// NewData returns a pointer to new keyvalue data with default values.
func (dtype *Type) NewDataService(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (datastore.DataService, error) {
basedata, err := datastore.NewDataService(dtype, uuid, id, name, c)
if err != nil {
return nil, err
}
return &Data{basedata}, nil
}
// NewData returns a pointer to labelsz data.
func NewData(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (*Data, error) {
// See if we have a valid DataService ROI
var roistr string
roistr, found, err := c.GetString("ROI")
if err != nil {
return nil, err
}
if found {
parts := strings.Split(roistr, ",")
if len(parts) != 2 {
return nil, fmt.Errorf("bad ROI value (%q) expected %q", roistr, "<roiname>,<uuid>")
}
}
// Initialize the Data for this data type
basedata, err := datastore.NewDataService(dtype, uuid, id, name, c)
if err != nil {
return nil, err
}
data := &Data{
Data: basedata,
Properties: Properties{
StaticROI: roistr,
},
}
return data, nil
}
// NewData returns a pointer to new ROI data with default values.
func (dtype *Type) NewDataService(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (datastore.DataService, error) {
basedata, err := datastore.NewDataService(dtype, uuid, id, name, c)
if err != nil {
return nil, err
}
s, found, err := c.GetString("BlockSize")
if err != nil {
return nil, err
}
var blockSize dvid.Point3d
if found {
pt, err := dvid.StringToPoint(s, ",")
if err != nil {
return nil, err
}
if pt.NumDims() != 3 {
return nil, fmt.Errorf("BlockSize must be 3d, not %dd", pt.NumDims())
}
blockSize, _ = pt.(dvid.Point3d)
} else {
blockSize = dvid.Point3d{DefaultBlockSize, DefaultBlockSize, DefaultBlockSize}
}
d := &Data{
Data: basedata,
Properties: Properties{blockSize, math.MaxInt32, math.MinInt32},
ready: make(map[dvid.VersionID]bool),
}
return d, nil
}
// NewData returns a pointer to annotation data.
func NewData(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (*Data, error) {
// Initialize the Data for this data type
basedata, err := datastore.NewDataService(dtype, uuid, id, name, c)
if err != nil {
return nil, err
}
data := &Data{
Data: basedata,
Properties: Properties{},
}
return data, nil
}
// NewData returns a pointer to a new Voxels with default values.
func (dtype *Type) NewData(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (*Data, error) {
basedata, err := datastore.NewDataService(dtype, uuid, id, name, c)
if err != nil {
return nil, err
}
var p Properties
p.setDefault(dtype.values, dtype.interpolable)
if err := p.setByConfig(c); err != nil {
return nil, err
}
data := &Data{
Data: basedata,
Properties: p,
}
return data, nil
}
// NewData returns a pointer to labelvol data.
func NewData(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (*Data, error) {
// Initialize the Data for this data type
basedata, err := datastore.NewDataService(dtype, uuid, id, name, c)
if err != nil {
return nil, err
}
props := new(Properties)
props.setDefault()
if err := props.setByConfig(c); err != nil {
return nil, err
}
data := &Data{
Data: basedata,
Properties: *props,
}
data.Properties.MaxLabel = make(map[dvid.VersionID]uint64)
return data, nil
}
// NewData returns a pointer to labelvol data.
func NewData(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (*Data, error) {
// Make sure we have a valid labelvol source
s, found, err := c.GetString("Source")
if err != nil {
return nil, err
}
if !found {
return nil, fmt.Errorf("Cannot make labelsz data without valid 'Source' specifying an associated labelvol.")
}
srcname := dvid.InstanceName(s)
if _, err = labelvol.GetByUUID(uuid, srcname); err != nil {
return nil, err
}
c.Set("sync", s) // This will set base data sync list
// Initialize the Data for this data type
basedata, err := datastore.NewDataService(dtype, uuid, id, name, c)
if err != nil {
return nil, err
}
return &Data{basedata, srcname}, nil
}
// NewData returns a pointer to new googlevoxels data with default values.
func (dtype *Type) NewDataService(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (datastore.DataService, error) {
// Make sure we have needed volumeid and authentication key.
volumeid, found, err := c.GetString("volumeid")
if err != nil {
return nil, err
}
if !found {
return nil, fmt.Errorf("Cannot make googlevoxels data without valid 'volumeid' setting.")
}
jwtfile, found, err := c.GetString("jwtfile")
if err != nil {
return nil, err
}
if !found {
return nil, fmt.Errorf("Cannot make googlevoxels data without valid 'jwtfile' specifying path to JSON Web Token")
}
// Read in the JSON Web Token
jwtdata, err := ioutil.ReadFile(jwtfile)
if err != nil {
return nil, fmt.Errorf("Cannot load JSON Web Token file (%s): %v", jwtfile, err)
}
conf, err := google.JWTConfigFromJSON(jwtdata, "https://www.googleapis.com/auth/brainmaps")
if err != nil {
return nil, fmt.Errorf("Cannot establish JWT Config file from Google: %v", err)
}
client := conf.Client(oauth2.NoContext)
// Make URL call to get the available scaled volumes.
url := fmt.Sprintf("%s/volumes/%s", bmapsPrefix, volumeid)
resp, err := client.Get(url)
if err != nil {
return nil, fmt.Errorf("Error getting volume metadata from Google: %v", err)
}
if resp.StatusCode != http.StatusOK {
return nil, fmt.Errorf("Unexpected status code %d returned when getting volume metadata for %q", resp.StatusCode, volumeid)
}
metadata, err := ioutil.ReadAll(resp.Body)
if err != nil {
return nil, err
}
resp.Body.Close()
var m struct {
Geoms Geometries `json:"geometry"`
}
if err := json.Unmarshal(metadata, &m); err != nil {
return nil, fmt.Errorf("Error decoding volume JSON metadata: %v", err)
}
dvid.Infof("Successfully got geometries:\nmetadata:\n%s\nparsed JSON:\n%v\n", metadata, m)
// Compute the mapping from tile scale/orientation to scaled volume index.
geomMap := GeometryMap{}
// (1) Find the highest resolution geometry.
var highResIndex GeometryIndex
minVoxelSize := dvid.NdFloat32{10000, 10000, 10000}
for i, geom := range m.Geoms {
if geom.PixelSize[0] < minVoxelSize[0] || geom.PixelSize[1] < minVoxelSize[1] || geom.PixelSize[2] < minVoxelSize[2] {
minVoxelSize = geom.PixelSize
highResIndex = GeometryIndex(i)
}
}
dvid.Infof("Google voxels %q: found highest resolution was geometry %d: %s\n", name, highResIndex, minVoxelSize)
// (2) For all geometries, find out what the scaling is relative to the highest resolution pixel size.
for i, geom := range m.Geoms {
if i == int(highResIndex) {
geomMap[GSpec{0, XY}] = highResIndex
geomMap[GSpec{0, XZ}] = highResIndex
geomMap[GSpec{0, YZ}] = highResIndex
geomMap[GSpec{0, XYZ}] = highResIndex
} else {
scaleX := geom.PixelSize[0] / minVoxelSize[0]
scaleY := geom.PixelSize[1] / minVoxelSize[1]
scaleZ := geom.PixelSize[2] / minVoxelSize[2]
var shape Shape
switch {
case scaleX > scaleZ && scaleY > scaleZ:
shape = XY
case scaleX > scaleY && scaleZ > scaleY:
shape = XZ
case scaleY > scaleX && scaleZ > scaleX:
shape = YZ
default:
shape = XYZ
}
var mag float32
if scaleX > mag {
mag = scaleX
}
if scaleY > mag {
mag = scaleY
}
if scaleZ > mag {
mag = scaleZ
}
scaling := log2(mag)
geomMap[GSpec{scaling, shape}] = GeometryIndex(i)
dvid.Infof("%s at scaling %d set to geometry %d: resolution %s\n", shape, scaling, i, geom.PixelSize)
}
}
// Create a client that will be authorized and authenticated on behalf of the account.
// Initialize the googlevoxels data
basedata, err := datastore.NewDataService(dtype, uuid, id, name, c)
if err != nil {
return nil, err
}
data := &Data{
Data: basedata,
Properties: Properties{
VolumeID: volumeid,
JWT: string(jwtdata),
TileSize: DefaultTileSize,
GeomMap: geomMap,
Scales: m.Geoms,
HighResIndex: highResIndex,
},
client: client,
}
return data, nil
}
// NewData returns a pointer to new tile data with default values.
func (dtype *Type) NewDataService(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (datastore.DataService, error) {
// Make sure we have a valid DataService source
sourcename, found, err := c.GetString("Source")
if err != nil {
return nil, err
}
if !found {
return nil, fmt.Errorf("Cannot make imagetile data without valid 'Source' setting.")
}
// See if we want placeholder imagetile.
placeholder, found, err := c.GetBool("Placeholder")
if err != nil {
return nil, err
}
// Determine encoding for tile storage and this dictates what kind of compression we use.
encoding, found, err := c.GetString("Format")
if err != nil {
return nil, err
}
format := PNG
if found {
switch strings.ToLower(encoding) {
case "lz4":
format = LZ4
case "png":
format = PNG
case "jpg":
format = JPG
default:
return nil, fmt.Errorf("Unknown encoding specified: '%s' (should be 'lz4', 'png', or 'jpg'", encoding)
}
}
// Compression is determined by encoding. Inform user if there's a discrepancy.
var compression string
switch format {
case LZ4:
compression = "lz4"
case PNG:
compression = "none"
case JPG:
compression = "none"
}
compressConfig, found, err := c.GetString("Compression")
if err != nil {
return nil, err
}
if found && strings.ToLower(compressConfig) != compression {
return nil, fmt.Errorf("Conflict between specified compression '%s' and format '%s'. Suggest not dictating compression.",
compressConfig, encoding)
}
c.Set("Compression", compression)
// Initialize the imagetile data
basedata, err := datastore.NewDataService(dtype, uuid, id, name, c)
if err != nil {
return nil, err
}
data := &Data{
Data: basedata,
Properties: Properties{
Source: dvid.InstanceName(sourcename),
Placeholder: placeholder,
Encoding: format,
},
}
return data, nil
}
// NewData returns a pointer to new googlevoxels data with default values.
func (dtype *Type) NewDataService(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (datastore.DataService, error) {
// Make sure we have needed volumeid and authentication key.
volumeid, found, err := c.GetString("volumeid")
if err != nil {
return nil, err
}
if !found {
return nil, fmt.Errorf("Cannot make googlevoxels data without valid 'volumeid' setting.")
}
authkey, found, err := c.GetString("authkey")
if err != nil {
return nil, err
}
if !found {
return nil, fmt.Errorf("Cannot make googlevoxels data without valid 'authkey' setting.")
}
// Make URL call to get the available scaled volumes.
url := fmt.Sprintf("https://www.googleapis.com/brainmaps/v1beta1/volumes/%s?key=%s", volumeid, authkey)
resp, err := http.Get(url)
if err != nil {
return nil, fmt.Errorf("Error getting volume metadata from Google: %v", err)
}
if resp.StatusCode != http.StatusOK {
return nil, fmt.Errorf("Unexpected status code %d returned when getting volume metadata for %q", resp.StatusCode, volumeid)
}
metadata, err := ioutil.ReadAll(resp.Body)
if err != nil {
return nil, err
}
var m struct {
Geoms Geometries `json:"geometrys"`
}
if err := json.Unmarshal(metadata, &m); err != nil {
return nil, fmt.Errorf("Error decoding volume JSON metadata: %v", err)
}
// Compute the mapping from tile scale/orientation to scaled volume index.
tileMap := GeometryMap{}
// (1) Find the highest resolution geometry.
var highResIndex GeometryIndex
minVoxelSize := dvid.NdFloat32{10000, 10000, 10000}
for i, geom := range m.Geoms {
if geom.PixelSize[0] < minVoxelSize[0] || geom.PixelSize[1] < minVoxelSize[1] || geom.PixelSize[2] < minVoxelSize[2] {
minVoxelSize = geom.PixelSize
highResIndex = GeometryIndex(i)
}
}
dvid.Infof("Google voxels %q: found highest resolution was geometry %d: %s\n", name, highResIndex, minVoxelSize)
// (2) For all geometries, find out what the scaling is relative to the highest resolution pixel size.
for i, geom := range m.Geoms {
if i == int(highResIndex) {
tileMap[TileSpec{0, XY}] = highResIndex
tileMap[TileSpec{0, XZ}] = highResIndex
tileMap[TileSpec{0, YZ}] = highResIndex
} else {
scaleX := geom.PixelSize[0] / minVoxelSize[0]
scaleY := geom.PixelSize[1] / minVoxelSize[1]
scaleZ := geom.PixelSize[2] / minVoxelSize[2]
var plane TileOrientation
switch {
case scaleX > scaleZ && scaleY > scaleZ:
plane = XY
case scaleX > scaleY && scaleZ > scaleY:
plane = XZ
case scaleY > scaleX && scaleZ > scaleX:
plane = YZ
default:
dvid.Infof("Odd geometry skipped for Google voxels %q with pixel size: %s\n", name, geom.PixelSize)
dvid.Infof(" Scaling from highest resolution: %d x %d x %d\n", scaleX, scaleY, scaleZ)
continue
}
var mag float32
if scaleX > mag {
mag = scaleX
}
if scaleY > mag {
mag = scaleY
}
if scaleZ > mag {
mag = scaleZ
}
scaling := log2(mag)
tileMap[TileSpec{scaling, plane}] = GeometryIndex(i)
dvid.Infof("Plane %s at scaling %d set to geometry %d: resolution %s\n", plane, scaling, i, geom.PixelSize)
}
}
// Initialize the googlevoxels data
basedata, err := datastore.NewDataService(dtype, uuid, id, name, c)
if err != nil {
return nil, err
}
data := &Data{
Data: basedata,
Properties: Properties{
VolumeID: volumeid,
AuthKey: authkey,
TileSize: DefaultTileSize,
TileMap: tileMap,
Scales: m.Geoms,
HighResIndex: highResIndex,
},
}
return data, nil
}
