annotation

package
v1.0.0 Latest Latest
Warning

This package is not in the latest version of its module.

 Go to latest Published: Aug 18, 2023 License: BSD-3-Clause Imports: 26 Imported by: 2

Documentation

Overview

Package annotation supports point annotation management and queries.

Index

Constants

View Source 
const (
	Version  = "0.1"
	RepoURL  = "github.com/janelia-flyem/dvid/datatype/annotation"
	TypeName = "annotation"
)
View Source 
const (
	FormatFlatBuffers formatType = iota
	FormatProtobuf3
	FormatJSON
)
View Source 
const (
	ModifyElementsEvent = "ANNOTATION_MOD_ELEMENTS"
	SetElementsEvent    = "ANNOTATION_SET_ELEMENTS"
)

Annotation number change event identifiers.

Variables

View Source 
var (
	DefaultBlockSize int32   = 64 // labelblk.DefaultBlockSize
	DefaultRes       float32 = labelblk.DefaultRes
	DefaultUnits             = labelblk.DefaultUnits
)

Functions

func BlockTKeyRange 

func BlockTKeyRange() (min, max storage.TKey)

func BlockTKeyZRange added in v1.0.0 

func BlockTKeyZRange(begBlockCoord, endBlockCoord dvid.ChunkPoint3d) (min, max storage.TKey)

func DecodeBlockTKey 

func DecodeBlockTKey(tk storage.TKey) (pt dvid.ChunkPoint3d, err error)

func DecodeLabelTKey 

func DecodeLabelTKey(tk storage.TKey) (label uint64, err error)

func NewBlockTKey 

func NewBlockTKey(pt dvid.ChunkPoint3d) storage.TKey

func NewLabelTKey 

func NewLabelTKey(label uint64) storage.TKey

func NewTagTKey 

func NewTagTKey(tag Tag) (storage.TKey, error)

NewTagTKey returns a TKey for a given tag.

Types

type Data 

type Data struct {
	*datastore.Data
	Properties

	// Keep track of sync operations that could be updating the data.
	datastore.Updater

	sync.RWMutex // For CAS ops.  TODO: Make more specific (e.g., point locks) for efficiency.
	// contains filtered or unexported fields
}

Data instance of labelvol, label sparse volumes.

func GetByDataUUID 

func GetByDataUUID(dataUUID dvid.UUID) (*Data, error)

GetByDataUUID returns a pointer to annotation data given a data UUID.

func GetByUUIDName 

func GetByUUIDName(uuid dvid.UUID, name dvid.InstanceName) (*Data, error)

GetByUUIDName returns a pointer to annotation data given a version (UUID) and data name.

func NewData 

func NewData(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (*Data, error)

NewData returns a pointer to annotation data.

func (*Data) DeleteElement 

func (d *Data) DeleteElement(ctx *datastore.VersionedCtx, pt dvid.Point3d, kafkaOff bool) error

func (*Data) DescribeTKeyClass 

func (d *Data) DescribeTKeyClass(tkc storage.TKeyClass) string

DescribeTKeyClass returns a string explanation of what a particular TKeyClass is used for. Implements the datastore.TKeyClassDescriber interface.

func (*Data) DoRPC 

func (d *Data) DoRPC(req datastore.Request, reply *datastore.Response) error

DoRPC acts as a switchboard for RPC commands.

func (*Data) Equals 

func (d *Data) Equals(d2 *Data) bool

func (*Data) GetLabelJSON 

func (d *Data) GetLabelJSON(ctx *datastore.VersionedCtx, label uint64, addRels bool) ([]byte, error)

GetLabelJSON returns JSON for synapse elements in a given label.

func (*Data) GetROISynapses 

func (d *Data) GetROISynapses(ctx *datastore.VersionedCtx, roiSpec storage.FilterSpec) (Elements, error)

GetROISynapses returns synapse elements for a given ROI.

func (*Data) GetRegionSynapses 

func (d *Data) GetRegionSynapses(ctx *datastore.VersionedCtx, ext *dvid.Extents3d) (Elements, error)

GetRegionSynapses returns synapse elements for a given subvolume of image space.

func (*Data) GetSyncSubs 

func (d *Data) GetSyncSubs(synced dvid.Data) (subs datastore.SyncSubs, err error)

GetSyncSubs implements the datastore.Syncer interface. Returns a list of subscriptions to the sync data instance that will notify the receiver.

func (*Data) GetSyncedLabelvol 

func (d *Data) GetSyncedLabelvol() *labelvol.Data

func (*Data) GetTagJSON 

func (d *Data) GetTagJSON(ctx *datastore.VersionedCtx, tag Tag, addRels bool) (jsonBytes []byte, err error)

GetTagJSON returns JSON for synapse elements in a given tag.

func (*Data) GobDecode 

func (d *Data) GobDecode(b []byte) error

func (*Data) GobEncode 

func (d *Data) GobEncode() ([]byte, error)

func (*Data) Help 

func (d *Data) Help() string

func (*Data) InitDataHandlers 

func (d *Data) InitDataHandlers() error

InitDataHandlers launches goroutines to handle each labelblk instance's syncs.

func (*Data) MarshalJSON 

func (d *Data) MarshalJSON() ([]byte, error)

func (*Data) MoveElement 

func (d *Data) MoveElement(ctx *datastore.VersionedCtx, from, to dvid.Point3d, kafkaOff bool) error

func (*Data) ProcessLabelAnnotations 

func (d *Data) ProcessLabelAnnotations(v dvid.VersionID, f func(label uint64, elems ElementsNR)) error

ProcessLabelAnnotations will pass all annotations, label by label, to the given function.

func (*Data) RecreateDenormalizations 

func (d *Data) RecreateDenormalizations(ctx *datastore.VersionedCtx, inMemory, check bool)

RecreateDenormalizations will recreate label and tag denormalizations from the block-based elements.

func (*Data) ServeHTTP 

func (d *Data) ServeHTTP(uuid dvid.UUID, ctx *datastore.VersionedCtx, w http.ResponseWriter, r *http.Request) (activity map[string]interface{})

ServeHTTP handles all incoming HTTP requests for this data.

func (*Data) Shutdown 

func (d *Data) Shutdown(wg *sync.WaitGroup)

Shutdown terminates blocks until syncs are done then terminates background goroutines processing data.

func (*Data) StoreBlocks 

func (d *Data) StoreBlocks(ctx *datastore.VersionedCtx, r io.Reader, kafkaOff bool) (numBlocks int, err error)

StoreBlocks performs a synchronous store of synapses in JSON format, not returning until the data blocks are complete.

func (*Data) StoreElements 

func (d *Data) StoreElements(ctx *datastore.VersionedCtx, r io.Reader, kafkaOff bool) error

StoreElements performs a synchronous store of synapses in JSON format, not returning until the data and its denormalizations are complete.

func (*Data) StreamAll 

func (d *Data) StreamAll(ctx *datastore.VersionedCtx, w http.ResponseWriter) error

StreamAll returns all elements for this data instance.

func (*Data) StreamBlocks 

func (d *Data) StreamBlocks(ctx *datastore.VersionedCtx, w http.ResponseWriter, ext *dvid.Extents3d) error

StreamBlocks returns synapse elements for a given subvolume of image space.

type DeltaModifyElements 

type DeltaModifyElements struct {
	Add []ElementPos
	Del []ElementPos
}

DeltaModifyElements is a change in the elements assigned to a label. Need positions of elements because subscribers may have ROI filtering.

type DeltaSetElements 

type DeltaSetElements struct {
	Set []ElementPos
}

DeltaSetElements is a replacement of elements assigned to a label.

type Element 

type Element struct {
	ElementNR
	Rels Relationships
}

Element describes a synaptic element's properties, including Relationships.

func (Element) Copy 

func (e Element) Copy() *Element

type ElementNR 

type ElementNR struct {
	Pos  dvid.Point3d
	Kind ElementType
	Tags Tags              // Indexed
	Prop map[string]string // Non-Indexed
}

ElementNR describes a synaptic element's properties with No Relationships (NR), used for label and tag annotations while block-indexed annotations include the relationships.

func (ElementNR) Copy 

func (e ElementNR) Copy() *ElementNR

func (ElementNR) String 

func (e ElementNR) String() string

type ElementPos 

type ElementPos struct {
	Label uint64
	Kind  ElementType
	Pos   dvid.Point3d
}

ElementPos describes the label and kind of an annotation, useful for synchronizing changes in data to other data types like labelsz.

type ElementType 

type ElementType uint8

ElementType gives the type of a synaptic element. 

const (
	UnknownElem ElementType = iota
	PostSyn                 // Post-synaptic element
	PreSyn                  // Pre-synaptic element
	Gap                     // Gap junction
	Note                    // A note or bookmark with some description
)

func StringToElementType 

func StringToElementType(s string) ElementType

StringToElementType converts a string

func (ElementType) IsSynaptic 

func (e ElementType) IsSynaptic() bool

IsSynaptic returns true if the ElementType is some synaptic component.

func (ElementType) MarshalJSON 

func (e ElementType) MarshalJSON() ([]byte, error)

func (ElementType) String 

func (e ElementType) String() string

func (*ElementType) UnmarshalJSON 

func (e *ElementType) UnmarshalJSON(b []byte) error

type Elements 

type Elements []Element

Elements is a slice of Element, which includes relationships.

func (Elements) Len 

func (elems Elements) Len() int

func (Elements) Less 

func (elems Elements) Less(i, j int) bool

Less returns true if element[i] < element[j] where ordering is determined by Pos and Kind in that order. Relationships and Tags are not considered in ordering.

func (Elements) Normalize 

func (elems Elements) Normalize() Elements

Returns Elements that can be used for DeepEqual because all positions, relationships, and tags are sorted.

func (Elements) Swap 

func (elems Elements) Swap(i, j int)

type ElementsNR 

type ElementsNR []ElementNR

ElementsNR is a slice of elements without relationships.

func (ElementsNR) Len 

func (elems ElementsNR) Len() int

func (ElementsNR) Less 

func (elems ElementsNR) Less(i, j int) bool

Less returns true if element[i] < element[j] where ordering is determined by Pos and Kind in that order. Tags are not considered in ordering.

func (ElementsNR) Normalize 

func (elems ElementsNR) Normalize() ElementsNR

Normalize returns ElementsNR that can be used for DeepEqual because all positions and tags are sorted.

func (ElementsNR) Swap 

func (elems ElementsNR) Swap(i, j int)

type LabelElements 

type LabelElements map[uint64]ElementsNR

type LabelPoints 

type LabelPoints map[uint64][]dvid.Point3d

type Properties 

type Properties struct {
}

Properties are additional properties for data beyond those in standard datastore.Data.

type RelationType 

type RelationType uint8
const (
	UnknownRel RelationType = iota
	PostSynTo
	PreSynTo
	ConvergentTo
	GroupedWith
)

func (RelationType) MarshalJSON 

func (r RelationType) MarshalJSON() ([]byte, error)

func (*RelationType) UnmarshalJSON 

func (r *RelationType) UnmarshalJSON(b []byte) error

type Relationship 

type Relationship struct {
	Rel RelationType
	To  dvid.Point3d
}

Relationship is a link between two synaptic elements.

type Relationships 

type Relationships []Relationship

func (Relationships) Len 

func (r Relationships) Len() int

func (Relationships) Less 

func (r Relationships) Less(i, j int) bool

func (Relationships) Swap 

func (r Relationships) Swap(i, j int)

type Tag 

type Tag string

Tag is a string description of a synaptic element grouping, e.g., "convergent".

func DecodeTagTKey 

func DecodeTagTKey(tk storage.TKey) (Tag, error)

DecodeTagTKey returns the Tag corresponding to this type-specific key.

type Tags 

type Tags []Tag

func (Tags) Changes 

func (t Tags) Changes(t2 Tags) (removed, added Tags)

Changes returns tags removed or added from the receiver.

func (Tags) Len 

func (t Tags) Len() int

func (Tags) Less 

func (t Tags) Less(i, j int) bool

func (Tags) Removed 

func (t Tags) Removed(t2 Tags) Tags

Removed returns tags removed from the receiver.

func (Tags) Swap 

func (t Tags) Swap(i, j int)

type Type 

type Type struct {
	datastore.Type
}

func (*Type) Help 

func (dtype *Type) Help() string

func (*Type) NewDataService 

func (dtype *Type) NewDataService(uuid dvid.UUID, id dvid.InstanceID, name dvid.InstanceName, c dvid.Config) (datastore.DataService, error)

Source Files

View all Source files

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL
go.dev uses cookies from Google to deliver and enhance the quality of its services and to analyze traffic. Learn more.