Exemple #1
0
func (d *Data) processSplit(v dvid.VersionID, delta labels.DeltaSplit) {
	timedLog := dvid.NewTimeLog()

	mutID := d.NewMutationID()
	splitOpStart := labels.DeltaSplitStart{delta.OldLabel, delta.NewLabel}
	splitOpEnd := labels.DeltaSplitEnd{delta.OldLabel, delta.NewLabel}
	iv := dvid.InstanceVersion{d.DataUUID(), v}
	labels.SplitStart(iv, splitOpStart)

	d.StartUpdate()
	if delta.Split == nil {
		// Coarse Split
		for _, izyxStr := range delta.SortedBlocks {
			n := izyxStr.Hash(numBlockHandlers)
			d.MutAdd(mutID)
			op := splitOp{
				mutID:    mutID,
				oldLabel: delta.OldLabel,
				newLabel: delta.NewLabel,
				block:    izyxStr,
			}
			d.procCh[n] <- procMsg{op: op, v: v}
		}
	} else {
		// Fine Split
		for izyxStr, blockRLEs := range delta.Split {
			n := izyxStr.Hash(numBlockHandlers)
			d.MutAdd(mutID)
			op := splitOp{
				mutID:    mutID,
				oldLabel: delta.OldLabel,
				newLabel: delta.NewLabel,
				rles:     blockRLEs,
				block:    izyxStr,
			}
			d.procCh[n] <- procMsg{op: op, v: v}
		}
	}
	// Wait for all blocks to be split then mark end of split op.
	go func() {
		d.MutWait(mutID)
		d.MutDelete(mutID)
		labels.SplitStop(iv, splitOpEnd)
		timedLog.Debugf("labelblk sync complete for split of %d -> %d", delta.OldLabel, delta.NewLabel)
		d.StopUpdate()
		d.publishDownresCommit(v, mutID)
	}()
}
Exemple #2
0
// SplitCoarseLabels splits a portion of a label's voxels into a given split label or, if the given split
// label is 0, a new label, which is returned.  The input is a binary sparse volume defined by block
// coordinates and should be the smaller portion of a labeled region-to-be-split.
//
// EVENTS
//
// labels.SplitStartEvent occurs at very start of split and transmits labels.DeltaSplitStart struct.
//
// labels.SplitBlockEvent occurs for every block of a split label and transmits labels.DeltaSplit struct.
//
// labels.SplitEndEvent occurs at end of split and transmits labels.DeltaSplitEnd struct.
//
func (d *Data) SplitCoarseLabels(v dvid.VersionID, fromLabel, splitLabel uint64, r io.ReadCloser) (toLabel uint64, err error) {
	store, err := d.GetOrderedKeyValueDB()
	if err != nil {
		err = fmt.Errorf("Data type labelvol had error initializing store: %v\n", err)
		return
	}
	batcher, ok := store.(storage.KeyValueBatcher)
	if !ok {
		err = fmt.Errorf("Data type labelvol requires batch-enabled store, which %q is not\n", store)
		return
	}

	// Create a new label id for this version that will persist to store
	if splitLabel != 0 {
		toLabel = splitLabel
		dvid.Debugf("Splitting coarse subset of label %d into given label %d ...\n", fromLabel, splitLabel)
	} else {
		toLabel, err = d.NewLabel(v)
		if err != nil {
			return
		}
		dvid.Debugf("Splitting coarse subset of label %d into new label %d ...\n", fromLabel, toLabel)
	}

	evt := datastore.SyncEvent{d.DataUUID(), labels.SplitStartEvent}
	splitOpStart := labels.DeltaSplitStart{fromLabel, toLabel}
	splitOpEnd := labels.DeltaSplitEnd{fromLabel, toLabel}

	// Make sure we can split given current merges in progress
	if err := labels.SplitStart(d.getMergeIV(v), splitOpStart); err != nil {
		return toLabel, err
	}
	defer labels.SplitStop(d.getMergeIV(v), splitOpEnd)

	// Signal that we are starting a split.
	msg := datastore.SyncMessage{labels.SplitStartEvent, v, splitOpStart}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		return 0, err
	}

	// Read the sparse volume from reader.
	var splits dvid.RLEs
	splits, err = dvid.ReadRLEs(r)
	if err != nil {
		return
	}
	numBlocks, _ := splits.Stats()

	// Order the split blocks
	splitblks := make(dvid.IZYXSlice, numBlocks)
	n := 0
	for _, rle := range splits {
		p := rle.StartPt()
		run := rle.Length()
		for i := int32(0); i < run; i++ {
			izyx := dvid.IndexZYX{p[0] + i, p[1], p[2]}
			splitblks[n] = izyx.ToIZYXString()
			n++
		}
	}
	sort.Sort(splitblks)

	// Iterate through the split blocks, read the original block and change labels.
	// TODO: Modifications should be transactional since it's GET-PUT, therefore use
	// hash on block coord to direct it to block-specific goroutine; we serialize
	// requests to handle concurrency.
	ctx := datastore.NewVersionedCtx(d, v)
	batch := batcher.NewBatch(ctx)

	var toLabelSize uint64
	for _, splitblk := range splitblks {
		// Get original block
		tk := NewTKey(fromLabel, splitblk)
		val, err := store.Get(ctx, tk)
		if err != nil {
			return toLabel, err
		}
		if val == nil {
			return toLabel, fmt.Errorf("Split block %s is not part of original label %d", splitblk, fromLabel)
		}
		var rles dvid.RLEs
		if err := rles.UnmarshalBinary(val); err != nil {
			return toLabel, fmt.Errorf("Unable to unmarshal RLE for original labels in block %s", splitblk)
		}
		numVoxels, _ := rles.Stats()
		toLabelSize += numVoxels

		// Delete the old block and save the sparse volume but under a new label.
		batch.Delete(tk)
		tk2 := NewTKey(toLabel, splitblk)
		batch.Put(tk2, val)
	}

	if err := batch.Commit(); err != nil {
		dvid.Errorf("Batch PUT during split of %q label %d: %v\n", d.DataName(), fromLabel, err)
	}

	// Publish split event
	evt = datastore.SyncEvent{d.DataUUID(), labels.SplitLabelEvent}
	msg = datastore.SyncMessage{labels.SplitLabelEvent, v, labels.DeltaSplit{fromLabel, toLabel, nil, splitblks}}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		return 0, err
	}

	// Publish change in label sizes.
	delta := labels.DeltaNewSize{
		Label: toLabel,
		Size:  toLabelSize,
	}
	evt = datastore.SyncEvent{d.DataUUID(), labels.ChangeSizeEvent}
	msg = datastore.SyncMessage{labels.ChangeSizeEvent, v, delta}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		return 0, err
	}

	delta2 := labels.DeltaModSize{
		Label:      fromLabel,
		SizeChange: int64(-toLabelSize),
	}
	evt = datastore.SyncEvent{d.DataUUID(), labels.ChangeSizeEvent}
	msg = datastore.SyncMessage{labels.ChangeSizeEvent, v, delta2}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		return 0, err
	}

	// Publish split end
	evt = datastore.SyncEvent{d.DataUUID(), labels.SplitEndEvent}
	msg = datastore.SyncMessage{labels.SplitEndEvent, v, splitOpEnd}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		return 0, err
	}
	dvid.Infof("Split %d voxels from label %d to label %d\n", toLabelSize, fromLabel, toLabel)

	return toLabel, nil
}
Exemple #3
0
// SplitLabels splits a portion of a label's voxels into a given split label or, if the given split
// label is 0, a new label, which is returned.  The input is a binary sparse volume and should
// preferably be the smaller portion of a labeled region.  In other words, the caller should chose
// to submit for relabeling the smaller portion of any split.  It is assumed that the given split
// voxels are within the fromLabel set of voxels and will generate unspecified behavior if this is
// not the case.
//
// EVENTS
//
// labels.SplitStartEvent occurs at very start of split and transmits labels.DeltaSplitStart struct.
//
// labels.SplitBlockEvent occurs for every block of a split label and transmits labels.DeltaSplit struct.
//
// labels.SplitEndEvent occurs at end of split and transmits labels.DeltaSplitEnd struct.
//
func (d *Data) SplitLabels(v dvid.VersionID, fromLabel, splitLabel uint64, r io.ReadCloser) (toLabel uint64, err error) {
	store, err := d.GetOrderedKeyValueDB()
	if err != nil {
		err = fmt.Errorf("Data type labelvol had error initializing store: %v\n", err)
		return
	}
	batcher, ok := store.(storage.KeyValueBatcher)
	if !ok {
		err = fmt.Errorf("Data type labelvol requires batch-enabled store, which %q is not\n", store)
		return
	}

	// Create a new label id for this version that will persist to store
	if splitLabel != 0 {
		toLabel = splitLabel
		dvid.Debugf("Splitting subset of label %d into given label %d ...\n", fromLabel, splitLabel)
	} else {
		toLabel, err = d.NewLabel(v)
		if err != nil {
			return
		}
		dvid.Debugf("Splitting subset of label %d into new label %d ...\n", fromLabel, toLabel)
	}

	evt := datastore.SyncEvent{d.DataUUID(), labels.SplitStartEvent}
	splitOpStart := labels.DeltaSplitStart{fromLabel, toLabel}
	splitOpEnd := labels.DeltaSplitEnd{fromLabel, toLabel}

	// Make sure we can split given current merges in progress
	if err := labels.SplitStart(d.getMergeIV(v), splitOpStart); err != nil {
		return toLabel, err
	}
	defer labels.SplitStop(d.getMergeIV(v), splitOpEnd)

	// Signal that we are starting a split.
	msg := datastore.SyncMessage{labels.SplitStartEvent, v, splitOpStart}
	if err := datastore.NotifySubscribers(evt, msg); err != nil {
		return 0, err
	}

	// Read the sparse volume from reader.
	var split dvid.RLEs
	split, err = dvid.ReadRLEs(r)
	if err != nil {
		return
	}
	toLabelSize, _ := split.Stats()

	// Partition the split spans into blocks.
	var splitmap dvid.BlockRLEs
	splitmap, err = split.Partition(d.BlockSize)
	if err != nil {
		return
	}

	// Get a sorted list of blocks that cover split.
	splitblks := splitmap.SortedKeys()

	// Iterate through the split blocks, read the original block.  If the RLEs
	// are identical, just delete the original.  If not, modify the original.
	// TODO: Modifications should be transactional since it's GET-PUT, therefore use
	// hash on block coord to direct it to blockLabel, splitLabel-specific goroutine; we serialize
	// requests to handle concurrency.
	ctx := datastore.NewVersionedCtx(d, v)
	batch := batcher.NewBatch(ctx)

	for _, splitblk := range splitblks {

		// Get original block
		tk := NewTKey(fromLabel, splitblk)
		val, err := store.Get(ctx, tk)
		if err != nil {
			return toLabel, err
		}

		if val == nil {
			return toLabel, fmt.Errorf("Split RLEs at block %s are not part of original label %d", splitblk, fromLabel)
		}
		var rles dvid.RLEs
		if err := rles.UnmarshalBinary(val); err != nil {
			return toLabel, fmt.Errorf("Unable to unmarshal RLE for original labels in block %s", splitblk)
		}

		// Compare and process based on modifications required.
		remain, err := rles.Split(splitmap[splitblk])
		if err != nil {
			return toLabel, err
		}
		if len(remain) == 0 {
			batch.Delete(tk)
		} else {
			rleBytes, err := remain.MarshalBinary()
			if err != nil {
				return toLabel, fmt.Errorf("can't serialize remain RLEs for split of %d: %v\n", fromLabel, err)
			}
			batch.Put(tk, rleBytes)
		}
	}

	if err = batch.Commit(); err != nil {
		err = fmt.Errorf("Batch PUT during split of %q label %d: %v\n", d.DataName(), fromLabel, err)
		return
	}

	// Publish split event
	evt = datastore.SyncEvent{d.DataUUID(), labels.SplitLabelEvent}
	msg = datastore.SyncMessage{labels.SplitLabelEvent, v, labels.DeltaSplit{fromLabel, toLabel, splitmap, splitblks}}
	if err = datastore.NotifySubscribers(evt, msg); err != nil {
		return
	}

	// Write the split sparse vol.
	if err = d.writeLabelVol(v, toLabel, splitmap, splitblks); err != nil {
		return
	}

	// Publish change in label sizes.
	delta := labels.DeltaNewSize{
		Label: toLabel,
		Size:  toLabelSize,
	}
	evt = datastore.SyncEvent{d.DataUUID(), labels.ChangeSizeEvent}
	msg = datastore.SyncMessage{labels.ChangeSizeEvent, v, delta}
	if err = datastore.NotifySubscribers(evt, msg); err != nil {
		return
	}

	delta2 := labels.DeltaModSize{
		Label:      fromLabel,
		SizeChange: int64(-toLabelSize),
	}
	evt = datastore.SyncEvent{d.DataUUID(), labels.ChangeSizeEvent}
	msg = datastore.SyncMessage{labels.ChangeSizeEvent, v, delta2}
	if err = datastore.NotifySubscribers(evt, msg); err != nil {
		return
	}

	// Publish split end
	evt = datastore.SyncEvent{d.DataUUID(), labels.SplitEndEvent}
	msg = datastore.SyncMessage{labels.SplitEndEvent, v, splitOpEnd}
	if err = datastore.NotifySubscribers(evt, msg); err != nil {
		return
	}

	return toLabel, nil
}