labels

package
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 Go to latest Published: Aug 18, 2023 License: BSD-3-Clause Imports: 15 Imported by: 10

Documentation

Overview

Package labels supports label-based data types like labelblk, labelvol, labelsurf, labelsz, etc. Basic 64-bit label data and deltas are kept here so all label-based data types can use them without cyclic package dependencies, especially when writing code to synchronize across data instances.

Index

Constants

View Source 
const (
	IngestBlockEvent          = imageblk.IngestBlockEvent
	MutateBlockEvent          = imageblk.MutateBlockEvent
	DeleteBlockEvent          = imageblk.DeleteBlockEvent
	SparsevolStartEvent       = "SPARSEVOL_START"
	SparsevolModEvent         = "SPARSEVOL_MOD"
	SparsevolEndEvent         = "SPARSEVOL_END"
	ChangeSizeEvent           = "LABEL_SIZE_CHANGE"
	MergeStartEvent           = "MERGE_START"
	MergeBlockEvent           = "MERGE_BLOCK"
	MergeEndEvent             = "MERGE_END"
	SplitStartEvent           = "SPLIT_START"
	SplitLabelEvent           = "SPLIT_LABEL"
	SplitEndEvent             = "SPLIT_END"
	CleaveStartEvent          = "CLEAVE_START"
	CleaveLabelEvent          = "CLEAVE_LABEL"
	CleaveEndEvent            = "CLEAVE_END"
	SupervoxelSplitStartEvent = "SV_SPLIT_START"
	SupervoxelSplitEvent      = "SV_SPLIT"
	SupervoxelSplitEndEvent   = "SV_SPLIT_END"
)

Label change event identifiers

View Source 
const DefaultBlockSize = DefaultSubBlocksPerBlock * SubBlockSize
View Source 
const DefaultSubBlocksPerBlock = 8
View Source 
const (
	// MaxAllowedLabel is the largest label that should be allowed by DVID if we want
	// to take into account the maximum integer size within Javascript (due to its
	// underlying use of a double float for numbers, leading to max int = 2^53 - 1).
	// This would circumvent the need to use strings within JSON (e.g., the Google
	// solution) to represent integer labels that could exceed the max javascript
	// number.  It would require adding a value check on each label voxel of a
	// mutation request, which might be too much of a hit to handle an edge case.
	MaxAllowedLabel = 9007199254740991
)
View Source 
const MaxBlockSize = 1024 // N^3 < max uint32, so N <= 2^10
View Source 
const MaxSubBlockSize = MaxBlockSize / SubBlockSize
View Source 
const SubBlockSize = 8

Variables

This section is empty.

Functions

func BlockIndexToIZYXString 

func BlockIndexToIZYXString(zyx uint64) dvid.IZYXString

BlockIndexToIZYXString decodes a packed block index into an IZYXString. At most, each block int32 coordinate can be 20 bits.

func DecodeBlockIndex 

func DecodeBlockIndex(zyx uint64) (x, y, z int32)

DecodeBlockIndex decodes a packed block index into int32 coordinates. At most, each block int32 coordinate can be 20 bits.

func DownresLabels 

func DownresLabels(hires []byte, hisize dvid.Point3d) (lores []byte, err error)

DownresLabels takes an array of uint64 in []byte format and returns a 2x down-sampled array of uint64. An error is returned if size is not multiple of two or passed array is incorrect size.

func EncodeBlockIndex 

func EncodeBlockIndex(x, y, z int32) (zyx uint64)

EncodeBlockIndex converts signed (x,y,z) block coordinate into a single uint64, which is packed in ZYX order with MSB empty, the most-significant 21 bits is Z (21st bit is sign flag), next 21 bits is Y, then least-significant 21 bits is X.

func IZYXStringToBlockIndex 

func IZYXStringToBlockIndex(s dvid.IZYXString) (zyx uint64, err error)

IZYXStringToBlockIndex returns an encoded Block Index for a given IZYXString, returning an error if the IZYXString is formatted incorrectly.

func LogAffinity 

func LogAffinity(d dvid.Data, v dvid.VersionID, aff Affinity) error

func LogCleave 

func LogCleave(d dvid.Data, v dvid.VersionID, op CleaveOp) error

LogCleave logs the cleave of supervoxels to a label.

func LogMapping 

func LogMapping(d dvid.Data, v dvid.VersionID, op MappingOp) error

LogMapping logs the mapping of supervoxels to a label.

func LogMappings 

func LogMappings(d dvid.Data, v dvid.VersionID, ops *proto.MappingOps) error

LogMappings logs a collection of mapping operations to a UUID.

func LogMerge 

func LogMerge(d dvid.Data, v dvid.VersionID, op MergeOp) error

LogMerge logs the merge of supervoxels to a label.

func LogRenumber added in v0.9.17 

func LogRenumber(d dvid.Data, v dvid.VersionID, mutID, origLabel, newLabel uint64) error

LogRenumber logs the merge of supervoxels to a label.

func LogSplit 

func LogSplit(d dvid.Data, v dvid.VersionID, op SplitOp) error

LogSplit logs the split of a set of voxels from the underlying label.

func LogSupervoxelSplit 

func LogSupervoxelSplit(d dvid.Data, v dvid.VersionID, op SplitSupervoxelOp) error

LogSupervoxelSplit logs the split of a supervoxel into two separate supervoxels.

func MergeStart 

func MergeStart(iv dvid.InstanceVersion, op MergeOp) error

MergeStart handles label map caches during an active merge operation. Note that if there are multiple synced label instances, the InstanceVersion will always be the labelblk instance. Multiple merges into a single label are allowed, but chained merges are not. For example, you can merge label 1, 2, and 3 into 4, then later merge 6 into 4. However, you cannot concurrently merge label 4 into some other label because there can be a race condition between 3 -> 4 and 4 -> X.

func MergeStop 

func MergeStop(iv dvid.InstanceVersion, op MergeOp)

MergeStop marks the end of a merge operation.

func SplitStart 

func SplitStart(iv dvid.InstanceVersion, op DeltaSplitStart) error

SplitStart checks current label map to see if the split conflicts.

func SplitStop 

func SplitStop(iv dvid.InstanceVersion, op DeltaSplitEnd)

SplitStop marks the end of a split operation.

func StreamLog 

func StreamLog(d dvid.Data, v dvid.VersionID, ch chan storage.LogMessage) error

func WriteBinaryBlocks 

func WriteBinaryBlocks(mainLabel uint64, lbls Set, op *OutputOp, bounds dvid.Bounds)

WriteBinaryBlocks writes a compact serialization of a binarized Block to the supplied Writer. The serialization is a header + stream of blocks. The header is the following: 

 3 * uint32      values of gx, gy, and gz
 uint64          foreground label

The format of each binary block in the stream is detailed by the WriteBinaryBlock() function.

func WriteRLEs 

func WriteRLEs(lbls Set, op *OutputOp, bounds dvid.Bounds)

WriteRLEs, like WriteBinaryBlocks, writes a compact serialization of a binarized Block to the supplied Writer. In this case, the serialization uses little-endian encoded integers and RLEs with the repeating units of the following format: 

int32   Coordinate of run start (dimension 0)
int32   Coordinate of run start (dimension 1)
int32   Coordinate of run start (dimension 2)
int32   Length of run in X direction

The offset is the DVID space offset to the first voxel in the Block. After the RLEs have been written to the io.Writer, an error message is sent down the given errCh.

Types

type Affinity 

type Affinity struct {
	Label1 uint64
	Label2 uint64
	Value  float32
}

Affinity represents a float value associated with a two-tuple of labels.

type BinaryBlock 

type BinaryBlock struct {
	Offset dvid.Point3d // voxel offset for the first voxels in this block
	Size   dvid.Point3d
	Label  uint64
	Voxels []bool
}

func ReceiveBinaryBlocks 

func ReceiveBinaryBlocks(r io.Reader) ([]BinaryBlock, error)

ReceiveBinaryBlocks returns a slice of BinaryBlock, easily parseable but not necessarily optimally compressed format.

func (*BinaryBlock) Read 

func (b *BinaryBlock) Read(r io.Reader, gx, gy, gz int32, label uint64) error

func (BinaryBlock) String 

func (b BinaryBlock) String() string

type Block 

type Block struct {
	Labels []uint64     // labels in Block.
	Size   dvid.Point3d // # voxels in each dimension for this block

	NumSBLabels []uint16 // # of labels for each sub-block
	SBIndices   []uint32 // indices into Labels array
	SBValues    []byte   // compressed voxel values giving index into SBIndices.
	// contains filtered or unexported fields
}

Block is the unit of storage for compressed DVID labels. It is inspired by the Neuroglancer compression scheme and makes the following changes: (1) a block-level label list with sub-block indices into the list (minimal required bits vs 64 bits in original Neuroglancer scheme), (2) the number of bits for encoding values is not required to be a power of two. A block-level label list allows easy sharing of labels between sub-blocks, and sub-block storage can be more efficient due to the smaller index (at the cost of an indirection) and better encoded value packing (at the cost of byte alignment). In both cases memory is gained for increased computation.

Blocks cover nx * ny * nz voxels. This implementation allows any choice of nx, ny, and nz with two restrictions: (1) nx, ny, and nz must be a multiple of 8 greater than 16, and (2) the total number of labels cannot exceed the capacity of a uint32.

Internally, labels are stored in 8x8x8 sub-blocks. There are gx * gy * gz sub-blocks where gx = nx / 8; gy = ny / 8; gz = nz / 8.

The byte layout will be the following if there are N labels in the Block: 

     3 * uint32      values of gx, gy, and gz
     uint32          # of labels (N), cannot exceed uint32.
     N * uint64      packed labels in little-endian format.  Label 0 can be
							used to represent deleted labels, e.g., after a merge
							operation to avoid changing all sub-block indices.

     ----- Data below is only included if N > 1, otherwise it is a solid block.
           Nsb = # sub-blocks = gx * gy * gz

     Nsb * uint16        # of labels for sub-blocks (Ns[i]).
                             Each uint16 Ns[i] = # labels for sub-block i.
                             If Ns[i] == 0, the sub-block has no data
								(uninitialized), which is useful for constructing
								Blocks with sparse data.

     Nsb * Ns * uint32   label indices for sub-blocks where Ns = sum of Ns[i]
								over all sub-blocks. For each sub-block i, we have
								Ns[i] label indices of lBits.

     Nsb * values        sub-block indices for each voxel.
                             Data encompasses 512 * ceil(log2(Ns[i])) bits,
								padded so no two sub-blocks have indices in the
								same byte. At most we use 9 bits per voxel for up
								to the 512 labels in sub-block. A value gives the
								sub-block index which points to the index into
                             the N labels.  If Ns[i] <= 1, there are no values.
								If Ns[i] = 0, the 8x8x8 voxels are set to label 0.
								If Ns[i] = 1, all voxels are the given label index.

func MakeBlock 

func MakeBlock(uint64array []byte, bsize dvid.Point3d) (*Block, error)

MakeBlock returns a compressed label Block given a packed little-endian uint64 label array. It is the inverse of MakeLabelVolume(). There is no sharing of underlying memory between the returned Block and the given byte slice.

func MakeSolidBlock 

func MakeSolidBlock(label uint64, blockSize dvid.Point3d) *Block

MakeSolidBlock returns a Block that represents a single label of the given block size.

func SubvolumeToBlock 

func SubvolumeToBlock(sv *dvid.Subvolume, lbls []byte, idx dvid.IndexZYX, bsize dvid.Point3d) (*Block, error)

SubvolumeToBlock converts a portion of the given label array into a compressed Block. It accepts a packed little-endian uint64 label array and a description of its subvolume, i.e., its extents in dvid space, and returns a compressed Block for the given chunk when tiling dvid space with the given chunk size.

func (Block) CalcNumLabels 

func (b Block) CalcNumLabels(prev *Block) map[uint64]int32

CalcNumLabels calculates the change in the number of voxels under each non-zero label. If a previous Block is given, the change is calculated from the previous numbers.

func (Block) CompressGZIP 

func (b Block) CompressGZIP() ([]byte, error)

CompressGZIP returns a gzip compressed encoding of the serialized block data.

func (*Block) Downres 

func (b *Block) Downres(octants [8]*Block) error

Downres takes eight Blocks that represent higher-resolution octants (by 2x) of the receiving block, and modifies the receiving Block to be a half-resolution representation. If a given octant is a nil Block, the receiving Block is not modified for that portion of the higher-resolution octant.

func (*Block) DownresFast added in v0.9.17 

func (b *Block) DownresFast(octants [8]*Block) error

TODO -- Not completely working, so stick with DownresSlow() until this becomes rises in priority.

func (*Block) DownresSlow 

func (b *Block) DownresSlow(octants [8]*Block) error

DownresSlow is same as Downres() but uses simpler and more memory/compute-intensive approach to computing down-res block.

func (*Block) GetPointLabels 

func (b *Block) GetPointLabels(pts []dvid.Point3d) []uint64

GetPointLabels returns the labels associated with each point by traversing the compressed data. If the point is outside the block, a zero is returned.

func (Block) MakeLabelVolume 

func (b Block) MakeLabelVolume() (uint64array []byte, size dvid.Point3d)

MakeLabelVolume returns a byte slice with packed little-endian uint64 labels in ZYX order, i.e., a uint64 for each voxel where consecutive values are in the (x,y,z) order: (0,0,0), (1,0,0), (2,0,0) ... (0,1,0) There is no sharing of memory between the returned byte slice and the Block data.

func (Block) MarshalBinary 

func (b Block) MarshalBinary() ([]byte, error)

MarshalBinary implements the encoding.BinaryMarshaler interface. Note that for efficiency, the returned byte slice will share memory with the receiver Block.

func (*Block) MergeLabels 

func (b *Block) MergeLabels(op MergeOp) (merged *Block, err error)

MergeLabels returns a new block that has computed the given MergeOp.

func (*Block) ReplaceLabel 

func (b *Block) ReplaceLabel(target, newLabel uint64) (replace *Block, replaceSize uint64, err error)

ReplaceLabel replaces references to the target label with newLabel.

func (*Block) ReplaceLabels 

func (b *Block) ReplaceLabels(mapping map[uint64]uint64) (replace *Block, replaced bool, err error)

ReplaceLabels replaces labels according to mapping and doesn't compute sizes.

func (Block) StringDump 

func (b Block) StringDump(verbose bool) string

StringDump returns a string that lists pretty-printed data from the block.

func (*Block) UnmarshalBinary 

func (b *Block) UnmarshalBinary(data []byte) error

UnmarshalBinary implements the encoding.BinaryUnmarshaler interface. The source byte slice is copied into a new 8-byte aligned slice so the receiver block does not depend on the passed slice.

func (*Block) Value 

func (b *Block) Value(pos dvid.Point3d) uint64

Value returns the label for a voxel using its 3d location within block. If the given location is outside the block extent, label 0 is returned. Note that this function is inefficient for multi-voxel value retrieval.

func (Block) WriteGoogleCompression 

func (b Block) WriteGoogleCompression(w io.Writer) error

GoogleCompression writes label compression compliant with the Google Neuroglancer specification: https://goo.gl/IyQbzL

func (Block) WriteLabelVolume added in v1.0.0 

func (b Block) WriteLabelVolume(w io.Writer) error

WriteLabelVolume streams uncompressed, packed little-endian uint64 labels in ZYX order, i.e., a uint64 for each voxel where consecutive values are in the (x,y,z) order: (0,0,0), (1,0,0), (2,0,0) ... (0,1,0)

type CleaveOp 

type CleaveOp struct {
	MutID              uint64
	Target             uint64
	CleavedLabel       uint64
	CleavedSupervoxels []uint64
}

CleaveOp represents a cleave of a label using supervoxels.

type Counts 

type Counts struct {
	sync.RWMutex
	// contains filtered or unexported fields
}

Counts is a thread-safe type for counting label references.

func (*Counts) Decr 

func (c *Counts) Decr(label uint64)

Decr decrements the count for a label.

func (*Counts) Empty 

func (c *Counts) Empty() bool

Empty returns true if there are no counts.

func (*Counts) Incr 

func (c *Counts) Incr(label uint64)

Incr increments the count for a label.

func (*Counts) Value 

func (c *Counts) Value(label uint64) int

Value returns the count for a label.

type DeltaDeleteSize 

type DeltaDeleteSize struct {
	Label    uint64
	OldSize  uint64
	OldKnown bool // true if OldSize is valid, otherwise delete all size k/v for this label.
}

DeltaDeleteSize gives info to delete a label's size.

type DeltaMerge 

type DeltaMerge struct {
	MergeOp
	Blocks       dvid.IZYXSlice               // not nil if labelarray used.
	BlockMap     map[dvid.IZYXString]struct{} // not nil if labelblk used, to be deprecated.
	TargetVoxels uint64
	MergedVoxels uint64
}

DeltaMerge describes the labels and blocks affected by a merge operation. It is sent during a MergeBlockEvent.

type DeltaMergeEnd 

type DeltaMergeEnd struct {
	MergeOp
}

DeltaMergeEnd is the data sent during a MergeEndEvent.

type DeltaMergeStart 

type DeltaMergeStart struct {
	MergeOp
}

DeltaMergeStart is the data sent during a MergeStartEvent.

type DeltaModSize 

type DeltaModSize struct {
	Label      uint64
	SizeChange int64 // Adds to old label size
}

DeltaModSize gives info to modify an existing label size without knowing the old size.

type DeltaNewSize 

type DeltaNewSize struct {
	Label uint64
	Size  uint64
}

DeltaNewSize is a new label being introduced.

type DeltaReplaceSize 

type DeltaReplaceSize struct {
	Label   uint64
	OldSize uint64
	NewSize uint64
}

DeltaReplaceSize gives info to precisely remove an old label size and add the updated size.

type DeltaSparsevol 

type DeltaSparsevol struct {
	Label uint64
	Mods  dvid.BlockRLEs
}

DeltaSparsevol describes a change to an existing label.

type DeltaSplit 

type DeltaSplit struct {
	MutID        uint64
	OldLabel     uint64
	NewLabel     uint64
	Split        dvid.BlockRLEs
	SortedBlocks dvid.IZYXSlice
	SplitVoxels  uint64
}

DeltaSplit describes the voxels modified during a split operation. The Split field may be null if this is a coarse split only defined by block indices.

type DeltaSplitEnd 

type DeltaSplitEnd struct {
	OldLabel uint64
	NewLabel uint64
}

DeltaSplitEnd is the data sent during a SplitEndEvent.

type DeltaSplitStart 

type DeltaSplitStart struct {
	OldLabel uint64
	NewLabel uint64
}

DeltaSplitStart is the data sent during a SplitStartEvent.

type Index 

type Index struct {
	proto.LabelIndex
}

func (*Index) Add 

func (idx *Index) Add(idx2 *Index) error

Add adds the given Index to the receiver.

func (*Index) Cleave 

func (idx *Index) Cleave(cleaveLabel uint64, toCleave []uint64) (cleavedSize, remainSize uint64, cidx *Index)

Cleave the given supervoxels from an index and returns a new index, modifying both receiver and creating new cleaved index.

func (Index) Equal 

func (idx Index) Equal(idx2 Index) bool

Equal returns true if the receiver and passed Index are equivalent.

func (*Index) FitToBounds 

func (idx *Index) FitToBounds(bounds *dvid.OptionalBounds) error

FitToBounds modifies the receiver to fit the given optional block bounds.

func (*Index) GetBlockIndices 

func (idx *Index) GetBlockIndices() dvid.IZYXSlice

GetBlockIndices returns the block coordinates within the Index.

func (*Index) GetProcessedBlockIndices 

func (idx *Index) GetProcessedBlockIndices(scale uint8, bounds dvid.Bounds, supervoxel uint64) (dvid.IZYXSlice, error)

GetProcessedBlockIndices returns the blocks for an index, possibly bounded in and with down-res applied by the given scale. If supervoxel is 0, assumes that all blocks should be returned after the other restrictions, otherwise it screens for only blocks that contain the given supervoxel id.

func (*Index) GetSupervoxelCount 

func (idx *Index) GetSupervoxelCount(supervoxel uint64) (count uint64)

GetSupervoxelCount returns the # of voxels for a supervoxel in an Index. Note that the counts are uint64 because although each block might only hold a # of voxels < max uint32, a massive supervoxel could hold many more.

func (*Index) GetSupervoxelCounts 

func (idx *Index) GetSupervoxelCounts() (counts map[uint64]uint64)

GetSupervoxelCounts returns the # of voxels for each supervoxel in an Index. Note that the counts are uint64 because although each block might only hold a # of voxels < max uint32, a massive supervoxel could hold many more.

func (*Index) GetSupervoxels 

func (idx *Index) GetSupervoxels() Set

GetSupervoxels returns a set of supervoxels within the receiver Index.

func (*Index) GetSupervoxelsBlocks 

func (idx *Index) GetSupervoxelsBlocks(supervoxels Set) map[dvid.IZYXString]struct{}

GetSupervoxelsBlocks returns the blocks for a given list of supervoxels.

func (*Index) LimitToSupervoxel 

func (idx *Index) LimitToSupervoxel(supervoxel uint64) (*Index, error)

LimitToSupervoxel returns a copy of the index but with only the given supervoxel

func (*Index) ModifyBlocks 

func (idx *Index) ModifyBlocks(label uint64, sc SupervoxelChanges) error

ModifyBlocks modifies the receiver Index to incorporate supervoxel changes among the given blocks.

func (Index) NumVoxels 

func (idx Index) NumVoxels() uint64

NumVoxels returns the number of voxels for the Index.

func (Index) StringDump 

func (idx Index) StringDump(showMutationInfo bool) string

StringDump returns a description of the data within the Index. If showMutationInfo is true, the mutation ID and information about modification is also printed.

func (*Index) SupervoxelsPresent 

func (idx *Index) SupervoxelsPresent(supervoxels Set) (present map[uint64]bool)

SupervoxelsPresent checks whether each label from a Set are within the index.

type Mapping 

type Mapping struct {
	sync.RWMutex
	// contains filtered or unexported fields
}

Mapping is a thread-safe, mapping of labels to labels in both forward and backward direction. Mutation of a Mapping instance can only be done through labels.MergeCache.

func LabelMap 

func LabelMap(iv dvid.InstanceVersion) *Mapping

LabelMap returns a label mapping for a version of a data instance. If no label mapping is available, a nil is returned.

func (*Mapping) ConstituentLabels 

func (m *Mapping) ConstituentLabels(final uint64) Set

ConstituentLabels returns a set of labels that will be mapped to the given label. The set will always include the given label.

func (*Mapping) FinalLabel 

func (m *Mapping) FinalLabel(start uint64) (uint64, bool)

FinalLabel follows mappings from a start label until a final mapped label is reached.

func (*Mapping) Get 

func (m *Mapping) Get(label uint64) (uint64, bool)

Get returns the mapping or false if no mapping exists.

type MappingOp 

type MappingOp struct {
	MutID    uint64
	Mapped   uint64
	Original Set
}

MappingOp represents a mapping of a set of original labels into a mapped lapel.

func ReadMappingLog 

func ReadMappingLog(d dvid.Data, v dvid.VersionID) ([]MappingOp, error)

func (MappingOp) Marshal 

func (op MappingOp) Marshal() (serialization []byte, err error)

Marshal returns a proto.MappingOp serialization

type MergeOp 

type MergeOp struct {
	MutID  uint64
	Target uint64
	Merged Set
}

MergeOp represents the merging of a set of labels into a target label.

func (MergeOp) String 

func (op MergeOp) String() string

type MergeTuple 

type MergeTuple []uint64

MergeTuple represents a merge of labels. Its first element is the destination label and all later elements in the slice are labels to be merged. It's an easy JSON representation as a list of labels.

func (MergeTuple) Op 

func (t MergeTuple) Op() (MergeOp, error)

Op converts a MergeTuple into a MergeOp.

type OutputOp 

type OutputOp struct {
	sync.Mutex // lock on writing
	// contains filtered or unexported fields
}

OutputOp provides a way to communicate with writing goroutines, TODO: concurrency support on the given io.Writer.

func NewOutputOp 

func NewOutputOp(w io.Writer) *OutputOp

func (OutputOp) Finish 

func (op OutputOp) Finish() error

Finish signals all input to an OutputOp is done and waits for completion. Any error from the OutputOp is returned.

func (OutputOp) Process 

func (op OutputOp) Process(pb *PositionedBlock)

type PositionedBlock 

type PositionedBlock struct {
	Block
	BCoord dvid.IZYXString
}

PositionedBlock is a Block that also knows its position in DVID space via a chunk coordinate.

func (PositionedBlock) DoSplitWithStats 

func (pb PositionedBlock) DoSplitWithStats(op SplitOp, m *SVSplitMap, newLabelFunc func() (uint64, error)) (split *Block, counts map[uint64]SVSplitCount, err error)

DoSplitWithStats writes a new label into the RLEs defined by the split and returns how each supervoxel (counts key) was split. This is done by doing full expansion of block into uint64 array.

func (PositionedBlock) OffsetDVID 

func (pb PositionedBlock) OffsetDVID() (dvid.Point3d, error)

OffsetDVID returns the DVID voxel coordinate corresponding to the first voxel of the Block, i.e., the lowest (x,y,z).

func (PositionedBlock) Split 

func (pb PositionedBlock) Split(op SplitOp) (split *Block, keptSize, splitSize uint64, err error)

Split a target label using RLEs within a block. Only the target label is split. A nil split block is returned if target label is not within block. TODO: If RLEs continue to be used for splits, refactor / split up to make this more readable.

func (PositionedBlock) SplitStats 

func (pb PositionedBlock) SplitStats(rles dvid.RLEs, m *SVSplitMap, newLabelFunc func() (uint64, error)) (counts map[uint64]SVSplitCount, err error)

SplitStats checks voxels under the split RLEs and returns how each supervoxel should be split without doing a split. This is done by doing full expansion of block into uint64 array.

func (PositionedBlock) SplitSupervoxel 

func (pb PositionedBlock) SplitSupervoxel(op SplitSupervoxelOp) (split *Block, keptSize, splitSize uint64, err error)

SplitSupervoxel splits a target supervoxel using RLEs within a block.

func (PositionedBlock) SplitSupervoxels 

func (pb PositionedBlock) SplitSupervoxels(rles dvid.RLEs, svsplits map[uint64]SVSplit) (split *Block, err error)

SplitSupervoxels replaces all split supervoxels in a block with either a split label or a remain label depending on whether it falls under the split RLEs.

func (PositionedBlock) String 

func (pb PositionedBlock) String() string

func (*PositionedBlock) WriteBinaryBlock 

func (pb *PositionedBlock) WriteBinaryBlock(indices map[uint32]struct{}, hasBackground bool, op *OutputOp, bounds dvid.Bounds) error

WriteBinaryBlock writes the binary version of a Block to the supplied Writer, where the serialized data represents just the label voxels. By definition, a binary block has at most two labels (0 = background, 1 = given label) and encoding is a bit per voxel. The binary format is related to the Google and internal DVID label block compression but is simplified, the DVID space offset of the block is included, and the sub-block data are arranged to allow streaming.

Internally, the mask is stored in 8x8x8 sub-blocks. There are gx * gy * gz sub-blocks where gx = nx / 8; gy = ny / 8; gz = nz / 8, and (gx, gy, gz) is relayed in a header outside of the data returned by this function. For example, for a full sparse volume response, there would be a header followed by some number of these binary blocks.

The byte layout will be the following: 

3 * int32       offset of first voxel of Block in DVID space (x, y, z)
byte            content flag:
                0 = background ONLY  (no more data for this block)
                1 = foreground ONLY  (no more data for this block)
                2 = both background and foreground so stream of sub-blocks required.

Stream of gx * gy * gz sub-blocks with the following data:

byte            content flag:
                0 = background ONLY  (no more data for this sub-block)
                1 = foreground ONLY  (no more data for this sub-block)
                2 = both background and foreground so mask data required.
mask            64 byte bitmask where each voxel is 0 (background) or 1 (foreground)

type SVSplit 

type SVSplit struct {
	Split  uint64 // label corresponding to split sparse volume
	Remain uint64 // relabeling of supervoxel that remains after split
}

SVSplit provides labels after a supervoxel split

type SVSplitCount 

type SVSplitCount struct {
	SVSplit
	Voxels uint32 // number of voxels split
}

SVSplitCount provides both labels and the # voxels after a supervoxel split.

type SVSplitMap 

type SVSplitMap struct {
	sync.RWMutex
	Splits map[uint64]SVSplit
}

SVSplitMap is a thread-safe mapping of supervoxels labels to their new split labels.

type Set 

type Set map[uint64]struct{}

Set is a set of labels.

func NewSet 

func NewSet(lbls ...uint64) Set

Merge returns a set made of the given labels.

func (Set) Copy 

func (s Set) Copy() Set

Copy returns a duplicate of the Set.

func (Set) Exists 

func (s Set) Exists(i uint64) bool

Exists returns true if the given uint64 is present in the Set.

func (Set) Merge 

func (s Set) Merge(s2 Set)

Merge adds the elements in the given set to the receiver.

func (Set) String 

func (s Set) String() string

type SplitOp 

type SplitOp struct {
	MutID    uint64
	Target   uint64
	NewLabel uint64
	RLEs     dvid.RLEs
	Coarse   bool // true if the RLEs are block coords (coarse split), not voxels.
	SplitMap map[uint64]SVSplit
}

SplitOp represents a split with the sparse volume of the new label.

type SplitSupervoxelOp 

type SplitSupervoxelOp struct {
	MutID            uint64
	Supervoxel       uint64
	SplitSupervoxel  uint64
	RemainSupervoxel uint64
	Split            dvid.BlockRLEs
}

SplitSupervoxelOp describes a supervoxel split.

type SupervoxelChanges 

type SupervoxelChanges map[uint64]map[dvid.IZYXString]int32

SupervoxelChanges tabulates changes in voxels among supervoxels across blocks.

Source Files

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