Merge pull request #539 from saalfeldlab/perf/1.3.1

1.3.1

src/main/java/org/janelia/saalfeldlab/bdv/fx/viewer/render/MultiResolutionRendererGeneric.java

@@ -529,6 +529,8 @@ public int paint(
 			// if rendering was not cancelled...
 			if (success) {
 				if (createProjector) {
+					if (currentScreenScaleIndex >= screenImages.size() || reuseBufferScreenScale >= screenImages.size())
+						return -1;
 					final ArrayDeque<T> buffers = screenImages.get(currentScreenScaleIndex);
 					final T renderTarget = doubleBuffered ? buffers.pop() : buffers.peek();
 					final T unusedBuffer = display.setBufferedImageAndTransform(renderTarget, currentProjectorTransform);

src/main/java/org/janelia/saalfeldlab/bdv/fx/viewer/render/PainterThreadFx.java

@@ -45,36 +45,37 @@ public void run() {
 		while (this.isRunning) {
 			boolean paint;
 			synchronized (this) {
-				paint = this.pleaseRepaint;
-				this.pleaseRepaint = false;
+				paint = pleaseRepaint;
+				pleaseRepaint = false;
 			}
 
 			if (paint) {
 				try {
-					this.paintable.paint();
+					paintable.paint();
 				} catch (RejectedExecutionException var5) {
 				}
 			}
 
 			synchronized (this) {
 				try {
-					if (this.isRunning && !this.pleaseRepaint) {
-						this.wait();
+					if (isRunning && !pleaseRepaint) {
+						wait();
 					}
-					continue;
+					if (isRunning)
+						continue;
 				} catch (InterruptedException var7) {
+					System.out.println(Thread.currentThread().getName() + " interrupted");
 				}
 			}
-
 			return;
 		}
 	}
 
 	public void requestRepaint() {
 
 		synchronized (this) {
-			this.pleaseRepaint = true;
-			this.notify();
+			pleaseRepaint = true;
+			notify();
 		}
 	}
 
@@ -85,12 +86,10 @@ public interface Paintable {
 
 	public void stopRendering() {
 
-		synchronized (this) {
-			LOG.debug("Stop rendering now!");
-			this.isRunning = false;
-			this.notify();
-			LOG.debug("Notified on this ({})", this);
-		}
+		LOG.debug("Stop rendering now!");
+		isRunning = false;
+		interrupt();
+		LOG.debug("Notified on this ({})", this);
 	}
 
 }

src/main/java/org/janelia/saalfeldlab/paintera/data/mask/MaskedSource.java

@@ -779,6 +779,8 @@ public void resetMasks(final boolean clearOldMask) throws MaskInUse {
 			if (!canResetMask)
 				throw new MaskInUse("Cannot reset the mask.");
 
+			var mask = getCurrentMask();
+			if (mask != null && mask.shutdown != null) mask.shutdown.run();
 			setCurrentMask(null);
 			this.isBusy.set(true);
 		}

src/main/java/org/janelia/saalfeldlab/paintera/id/IdService.java

@@ -105,6 +105,11 @@ static long randomTemporaryId() {
 		return randomTemps.findFirst().getAsLong();
 	}
 
+	static boolean isTemporary(final long id) {
+
+		return id > FIRST_TEMPORARY_ID && id < LAST_TEMPORARY_ID;
+	}
+
 	class IdServiceNotProvided implements IdService {
 
 		@Override

src/main/java/org/janelia/saalfeldlab/paintera/state/LabelSourceStateIdSelectorHandler.java

@@ -185,6 +185,12 @@ public List<ActionSet> makeActionSets(KeyTracker keyTracker, Supplier<ViewerPane
 		};
 	}
 
+	public long activateCurrentOrNext() {
+		if (selectedIds.isLastSelectionValid())
+			return selectedIds.getLastSelection();
+		else return nextId(true);
+	}
+
 	public long nextId() {
 
 		return nextId(true);

src/main/java/org/janelia/saalfeldlab/paintera/stream/AbstractHighlightingARGBStream.java

@@ -70,11 +70,11 @@ public abstract class AbstractHighlightingARGBStream extends ObservableWithListe
 	private final BooleanProperty colorFromSegmentId = new SimpleBooleanProperty();
 
 	protected final TLongIntHashMap explicitlySpecifiedColors = new TLongIntHashMap();
-	protected final TLongIntHashMap overrideAlpha = new TLongIntHashMap(
+	public final TLongIntHashMap overrideAlpha = new TLongIntHashMap(
 			Constants.DEFAULT_CAPACITY,
 			Constants.DEFAULT_LOAD_FACTOR,
 			Label.INVALID,
-			0
+			-1
 	);
 
 	public AbstractHighlightingARGBStream(
@@ -295,8 +295,10 @@ public boolean getHideLockedSegments() {
 	public void specifyColorExplicitly(final long segmentId, final int color, final boolean overrideAlpha) {
 
 		this.explicitlySpecifiedColors.put(segmentId, color);
-		if (overrideAlpha)
-			this.overrideAlpha.put(segmentId, 1);
+		if (overrideAlpha) {
+			var alpha = color >>> 24;
+			this.overrideAlpha.put(segmentId, alpha);
+		}
 		clearCache();
 	}
 

src/main/java/org/janelia/saalfeldlab/paintera/stream/AbstractSaturatedHighlightingARGBStream.java

@@ -72,16 +72,18 @@ protected int argbImpl(final long fragmentId, final boolean colorFromSegmentId)
 		} else if (lockedSegments.isLocked(segmentId) && hideLockedSegments) {
 			argb = argb & 0x00ffffff;
 		} else {
-			if (overrideAlpha.get(assigned) != 1) {
-				var a = alpha;
+			int alphaOverride = overrideAlpha.get(assigned);
+			int actualAlpha = alpha;
+			if (alphaOverride == overrideAlpha.getNoEntryValue()) {
 				if (isActiveSegment) {
 					if (isActiveFragment(fragmentId))
-						a = activeFragmentAlpha;
+						actualAlpha = activeFragmentAlpha;
 					else
-						a = activeSegmentAlpha;
+						actualAlpha = activeSegmentAlpha;
 				}
-				argb = argb & 0x00ffffff | a;
-			}
+			} else
+				actualAlpha = alphaOverride << 24;
+			argb = argb & 0x00ffffff | actualAlpha;
 		}
 
 		return argb;

src/main/java/org/janelia/saalfeldlab/util/n5/N5Data.java

@@ -800,7 +800,7 @@ public static void createEmptyLabelDataset(
 			throw new IOException(String.format("Unique labels group `%s' exists in container `%s' -- conflict likely.", uniqueLabelsGroup, container));
 
 		n5.setAttribute(group, N5Helpers.PAINTERA_DATA_KEY, pd);
-		n5.setAttribute(group, N5Helpers.MAX_ID_KEY, 1L);
+		n5.setAttribute(group, N5Helpers.MAX_ID_KEY, 0L);
 
 		final String dataGroup = String.format("%s/data", group);
 		n5.createGroup(dataGroup);
@@ -828,15 +828,16 @@ public static void createEmptyLabelDataset(
 
 			final String dataset = String.format(scaleDatasetPattern, scaleLevel);
 			final String uniqeLabelsDataset = String.format(scaleUniqueLabelsPattern, scaleLevel);
-			n5.createDataset(dataset, scaledDimensions, blockSize, DataType.UINT8, new GzipCompression());
-			n5.createDataset(uniqeLabelsDataset, scaledDimensions, blockSize, DataType.UINT64, new GzipCompression());
 
 			if (labelMultisetType) {
+				n5.createDataset(dataset, scaledDimensions, blockSize, DataType.UINT8, new GzipCompression());
 				final int maxNum = downscaledLevel < 0 ? -1 : maxNumEntries[downscaledLevel];
 				n5.setAttribute(dataset, N5Helpers.MAX_NUM_ENTRIES_KEY, maxNum);
 				n5.setAttribute(dataset, N5Helpers.IS_LABEL_MULTISET_KEY, true);
-			}
+			} else
+				n5.createDataset(dataset, scaledDimensions, blockSize, DataType.UINT64, new GzipCompression());
 
+			n5.createDataset(uniqeLabelsDataset, scaledDimensions, blockSize, DataType.UINT64, new GzipCompression());
 			if (scaleLevel != 0) {
 				n5.setAttribute(dataset, N5Helpers.DOWNSAMPLING_FACTORS_KEY, accumulatedFactors);
 				n5.setAttribute(uniqeLabelsDataset, N5Helpers.DOWNSAMPLING_FACTORS_KEY, accumulatedFactors);

src/main/kotlin/org/janelia/saalfeldlab/paintera/cache/SamEmbeddingLoaderCache.kt

@@ -198,6 +198,7 @@ object SamEmbeddingLoaderCache : AsyncCacheWithLoader<RenderUnitState, OnnxTenso
 			result.image?.let { img ->
 				ImageIO.write(SwingFXUtils.fromFXImage(img, null), "png", predictionImagePngOutputStream)
 				predictionImagePngOutputStream.close()
+				sharedQueue.shutdown()
 				imageRenderer.stopRendering()
 			}
 		}

src/main/kotlin/org/janelia/saalfeldlab/paintera/control/ShapeInterpolationController.kt

@@ -666,6 +666,7 @@ class ShapeInterpolationController<D : IntegerType<D>>(
 
 			/* Replace old slice info */
 			slicesAndInterpolants.removeSlice(oldSlice)
+			oldSlice.mask.shutdown?.run()
 
 			val newSlice = SliceInfo(
 				newMask,

src/main/kotlin/org/janelia/saalfeldlab/paintera/control/modes/ShapeInterpolationMode.kt

@@ -130,7 +130,9 @@ class ShapeInterpolationMode<D : IntegerType<D>>(val controller: ShapeInterpolat
 
 	override fun exit() {
 		super.exit()
+
 		SamEmbeddingLoaderCache.stopNavigationBasedRequests()
+		SamEmbeddingLoaderCache.invalidateAll()
 		paintera.baseView.disabledPropertyBindings.remove(controller)
 		controller.resetFragmentAlpha()
 		activeViewerProperty.removeListener(toolTriggerListener)
@@ -559,9 +561,36 @@ internal class SamSliceCache : HashMap<Float, SamSliceInfo>() {
 	operator fun minusAssign(key: Double) {
 		remove(key.toFloat())
 	}
+
 	operator fun minusAssign(key: Float) {
 		remove(key)
 	}
+
+	override fun clear() {
+		values.forEach {
+			it.mask.shutdown?.run()
+		}
+		super.clear()
+	}
+
+	override fun remove(key: Float): SamSliceInfo? {
+		return super.remove(key)?.also {
+			it.mask.shutdown?.run()
+		}
+	}
+
+	override fun remove(key: Float, value: SamSliceInfo): Boolean {
+		return if (super.remove(key, value)) {
+			value.mask.shutdown?.run()
+			true
+		} else false
+	}
+
+	override fun put(key: Float, value: SamSliceInfo): SamSliceInfo? {
+		return super.put(key, value)?.also {
+			it.mask.shutdown?.run()
+		}
+	}
 }
 
 internal data class SamSliceInfo(val renderState: RenderUnitState, val mask: ViewerMask, var prediction: SamPredictor.PredictionRequest, var sliceInfo: ShapeInterpolationController.SliceInfo?, var locked: Boolean = false) {

src/main/kotlin/org/janelia/saalfeldlab/paintera/control/tools/paint/SamTool.kt

@@ -49,8 +49,6 @@ import net.imglib2.view.Views
 import org.apache.commons.io.output.NullPrintStream
 import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerPanelFX
 import org.janelia.saalfeldlab.control.VPotControl
-import org.janelia.saalfeldlab.fx.Tasks
-import org.janelia.saalfeldlab.fx.UtilityTask
 import org.janelia.saalfeldlab.fx.actions.*
 import org.janelia.saalfeldlab.fx.actions.ActionSet.Companion.installActionSet
 import org.janelia.saalfeldlab.fx.extensions.LazyForeignValue
@@ -94,7 +92,6 @@ import org.janelia.saalfeldlab.paintera.util.IntervalHelpers.Companion.smallestC
 import org.janelia.saalfeldlab.paintera.util.algorithms.otsuThresholdPrediction
 import org.janelia.saalfeldlab.util.*
 import java.util.concurrent.CancellationException
-import java.util.concurrent.ForkJoinPool
 import java.util.concurrent.LinkedBlockingQueue
 import kotlin.collections.List
 import kotlin.collections.MutableList
@@ -207,7 +204,7 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 			originalWritableVolatileBackingImage = field?.volatileViewerImg?.writableSource
 		}
 
-	private var predictionTask: UtilityTask<Unit>? = null
+	private var predictionJob : Job = Job().apply { complete() }
 
 	internal val lastPredictionProperty = SimpleObjectProperty<SamTaskInfo?>(null)
 	var lastPrediction by lastPredictionProperty.nullable()
@@ -299,8 +296,7 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 	internal fun cleanup() {
 		clearPromptDrawings()
 		currentLabelToPaint = Label.INVALID
-		predictionTask?.cancel()
-		predictionTask = null
+		predictionJob.cancel()
 		if (unwrapResult) {
 			if (!maskProvided) {
 				maskedSource?.resetMasks()
@@ -833,8 +829,8 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 	}
 
 	open fun requestPrediction(promptPoints: List<SamPoint>, estimateThreshold: Boolean = true) {
-		if (predictionTask == null || predictionTask?.isCancelled == true) {
-			startPredictionTask()
+		if (!predictionJob.isActive) {
+			startPredictionJob()
 		}
 		currentPredictionRequest = SamPredictor.points(promptPoints.toList()) to estimateThreshold
 	}
@@ -849,25 +845,25 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 	private var embeddingRequest: Deferred<OnnxTensor>? = null
 
 	private var currentPrediction: SamPredictor.SamPrediction? = null
-	private fun startPredictionTask() {
+	private fun startPredictionJob() {
 		val maskSource = maskedSource ?: return
-		val task = Tasks.createTask { task ->
+		predictionJob = SAM_TASK_SCOPE.launch {
 			val session = createOrtSessionTask.get()
 			val imageEmbedding = try {
 				runBlocking {
 					isBusy = true
 					embeddingRequest!!.await()
 				}
 			} catch (e: InterruptedException) {
-				if (!task.isCancelled) throw e
-				return@createTask
+				if (coroutineContext.isActive) throw e
+				return@launch
 			} catch (e: CancellationException) {
-				return@createTask
+				return@launch
 			} finally {
 				isBusy = false
 			}
 			val predictor = SamPredictor(ortEnv, session, imageEmbedding, imgWidth to imgHeight)
-			while (!task.isCancelled) {
+			while (coroutineContext.isActive) {
 				val predictionPair = predictionQueue.take()
 				val (predictionRequest, estimateThreshold) = predictionPair
 				val points = (predictionRequest as SparsePrediction).points
@@ -933,7 +929,7 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 				} catch (e: InterruptedException) {
 					System.setErr(stdErr)
 					LOG.debug(e) { "Connected Components Interrupted During SAM" }
-					task.cancel()
+					cancel("Connected Components Interrupted During SAM" )
 					continue
 				} finally {
 					System.setErr(stdErr)
@@ -1048,8 +1044,6 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 				lastPrediction = SamTaskInfo(maskSource, predictionIntervalInViewerSpace, imageEmbedding, predictionRequest)
 			}
 		}
-		predictionTask = task
-		task.submit(SAM_TASK_SERVICE)
 	}
 
 	private fun setBestEstimatedThreshold(interval: Interval? = null) {
@@ -1140,15 +1134,7 @@ open class SamTool(activeSourceStateProperty: SimpleObjectProperty<SourceState<*
 
 		private val LOG = KotlinLogging.logger { }
 
-		internal val SAM_TASK_SERVICE = ForkJoinPool.ForkJoinWorkerThreadFactory { pool: ForkJoinPool ->
-			val worker = ForkJoinPool.defaultForkJoinWorkerThreadFactory.newThread(pool)
-			worker.isDaemon = true
-			worker.priority = 4
-			worker.name = "sam-task-" + worker.poolIndex
-			worker
-		}.let { factory ->
-			ForkJoinPool(max(4.0, 4 * (Runtime.getRuntime().availableProcessors()).toDouble()).toInt(), factory, null, false)
-		}
+		internal val SAM_TASK_SCOPE = CoroutineScope(Dispatchers.IO + Job())
 
 
 		private fun calculateTargetScreenScaleFactor(viewer: ViewerPanelFX): Double {