Merge pull request #546 from saalfeldlab/wip/perf/memory

Wip/perf/memory

pom.xml

@@ -10,7 +10,7 @@
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>paintera</artifactId>
-	<version>1.3.5-SNAPSHOT</version>
+	<version>1.4.0-SNAPSHOT</version>
 
 	<name>Paintera</name>
 	<description>New Era Painting and annotation tool</description>
@@ -58,16 +58,18 @@
 
 		<!-- JavaFx Version-->
 		<javafx.version>22.0.1</javafx.version>
-		<saalfx.version>2.0.0</saalfx.version>
+		<saalfx.version>2.1.0</saalfx.version>
 		<testfx.version>4.0.16-alpha</testfx.version>
 
 		<alphanumeric-comparator.version>1.4.1</alphanumeric-comparator.version>
 		<dokka.version>1.4.30</dokka.version>
 
+
 		<main-class>org.janelia.saalfeldlab.paintera.Paintera</main-class>
 		<app.name>Paintera</app.name>
 		<app.package>paintera</app.package>
-		<app.version>1.3.4</app.version>
+		<app.version>1.4.0</app.version>
+
 		<jvm.modules>javafx.base,javafx.controls,javafx.fxml,javafx.media,javafx.swing,javafx.web,javafx.graphics,java.naming,java.management,java.sql</jvm.modules>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<windows.upgrade.uuid>f918b6f9-8685-4b50-9fbd-9be7a1209249</windows.upgrade.uuid>
@@ -79,8 +81,7 @@
 		<n5-aws-s3.version>4.2.1</n5-aws-s3.version>
 		<n5-google-cloud>4.1.1</n5-google-cloud>
 		<n5-zarr.version>1.3.5</n5-zarr.version>
-
-		<imglib2-label-multisets.version>0.14.0</imglib2-label-multisets.version>
+		<imglib2-label-multisets.version>0.15.0</imglib2-label-multisets.version>
 
 		<maven-compiler-plugin.version>3.13.0</maven-compiler-plugin.version>
 		<enforcer.skip>true</enforcer.skip>
@@ -332,15 +333,14 @@
 			<artifactId>scripting-groovy</artifactId>
 			<exclusions>
 				<exclusion>
-					<groupId>org.codehaus.groovy</groupId>
+					<groupId>org.apache.groovy</groupId>
 					<artifactId>groovy</artifactId>
 				</exclusion>
 			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.groovy</groupId>
 			<artifactId>groovy</artifactId>
-			<version>${groovy.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.scijava</groupId>
@@ -687,7 +687,7 @@
 					<artifactId>maven-surefire-plugin</artifactId>
 					<configuration>
 						<forkCount>1</forkCount>
-						<argLine>-Dtestfx.robot=glass -Dglass.platform=Monocle -Dmonocle.platform=Headless -Dprism.order=sw</argLine>
+						<argLine>-Dtestfx.robot=glass -Dglass.platform=Monocle -Dmonocle.platform=Headless -Dprism.order=sw --enable-preview</argLine>
 					</configuration>
 				</plugin>
 			</plugins>
@@ -707,6 +707,9 @@
 					<annotationProcessors>
 						<annotationProcessor>org.scijava.annotations.AnnotationProcessor</annotationProcessor>
 					</annotationProcessors>
+					<source>21</source>
+					<target>21</target>
+					<compilerArgs>--enable-preview</compilerArgs>
 				</configuration>
 			</plugin>
 			<plugin>
@@ -910,6 +913,16 @@
 					</execution>
 				</executions>
 			</plugin>
+			<plugin>
+				<groupId>org.jetbrains.kotlin</groupId>
+				<artifactId>kotlin-maven-plugin</artifactId>
+				<version>${kotlin.version}</version>
+				<configuration>
+					<javacOptions>
+						<javacOption>--enable-preview</javacOption>
+					</javacOptions>
+				</configuration>
+			</plugin>
 		</plugins>
 	</build>
 	<profiles>
@@ -999,9 +1012,6 @@
 								<phase>none</phase>
 							</execution>
 						</executions>
-						<configuration>
-							<jvmTarget>11</jvmTarget>
-						</configuration>
 					</plugin>
 				</plugins>
 			</build>

src/main/java/org/janelia/saalfeldlab/bdv/fx/viewer/ViewerPanelFX.java

@@ -192,7 +192,9 @@ public ViewerPanelFX(
 		heightProperty().subscribe(height -> renderUnit.setDimensions((long)getWidth(), height.longValue()));
 
 		visibleProperty().subscribe(visible -> {
-			if (!visible)
+			if (visible)
+				renderUnit.setDimensions((long)getWidth(), (long)getHeight());
+			else
 				renderUnit.stopRendering();
 		});
 

src/main/java/org/janelia/saalfeldlab/bdv/fx/viewer/ViewerState.java

@@ -105,11 +105,14 @@ public boolean isVisible() {
 
 	public synchronized int getBestMipMapLevel() {
 
-		final var currentSource = Paintera.getPaintera().getBaseView().sourceInfo().currentSourceProperty().get();
+		return  getBestMipMapLevel(Paintera.getPaintera().getBaseView().sourceInfo().currentSourceProperty().get());
+	}
+
+	public int getBestMipMapLevel(Source<?> source) {
 
 		final AffineTransform3D screenScaleTransform = new AffineTransform3D();
 		viewer.getRenderUnit().getScreenScaleTransform(0, screenScaleTransform);
-		return getBestMipMapLevel(screenScaleTransform, currentSource);
+		return getBestMipMapLevel(screenScaleTransform, source);
 	}
 
 	public synchronized ViewerState copy() {

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

@@ -16,8 +16,6 @@ public final class PainterThreadFx extends Thread {
 
 	private boolean isRunning;
 
-	private long lastUpdate = -1;
-	private long targetFrameRateMs = 1000 / 60;
 
 	public PainterThreadFx(PainterThreadFx.Paintable paintable) {
 

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

@@ -41,14 +41,23 @@ public abstract class RenderUnit implements PainterThreadFx.Paintable {
 	protected PainterThreadFx painterThread;
 	protected boolean useVolatileIfAvailable = true;
 
-	public RenderUnit(final ThreadGroup threadGroup, final Function<Source<?>, Interpolation> interpolation, final AccumulateProjectorFactory<ARGBType> accumulateProjectorFactory, final CacheControl cacheControl, final long targetRenderNanos, final TaskExecutor renderingTaskExecutor) {
+	public RenderUnit(
+			final ThreadGroup threadGroup,
+			final Function<Source<?>, Interpolation> interpolation,
+			final AccumulateProjectorFactory<ARGBType> accumulateProjectorFactory,
+			final CacheControl cacheControl,
+			final long targetRenderNanos,
+			final TaskExecutor renderingTaskExecutor,
+			final boolean useVolatileIfAvailable
+			) {
 
 		this.threadGroup = threadGroup;
 		this.interpolation = interpolation;
 		this.accumulateProjectorFactory = accumulateProjectorFactory;
 		this.cacheControl = cacheControl;
 		this.targetRenderNanos = targetRenderNanos;
 		this.renderingTaskExecutor = renderingTaskExecutor;
+		this.useVolatileIfAvailable = useVolatileIfAvailable;
 	}
 
 	public void stopRendering() {

src/main/java/org/janelia/saalfeldlab/fx/ortho/OrthogonalViews.java

@@ -26,6 +26,7 @@
 import java.util.List;
 import java.util.concurrent.ForkJoinPool;
 import java.util.concurrent.ForkJoinWorkerThread;
+import java.util.concurrent.atomic.AtomicInteger;
 import java.util.function.Consumer;
 import java.util.function.Function;
 import java.util.stream.Collectors;
@@ -147,12 +148,12 @@ public OrthogonalViews(
 			final Function<Source<?>, Interpolation> interpolation) {
 
 		this.manager = manager;
-
+		final var count = new AtomicInteger();
 		final ForkJoinPool.ForkJoinWorkerThreadFactory factory = pool -> {
 			final ForkJoinWorkerThread worker = ForkJoinPool.defaultForkJoinWorkerThreadFactory.newThread(pool);
 			worker.setDaemon(true);
 			worker.setPriority(4);
-			worker.setName("render-thread-" + worker.getPoolIndex());
+			worker.setName("render-thread-" + count.getAndIncrement());
 			return worker;
 		};
 

src/main/java/org/janelia/saalfeldlab/paintera/PainteraBaseView.java

@@ -63,6 +63,7 @@
 import java.util.concurrent.Executors;
 import java.util.concurrent.ForkJoinPool;
 import java.util.concurrent.ForkJoinWorkerThread;
+import java.util.concurrent.atomic.AtomicInteger;
 
 /**
  * Contains all the things necessary to build a Paintera UI, most importantly:
@@ -123,15 +124,16 @@ public class PainteraBaseView {
 	private final ExecutorService propagationQueue;
 
 	{
+		final AtomicInteger count = new AtomicInteger();
 		final ForkJoinPool.ForkJoinWorkerThreadFactory factory = pool -> {
 			final ForkJoinWorkerThread worker = ForkJoinPool.defaultForkJoinWorkerThreadFactory.newThread(pool);
 			worker.setDaemon(true);
 			worker.setPriority(4);
-			worker.setName("propagation-queue-" + worker.getPoolIndex());
+			worker.setName("propagation-queue-" + count.getAndIncrement());
 			return worker;
 		};
 
-		propagationQueue = new ForkJoinPool(Math.max(1, Runtime.getRuntime().availableProcessors() - 2), factory, null, false);
+		propagationQueue = new ForkJoinPool(Math.max(1, Runtime.getRuntime().availableProcessors() - 2), factory, (thread, throwable) -> throwable.printStackTrace(), false);
 
 	}
 
@@ -382,7 +384,7 @@ public <D extends RealType<D> & NativeType<D>, T extends AbstractVolatileNativeR
 			final String name) {
 
 		final ConnectomicsRawState<D, T> state = new ConnectomicsRawState<D, T>(
-				new RaiBackendRaw<D, T>(data, resolution, offset, "test"),
+				new RaiBackendRaw<>(data, resolution, offset, "test"),
 				getQueue(),
 				getQueue().getNumPriorities() - 1,
 				name
@@ -486,7 +488,7 @@ public <D extends RealType<D> & NativeType<D>, T extends AbstractVolatileNativeR
 			final String name,
 			LabelBlockLookup labelBlockLookup) {
 
-		return this.addConnectomicsLabelSource(
+		return addConnectomicsLabelSource(
 				new RandomAccessibleInterval[]{data},
 				new double[][]{resolution},
 				new double[][]{offset},
@@ -560,7 +562,7 @@ public static int reasonableNumFetcherThreads() {
 	 */
 	public ExecutorService getMeshManagerExecutorService() {
 
-		return this.meshManagerExecutorService;
+		return meshManagerExecutorService;
 	}
 
 	/**

src/main/java/org/janelia/saalfeldlab/paintera/control/OrthoViewCoordinateDisplayListener.java

@@ -1,5 +1,6 @@
 package org.janelia.saalfeldlab.paintera.control;
 
+import bdv.viewer.Source;
 import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerPanelFX;
 import bdv.viewer.TransformListener;
 import javafx.beans.property.ObjectProperty;
@@ -35,16 +36,19 @@ public class OrthoViewCoordinateDisplayListener {
 
 	private final ObjectProperty<OrthogonalViews.ViewerAndTransforms> activeViewerProperty = new SimpleObjectProperty<>();
 
+	private final ObservableValue<Source<?>> currentSource;
+
 	public OrthoViewCoordinateDisplayListener(
 			final Consumer<RealPoint> submitViewerCoordinate,
 			final Consumer<RealPoint> submitWorldCoordinate,
-			final Consumer<RealPoint> submitSourceCoordinate
+			final Consumer<RealPoint> submitSourceCoordinate,
+			final ObservableValue<Source<?>> currentSource
 	) {
 
-		super();
 		this.submitViewerCoordinate = submitViewerCoordinate;
 		this.submitWorldCoordinate = submitWorldCoordinate;
 		this.submitSourceCoordinate = submitSourceCoordinate;
+		this.currentSource = currentSource;
 		activeViewerProperty.addListener((obs, exiting, entering) -> {
 			if (Objects.nonNull(exiting)) {
 				removeHandlers(exiting.viewer());
@@ -58,8 +62,7 @@ public OrthoViewCoordinateDisplayListener(
 	public void addHandlers(ViewerPanelFX viewer) {
 
 		if (!this.listeners.containsKey(viewer)) {
-			final CoordinateDisplayListener coordinateListener = new CoordinateDisplayListener(viewer, submitViewerCoordinate, submitWorldCoordinate,
-					submitSourceCoordinate);
+			final CoordinateDisplayListener coordinateListener = new CoordinateDisplayListener(viewer, currentSource, submitViewerCoordinate, submitWorldCoordinate, submitSourceCoordinate);
 			final var coordinateUpdate = painteraActionSet("coordinate update", null, actionSet -> {
 				actionSet.addMouseAction(MouseEvent.MOUSE_MOVED, action -> {
 					action.setConsume(false);

src/main/java/org/janelia/saalfeldlab/paintera/control/OrthogonalViewsValueDisplayListener.java

@@ -18,7 +18,7 @@
 
 public class OrthogonalViewsValueDisplayListener {
 
-	private final Map<ViewerPanelFX, ValueDisplayListener> listeners = new HashMap<>();
+	private final Map<ViewerPanelFX, ValueDisplayListener<?>> listeners = new HashMap<>();
 
 	private final Consumer<String> submitValue;
 
@@ -49,21 +49,24 @@ public OrthogonalViewsValueDisplayListener(
 
 	public void addHandlers(ViewerPanelFX viewer) {
 
-		if (!this.listeners.containsKey(viewer))
-			this.listeners.put(viewer, new ValueDisplayListener(viewer, currentSource, interpolation, submitValue));
-		viewer.getDisplay().addEventFilter(MouseEvent.MOUSE_MOVED, this.listeners.get(viewer));
-		viewer.addTransformListener(this.listeners.get(viewer));
+		listeners.putIfAbsent(viewer, new ValueDisplayListener<>(viewer, currentSource, interpolation, submitValue));
+
+		viewer.getDisplay().addEventFilter(MouseEvent.MOUSE_MOVED, listeners.get(viewer));
+		viewer.addTransformListener(listeners.get(viewer));
 	}
 
 	public void removeHandlers(ViewerPanelFX viewer) {
 
-		viewer.getDisplay().removeEventHandler(MouseEvent.MOUSE_MOVED, this.listeners.get(viewer));
-		viewer.removeTransformListener(this.listeners.get(viewer));
+		listeners.computeIfPresent(viewer, (key, vdl) -> {
+			viewer.getDisplay().removeEventHandler(MouseEvent.MOUSE_MOVED, vdl);
+			viewer.removeTransformListener(vdl);
+			return null;
+		});
 		submitValue.accept("");
 	}
 
 	public void bindActiveViewer(ObservableValue<OrthogonalViews.ViewerAndTransforms> activeViewerObservable) {
 		/* Binding would be neater here, but inexplicably, doesn't work? */
-		activeViewerObservable.addListener((obs, oldv, newv) -> activeViewerProperty.set(newv));
+		activeViewerObservable.subscribe(activeViewerProperty::set);
 	}
 }

src/main/java/org/janelia/saalfeldlab/paintera/control/assignment/FragmentSegmentAssignmentOnlyLocal.java

@@ -135,7 +135,7 @@ public synchronized void persist() throws UnableToPersist {
 	}
 
 	@Override
-	public synchronized long getSegment(final long fragmentId) {
+	public long getSegment(final long fragmentId) {
 
 		final long id;
 		final long segmentId = fragmentToSegmentMap.get(fragmentId);