// DownRes downsamples 2d Voxels data by averaging where the down-magnification are
// integers. If the source image size in Voxels is not an integral multiple of the
// reduction factor, the edge voxels on the right and bottom side are truncated.
// This function modifies the Voxels data. An error is returned if a non-2d Voxels
// receiver is used.
func (v *Voxels) DownRes(magnification dvid.Point) error {
if v.DataShape().ShapeDimensions() != 2 {
return fmt.Errorf("ImageDownres() only supports 2d images at this time.")
}
// Calculate new dimensions and allocate.
srcW := v.Size().Value(0)
srcH := v.Size().Value(1)
reduceW, reduceH, err := v.DataShape().GetSize2D(magnification)
if err != nil {
return err
}
dstW := srcW / reduceW
dstH := srcH / reduceH
// Reduce the image.
img, err := v.GetImage2d()
if err != nil {
return err
}
img, err = img.ScaleImage(int(dstW), int(dstH))
if err != nil {
return err
}
// Set data and dimensions to downres data.
v.data = []byte(img.Data())
geom, err := dvid.NewOrthogSlice(v.DataShape(), v.StartPoint(), dvid.Point2d{dstW, dstH})
if err != nil {
return err
}
v.Geometry = geom
v.stride = dstW * v.values.BytesPerElement()
return nil
}
// Loads a XY oriented image at given offset, returning Voxels.
func (d *Data) loadXYImage(filename string, offset dvid.Point) (*Voxels, error) {
img, _, err := dvid.GoImageFromFile(filename)
if err != nil {
return nil, err
}
slice, err := dvid.NewOrthogSlice(dvid.XY, offset, dvid.RectSize(img.Bounds()))
if err != nil {
return nil, fmt.Errorf("Unable to determine slice: %v", err)
}
vox, err := d.NewVoxels(slice, img)
if err != nil {
return nil, err
}
storage.FileBytesRead <- len(vox.Data())
return vox, nil
}
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
}
// 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
}