// NewLabels returns labelblk Labels, a representation of externally usable subvolume
// or slice data, given some geometry and optional image data.
// If img is passed in, the function will initialize Voxels with data from the image.
// Otherwise, it will allocate a zero buffer of appropriate size.
//
// TODO : Unlike the standard imageblk.NewVoxels, the labelblk version can modify the
// labels based on the z-coordinate of the given geometry for Raveler labeling.
// This will be removed when Raveler-specific labels are moved outside DVID.
func (d *Data) NewLabels(geom dvid.Geometry, img interface{}) (*Labels, error) {
bytesPerVoxel := d.Properties.Values.BytesPerElement()
stride := geom.Size().Value(0) * bytesPerVoxel
var data []byte
if img == nil {
numVoxels := geom.NumVoxels()
if numVoxels <= 0 {
return nil, fmt.Errorf("Illegal geometry requested: %s", geom)
}
requestSize := int64(bytesPerVoxel) * numVoxels
if requestSize > server.MaxDataRequest {
return nil, fmt.Errorf("Requested payload (%d bytes) exceeds this DVID server's set limit (%d)",
requestSize, server.MaxDataRequest)
}
data = make([]byte, requestSize)
} else {
switch t := img.(type) {
case image.Image:
var inputBytesPerVoxel, actualStride int32
var err error
data, inputBytesPerVoxel, actualStride, err = dvid.ImageData(t)
if err != nil {
return nil, err
}
if actualStride != stride {
// Need to do some conversion here.
switch d.Labeling {
case Standard64bit:
data, err = d.convertTo64bit(geom, data, int(inputBytesPerVoxel), int(actualStride))
if err != nil {
return nil, err
}
case RavelerLabel:
data, err = d.addLabelZ(geom, data, actualStride)
if err != nil {
return nil, err
}
default:
return nil, fmt.Errorf("unexpected label type in labelblk: %s", d.Labeling)
}
}
case []byte:
data = t
actualLen := int64(len(data))
expectedLen := int64(bytesPerVoxel) * geom.NumVoxels()
if actualLen != expectedLen {
return nil, fmt.Errorf("labels data was %d bytes, expected %d bytes for %s",
actualLen, expectedLen, geom)
}
default:
return nil, fmt.Errorf("unexpected image type given to NewVoxels(): %T", t)
}
}
labels := &Labels{
imageblk.NewVoxels(geom, d.Properties.Values, data, stride),
}
return labels, nil
}
// NewVoxels returns Voxels with given geometry and optional image data.
// If img is passed in, the function will initialize the Voxels with data from the image.
// Otherwise, it will allocate a zero buffer of appropriate size.
func (d *Data) NewVoxels(geom dvid.Geometry, img interface{}) (*Voxels, error) {
bytesPerVoxel := d.Properties.Values.BytesPerElement()
stride := geom.Size().Value(0) * bytesPerVoxel
voxels := &Voxels{
Geometry: geom,
values: d.Properties.Values,
stride: stride,
}
if img == nil {
numVoxels := geom.NumVoxels()
if numVoxels <= 0 {
return nil, fmt.Errorf("Illegal geometry requested: %s", geom)
}
requestSize := int64(bytesPerVoxel) * numVoxels
if requestSize > server.MaxDataRequest {
return nil, fmt.Errorf("Requested payload (%d bytes) exceeds this DVID server's set limit (%d)",
requestSize, server.MaxDataRequest)
}
voxels.data = make([]uint8, requestSize)
} else {
switch t := img.(type) {
case image.Image:
var actualStride int32
var err error
voxels.data, _, actualStride, err = dvid.ImageData(t)
if err != nil {
return nil, err
}
if actualStride < stride {
return nil, fmt.Errorf("Too little data in input image (expected stride %d)", stride)
}
voxels.stride = actualStride
case []byte:
voxels.data = t
actualLen := int64(len(voxels.data))
expectedLen := int64(bytesPerVoxel) * geom.NumVoxels()
if actualLen != expectedLen {
return nil, fmt.Errorf("voxels data was %d bytes, expected %d bytes for %s",
actualLen, expectedLen, geom)
}
default:
return nil, fmt.Errorf("Unexpected image type given to NewVoxels(): %T", t)
}
}
return voxels, nil
}
// Convert a 32-bit label into a 64-bit label by adding the Z coordinate into high 32 bits.
// Also drops the high byte (alpha channel) since Raveler labels only use 24-bits.
func (d *Data) addLabelZ(geom dvid.Geometry, data32 []uint8, stride int32) ([]byte, error) {
if len(data32)%4 != 0 {
return nil, fmt.Errorf("expected 4 byte/voxel alignment but have %d bytes!", len(data32))
}
coord := geom.StartPoint()
if coord.NumDims() < 3 {
return nil, fmt.Errorf("expected n-d (n >= 3) offset for image. Got %d dimensions.",
coord.NumDims())
}
superpixelBytes := make([]byte, 8, 8)
binary.BigEndian.PutUint32(superpixelBytes[0:4], uint32(coord.Value(2)))
nx := int(geom.Size().Value(0))
ny := int(geom.Size().Value(1))
numBytes := nx * ny * 8
data64 := make([]byte, numBytes, numBytes)
dstI := 0
for y := 0; y < ny; y++ {
srcI := y * int(stride)
for x := 0; x < nx; x++ {
if data32[srcI] == 0 && data32[srcI+1] == 0 && data32[srcI+2] == 0 {
copy(data64[dstI:dstI+8], ZeroBytes())
} else {
superpixelBytes[5] = data32[srcI+2]
superpixelBytes[6] = data32[srcI+1]
superpixelBytes[7] = data32[srcI]
copy(data64[dstI:dstI+8], superpixelBytes)
}
// NOTE: we skip the 4th byte (alpha) at srcI+3
//a := uint32(data32[srcI+3])
//b := uint32(data32[srcI+2])
//g := uint32(data32[srcI+1])
//r := uint32(data32[srcI+0])
//spid := (b << 16) | (g << 8) | r
srcI += 4
dstI += 8
}
}
return data64, nil
}
// GetImage returns an image given a 2d orthogonal image description. Since imagetile tiles
// have precomputed XY, XZ, and YZ orientations, reconstruction of the desired image should
// be much faster than computing the image from voxel blocks.
func (d *Data) GetImage(ctx storage.Context, src *imageblk.Data, geom dvid.Geometry, isotropic bool) (*dvid.Image, error) {
// Iterate through tiles that intersect our geometry.
if d.Levels == nil || len(d.Levels) == 0 {
return nil, fmt.Errorf("%s has no specification for tiles at highest resolution",
d.DataName())
}
levelSpec := d.Levels[0]
minSlice, err := dvid.Isotropy2D(src.VoxelSize, geom, isotropic)
if err != nil {
return nil, err
}
// Create an image of appropriate size and type using source's ExtData creation.
dstW := minSlice.Size().Value(0)
dstH := minSlice.Size().Value(1)
dst, err := src.BlankImage(dstW, dstH)
if err != nil {
return nil, err
}
// Read each tile that intersects the geometry and store into final image.
slice := minSlice.DataShape()
tileW, tileH, err := slice.GetSize2D(levelSpec.TileSize)
if err != nil {
return nil, err
}
tileSize := dvid.Point2d{tileW, tileH}
minPtX, minPtY, err := slice.GetSize2D(minSlice.StartPoint())
if err != nil {
return nil, err
}
wg := new(sync.WaitGroup)
topLeftGlobal := dvid.Point2d{minPtX, minPtY}
tilePt := topLeftGlobal.Chunk(tileSize)
bottomRightGlobal := tilePt.MaxPoint(tileSize).(dvid.Point2d)
y0 := int32(0)
y1 := bottomRightGlobal[1] - minPtY + 1
for y0 < dstH {
x0 := int32(0)
x1 := bottomRightGlobal[0] - minPtX + 1
for x0 < dstW {
wg.Add(1)
go func(x0, y0, x1, y1 int32) {
defer wg.Done()
// Get this tile from datastore
tileCoord, err := slice.PlaneToChunkPoint3d(x0, y0, minSlice.StartPoint(), levelSpec.TileSize)
goImg, err := d.GetTile(ctx, slice, 0, dvid.IndexZYX(tileCoord))
if err != nil || goImg == nil {
return
}
// Get tile space coordinate for top left.
curStart := dvid.Point2d{x0 + minPtX, y0 + minPtY}
p := curStart.PointInChunk(tileSize)
ptInTile := image.Point{int(p.Value(0)), int(p.Value(1))}
// Paste the pertinent rectangle from this tile into our destination.
r := image.Rect(int(x0), int(y0), int(x1), int(y1))
draw.Draw(dst.GetDrawable(), r, goImg, ptInTile, draw.Src)
}(x0, y0, x1, y1)
x0 = x1
x1 += tileW
}
y0 = y1
y1 += tileH
}
wg.Wait()
if isotropic {
dstW := int(geom.Size().Value(0))
dstH := int(geom.Size().Value(1))
dst, err = dst.ScaleImage(dstW, dstH)
if err != nil {
return nil, err
}
}
return dst, nil
}
// Convert raw image data into a 2d array of 64-bit labels
func (d *Data) convertTo64bit(geom dvid.Geometry, data []uint8, bytesPerVoxel, stride int) ([]byte, error) {
nx := int(geom.Size().Value(0))
ny := int(geom.Size().Value(1))
numBytes := nx * ny * 8
data64 := make([]byte, numBytes, numBytes)
var byteOrder binary.ByteOrder
if geom.DataShape().ShapeDimensions() == 2 {
byteOrder = binary.BigEndian // This is the default for PNG
} else {
byteOrder = binary.LittleEndian
}
switch bytesPerVoxel {
case 1:
dstI := 0
for y := 0; y < ny; y++ {
srcI := y * stride
for x := 0; x < nx; x++ {
binary.LittleEndian.PutUint64(data64[dstI:dstI+8], uint64(data[srcI]))
srcI++
dstI += 8
}
}
case 2:
dstI := 0
for y := 0; y < ny; y++ {
srcI := y * stride
for x := 0; x < nx; x++ {
value := byteOrder.Uint16(data[srcI : srcI+2])
binary.LittleEndian.PutUint64(data64[dstI:dstI+8], uint64(value))
srcI += 2
dstI += 8
}
}
case 4:
dstI := 0
for y := 0; y < ny; y++ {
srcI := y * stride
for x := 0; x < nx; x++ {
value := byteOrder.Uint32(data[srcI : srcI+4])
binary.LittleEndian.PutUint64(data64[dstI:dstI+8], uint64(value))
srcI += 4
dstI += 8
}
}
case 8:
dstI := 0
for y := 0; y < ny; y++ {
srcI := y * stride
for x := 0; x < nx; x++ {
value := byteOrder.Uint64(data[srcI : srcI+8])
binary.LittleEndian.PutUint64(data64[dstI:dstI+8], uint64(value))
srcI += 8
dstI += 8
}
}
default:
return nil, fmt.Errorf("could not convert to 64-bit label given %d bytes/voxel", bytesPerVoxel)
}
return data64, nil
}