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
}
// 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
}
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
}