example #20
0
// LoadLocal adds image data to a version node.  See HelpMessage for example of
// command-line use of "load local".
func (d *Data) LoadLocal(request datastore.Request, reply *datastore.Response) error {
	timedLog := dvid.NewTimeLog()

	// Parse the request
	var uuidStr, dataName, cmdStr, sourceStr, filename string
	_ = request.CommandArgs(1, &uuidStr, &dataName, &cmdStr, &sourceStr, &filename)

	// Get the uuid from a uniquely identifiable string
	uuid, versionID, err := datastore.MatchingUUID(uuidStr)
	if err != nil {
		return fmt.Errorf("Could not find node with UUID %s: %v", uuidStr, err)
	}

	// Load the V3D Raw file.
	ext := filepath.Ext(filename)
	switch ext {
	case ".raw", ".v3draw":
	default:
		return fmt.Errorf("Unknown extension '%s' when expected V3D Raw file", ext)
	}
	file, err := os.Open(filename)
	if err != nil {
		return err
	}
	unmarshaler := V3DRawMarshaler{}
	channels, err := unmarshaler.UnmarshalV3DRaw(file)
	if err != nil {
		return err
	}

	// Store the metadata
	d.NumChannels = len(channels)
	d.Properties.Values = make(dvid.DataValues, d.NumChannels)
	if d.NumChannels > 0 {
		reply.Text = fmt.Sprintf("Loaded %s into data '%s': found %d channels\n",
			d.DataName(), filename, d.NumChannels)
		reply.Text += fmt.Sprintf(" %s", channels[0])
	} else {
		reply.Text = fmt.Sprintf("Found no channels in file %s\n", filename)
		return nil
	}
	for i, channel := range channels {
		d.Properties.Values[i] = channel.Voxels.Values()[0]
	}

	// Get repo and save it.
	if err := datastore.SaveDataByUUID(uuid, d); err != nil {
		return err
	}

	// PUT each channel of the file into the datastore using a separate data name.
	for _, channel := range channels {
		dvid.Infof("Processing channel %d... \n", channel.channelNum)
		err = d.PutVoxels(versionID, channel.Voxels, nil)
		if err != nil {
			return err
		}
	}

	// Create a RGB composite from the first 3 channels.  This is considered to be channel 0
	// or can be accessed with the base data name.
	dvid.Infof("Creating composite image from channels...\n")
	err = d.storeComposite(versionID, channels)
	if err != nil {
		return err
	}

	timedLog.Infof("RPC load local '%s' completed", filename)
	return nil
}
Example #21
0
// PutLocal adds image data to a version node, altering underlying blocks if the image
// intersects the block.
//
// The image filename glob MUST BE absolute file paths that are visible to the server.
// This function is meant for mass ingestion of large data files, and it is inappropriate
// to read gigabytes of data just to send it over the network to a local DVID.
func (d *Data) PutLocal(request datastore.Request, reply *datastore.Response) error {
	timedLog := dvid.NewTimeLog()

	// Parse the request
	var uuidStr, dataName, cmdStr, sourceStr, planeStr, offsetStr string
	filenames := request.CommandArgs(1, &uuidStr, &dataName, &cmdStr, &sourceStr,
		&planeStr, &offsetStr)
	if len(filenames) == 0 {
		return fmt.Errorf("Need to include at least one file to add: %s", request)
	}

	// Get offset
	offset, err := dvid.StringToPoint(offsetStr, ",")
	if err != nil {
		return fmt.Errorf("Illegal offset specification: %s: %v", offsetStr, err)
	}

	// Get list of files to add
	var addedFiles string
	if len(filenames) == 1 {
		addedFiles = filenames[0]
	} else {
		addedFiles = fmt.Sprintf("filenames: %s [%d more]", filenames[0], len(filenames)-1)
	}
	dvid.Debugf(addedFiles + "\n")

	// Get plane
	plane, err := dvid.DataShapeString(planeStr).DataShape()
	if err != nil {
		return err
	}

	// Get Repo and IDs
	uuid, versionID, err := datastore.MatchingUUID(uuidStr)
	if err != nil {
		return err
	}

	// Load and PUT each image.
	numSuccessful := 0
	for _, filename := range filenames {
		sliceLog := dvid.NewTimeLog()
		img, _, err := dvid.GoImageFromFile(filename)
		if err != nil {
			return fmt.Errorf("Error after %d images successfully added: %v", numSuccessful, err)
		}
		slice, err := dvid.NewOrthogSlice(plane, offset, dvid.RectSize(img.Bounds()))
		if err != nil {
			return fmt.Errorf("Unable to determine slice: %v", err)
		}

		vox, err := d.NewVoxels(slice, img)
		if err != nil {
			return err
		}
		storage.FileBytesRead <- len(vox.Data())
		if err = d.PutVoxels(versionID, vox, nil); err != nil {
			return err
		}
		sliceLog.Debugf("%s put local %s", d.DataName(), slice)
		numSuccessful++
		offset = offset.Add(dvid.Point3d{0, 0, 1})
	}

	if err := datastore.AddToNodeLog(uuid, []string{request.Command.String()}); err != nil {
		return err
	}
	timedLog.Infof("RPC put local (%s) completed", addedFiles)
	return nil
}
Example #22
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())
	}
}
Example #23
0
func (d *Data) serveTile(w http.ResponseWriter, r *http.Request, geom *GoogleSubvolGeom, formatStr string, noblanks bool) error {
	// If it's outside, write blank tile unless user wants no blanks.
	if geom.outside {
		if noblanks {
			http.NotFound(w, r)
			return fmt.Errorf("Requested tile is outside of available volume.")
		}
		img, err := d.getBlankTileImage(geom)
		if err != nil {
			return err
		}
		return dvid.WriteImageHttp(w, img, formatStr)
	}

	// If we are within volume, get data from Google.
	url, err := geom.GetURL(d.VolumeID, formatStr)
	if err != nil {
		return err
	}

	timedLog := dvid.NewTimeLog()
	client, err := d.GetClient()
	if err != nil {
		dvid.Errorf("Can't get OAuth2 connection to Google: %v\n", err)
		return err
	}
	resp, err := client.Get(url)
	if err != nil {
		return err
	}
	timedLog.Infof("PROXY HTTP to Google: %s, returned response %d", url, resp.StatusCode)
	defer resp.Body.Close()

	// Set the image header
	if err := dvid.SetImageHeader(w, formatStr); err != nil {
		return err
	}

	// If it's on edge, we need to pad the tile to the tile size.
	if geom.edge {
		// We need to read whole thing in to pad it.
		data, err := ioutil.ReadAll(resp.Body)
		timedLog.Infof("Got edge tile from Google, %d bytes\n", len(data))
		if err != nil {
			return err
		}
		paddedData, err := geom.padData(data)
		if err != nil {
			return err
		}
		_, err = w.Write(paddedData)
		return err
	}

	// If we aren't on edge or outside, our return status should be OK.
	if resp.StatusCode != http.StatusOK {
		return fmt.Errorf("Unexpected status code %d on tile request (%q, volume id %q)", resp.StatusCode, d.DataName(), d.VolumeID)
	}

	// Just send the data as we get it from Google in chunks.
	respBytes := 0
	const BufferSize = 32 * 1024
	buf := make([]byte, BufferSize)
	for {
		n, err := resp.Body.Read(buf)
		respBytes += n
		eof := (err == io.EOF)
		if err != nil && !eof {
			return err
		}
		if _, err = w.Write(buf[:n]); err != nil {
			return err
		}
		if f, ok := w.(http.Flusher); ok {
			f.Flush()
		}
		if eof {
			break
		}
	}
	timedLog.Infof("Got non-edge tile from Google, %d bytes\n", respBytes)
	return nil
}
Example #24
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())
	}
}
Example #25
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)
}
Example #26
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
	}

	var comment string
	action := strings.ToLower(r.Method)

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

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

	case "keys":
		keyList, err := d.GetKeys(ctx)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		jsonBytes, err := json.Marshal(keyList)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-Type", "application/json")
		fmt.Fprintf(w, string(jsonBytes))
		comment = "HTTP GET keys"

	case "keyrange":
		if len(parts) < 6 {
			server.BadRequest(w, r, "expect beginning and end keys to follow 'keyrange' endpoint")
			return
		}

		// Return JSON list of keys
		keyBeg := parts[4]
		keyEnd := parts[5]
		keyList, err := d.GetKeysInRange(ctx, keyBeg, keyEnd)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		jsonBytes, err := json.Marshal(keyList)
		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 keyrange [%q, %q]", keyBeg, keyEnd)

	case "key":
		if len(parts) < 5 {
			server.BadRequest(w, r, "expect key string to follow 'key' endpoint")
			return
		}
		keyStr := parts[4]

		switch action {
		case "get":
			// Return value of single key
			value, found, err := d.GetData(ctx, keyStr)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if !found {
				http.Error(w, fmt.Sprintf("Key %q not found", keyStr), http.StatusNotFound)
				return
			}
			if value != nil || len(value) > 0 {
				_, err = w.Write(value)
				if err != nil {
					server.BadRequest(w, r, err)
					return
				}
				w.Header().Set("Content-Type", "application/octet-stream")
			}
			comment = fmt.Sprintf("HTTP GET key %q of keyvalue %q: %d bytes (%s)\n", keyStr, d.DataName(), len(value), url)

		case "delete":
			if err := d.DeleteData(ctx, keyStr); err != nil {
				server.BadRequest(w, r, err)
				return
			}
			comment = fmt.Sprintf("HTTP DELETE data with key %q of keyvalue %q (%s)\n", keyStr, d.DataName(), url)

		case "post":
			data, err := ioutil.ReadAll(r.Body)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			err = d.PutData(ctx, keyStr, data)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			comment = fmt.Sprintf("HTTP POST keyvalue '%s': %d bytes (%s)\n", d.DataName(), len(data), url)
		default:
			server.BadRequest(w, r, "key endpoint does not support %q HTTP verb", action)
			return
		}

	default:
		server.BadRequest(w, r, "unknown action %q requested", parts[3])
		return
	}

	timedLog.Infof(comment)
}
Example #27
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 "sync":
		if action != "post" {
			server.BadRequest(w, r, "Only POST allowed to sync endpoint")
			return
		}
		replace := r.URL.Query().Get("replace") == "true"
		if err := datastore.SetSyncByJSON(d, uuid, replace, r.Body); err != nil {
			server.BadRequest(w, r, err)
			return
		}

	case "label":
		if action != "get" {
			server.BadRequest(w, r, "Only GET action is available on 'label' endpoint.")
			return
		}
		if len(parts) < 5 {
			server.BadRequest(w, r, "Must include label after 'label' endpoint.")
			return
		}
		label, err := strconv.ParseUint(parts[4], 10, 64)
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if label == 0 {
			server.BadRequest(w, r, "Label 0 is protected background value and cannot be used for query.")
			return
		}
		queryStrings := r.URL.Query()
		jsonBytes, err := d.GetLabelJSON(ctx, label, queryStrings.Get("relationships") == "true")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-type", "application/json")
		if _, err := w.Write(jsonBytes); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: get synaptic elements for label %d (%s)", r.Method, label, r.URL)

	case "tag":
		if action != "get" {
			server.BadRequest(w, r, "Only GET action is available on 'tag' endpoint.")
			return
		}
		if len(parts) < 5 {
			server.BadRequest(w, r, "Must include tag string after 'tag' endpoint.")
			return
		}
		tag := Tag(parts[4])
		queryStrings := r.URL.Query()
		jsonBytes, err := d.GetTagJSON(ctx, tag, queryStrings.Get("relationships") == "true")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		w.Header().Set("Content-type", "application/json")
		if _, err := w.Write(jsonBytes); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: get synaptic elements for tag %s (%s)", r.Method, tag, r.URL)

	case "elements":
		switch action {
		case "get":
			// GET <api URL>/node/<UUID>/<data name>/elements/<size>/<offset>
			if len(parts) < 6 {
				server.BadRequest(w, r, "Expect size and offset to follow 'elements' in GET request")
				return
			}
			sizeStr, offsetStr := parts[4], parts[5]
			ext3d, err := dvid.NewExtents3dFromStrings(offsetStr, sizeStr, "_")
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			elements, err := d.GetRegionSynapses(ctx, ext3d)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			w.Header().Set("Content-type", "application/json")
			jsonBytes, err := json.Marshal(elements)
			if err != nil {
				server.BadRequest(w, r, err)
				return
			}
			if _, err := w.Write(jsonBytes); err != nil {
				server.BadRequest(w, r, err)
				return
			}
			timedLog.Infof("HTTP %s: synapse elements in subvolume (size %s, offset %s) (%s)", r.Method, sizeStr, offsetStr, r.URL)

		case "post":
			if err := d.StoreSynapses(ctx, r.Body); err != nil {
				server.BadRequest(w, r, err)
				return
			}
		default:
			server.BadRequest(w, r, "Only GET or POST action is available on 'elements' endpoint.")
			return
		}

	case "element":
		// DELETE <api URL>/node/<UUID>/<data name>/element/<coord>
		if action != "delete" {
			server.BadRequest(w, r, "Only DELETE action is available on 'element' endpoint.")
			return
		}
		if len(parts) < 5 {
			server.BadRequest(w, r, "Must include coordinate after DELETE on 'element' endpoint.")
			return
		}
		pt, err := dvid.StringToPoint3d(parts[4], "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if err := d.DeleteElement(ctx, pt); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: delete synaptic element at %s (%s)", r.Method, pt, r.URL)

	case "move":
		// POST <api URL>/node/<UUID>/<data name>/move/<from_coord>/<to_coord>
		if action != "post" {
			server.BadRequest(w, r, "Only POST action is available on 'move' endpoint.")
			return
		}
		if len(parts) < 6 {
			server.BadRequest(w, r, "Must include 'from' and 'to' coordinate after 'move' endpoint.")
			return
		}
		fromPt, err := dvid.StringToPoint3d(parts[4], "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		toPt, err := dvid.StringToPoint3d(parts[5], "_")
		if err != nil {
			server.BadRequest(w, r, err)
			return
		}
		if err := d.MoveElement(ctx, fromPt, toPt); err != nil {
			server.BadRequest(w, r, err)
			return
		}
		timedLog.Infof("HTTP %s: move synaptic element from %s to %s (%s)", r.Method, fromPt, toPt, r.URL)

	default:
		server.BadAPIRequest(w, r, d)
	}
}
Example #28
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)
}
Example #29
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())
	}
}
Example #30
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())
	}
}