Merge pull request #543 from saalfeldlab/perf/1.4.0

Perf/1.4.0
saalfeldlab · Jul 26, 2024 · b0459b3 · b0459b3
2 parents 93e59c0 + 538be00
commit b0459b3
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Showing 35 changed files with 1,002 additions and 1,563 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>37.0.0</version>
+		<version>38.0.1</version>
 	</parent>
 
 	<groupId>org.janelia.saalfeldlab</groupId>
@@ -29,7 +29,6 @@
 	<properties>
 		<!-- allows passing in command line argument to javafx:run via `-Dpaintera.commandline.args="....."`-->
 		<paintera.commandline.args />
-		<scijava.jvm.version>21</scijava.jvm.version>
 
 		<main-class>org.janelia.saalfeldlab.paintera.Paintera</main-class>
 		<license.licenseName>GNU General Public License v2.0</license.licenseName>
@@ -41,6 +40,8 @@
 
 		<package-name>org.janelia.saalfeldlab.paintera</package-name>
 
+		<!-- java -->
+		<scijava.jvm.version>21</scijava.jvm.version>
 		<!-- kotlin -->
 		<kotlin.version>1.9.24</kotlin.version>
 		<kotlin.compiler.incremental>true</kotlin.compiler.incremental>
@@ -51,14 +52,13 @@
 		<javadoc.skip>true</javadoc.skip>
 		<maven.javadoc.skip>${javadoc.skip}</maven.javadoc.skip>
 
-
 		<janino.version>3.0.7</janino.version>
 		<logback.version>1.4.12</logback.version>
 		<slf4j.version>2.0.0</slf4j.version>
 
 		<!-- JavaFx Version-->
 		<javafx.version>22.0.1</javafx.version>
-		<saalfx.version>1.4.2</saalfx.version>
+		<saalfx.version>2.0.0-SNAPSHOT</saalfx.version>
 		<testfx.version>4.0.16-alpha</testfx.version>
 
 		<alphanumeric-comparator.version>1.4.1</alphanumeric-comparator.version>
@@ -74,14 +74,12 @@
 		<macos.sign />
 		<macos.sign.identity />
 
-		<!--N5 versions. Should match with versions pinned by n5-universe -->
-		<n5.version>3.2.0</n5.version>
-		<n5-hdf5.version>2.2.0</n5-hdf5.version>
-		<n5-google-cloud.version>4.1.0</n5-google-cloud.version>
-		<n5-aws-s3.version>4.2.0</n5-aws-s3.version>
-		<n5-zarr.version>1.3.4</n5-zarr.version>
-		<n5-imglib2.version>7.0.0</n5-imglib2.version>
-		<n5-universe.version>1.6.0</n5-universe.version>
+		<!-- N5 (Only specify if newer versions available than in pom-scijava) -->
+		<n5.version>3.3.0</n5.version>
+		<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>
 
 		<maven-compiler-plugin.version>3.13.0</maven-compiler-plugin.version>
@@ -319,17 +317,6 @@
 			<artifactId>commons-io</artifactId>
 		</dependency>
 
-		<dependency>
-			<groupId>io.reactivex.rxjava2</groupId>
-			<artifactId>rxjavafx</artifactId>
-			<version>2.2.2</version>
-		</dependency>
-		<dependency>
-			<groupId>io.reactivex.rxjava2</groupId>
-			<artifactId>rxjava</artifactId>
-			<version>2.1.6</version>
-		</dependency>
-
 		<!--		scripting-->
 		<dependency>
 			<groupId>org.scijava</groupId>
@@ -351,7 +338,7 @@
 			</exclusions>
 		</dependency>
 		<dependency>
-			<groupId>org.codehaus.groovy</groupId>
+			<groupId>org.apache.groovy</groupId>
 			<artifactId>groovy</artifactId>
 			<version>${groovy.version}</version>
 		</dependency>
@@ -568,7 +555,7 @@
 			<email>hanslovskyp@janelia.hhmi.org</email>
 			<url />
 			<organization>HHMI Janelia</organization>
-			<organizationUrl>http://janelia.org/</organizationUrl>
+			<organizationUrl>https://janelia.org/</organizationUrl>
 			<roles>
 				<role>founder</role>
 				<role>lead</role>

diff --git a/src/main/java/org/janelia/saalfeldlab/bdv/fx/viewer/scalebar/ScaleBarOverlayRenderer.java b/src/main/java/org/janelia/saalfeldlab/bdv/fx/viewer/scalebar/ScaleBarOverlayRenderer.java
@@ -1,12 +1,12 @@
 package org.janelia.saalfeldlab.bdv.fx.viewer.scalebar;
 
-import org.janelia.saalfeldlab.bdv.fx.viewer.render.OverlayRendererGeneric;
 import bdv.viewer.TransformListener;
 import javafx.geometry.Bounds;
 import javafx.scene.canvas.GraphicsContext;
 import javafx.scene.text.Text;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.util.LinAlgHelpers;
+import org.janelia.saalfeldlab.bdv.fx.viewer.render.OverlayRendererGeneric;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -25,8 +25,6 @@ public class ScaleBarOverlayRenderer implements OverlayRendererGeneric<GraphicsC
 
 	private final ScaleBarOverlayConfig config;
 
-	//	private final DecimalFormat format = new DecimalFormat("0.####");
-
 	/**
 	 * For finding the value to display on the scalebar: into how many parts is
 	 * each power of ten divided? For example, 4 means the following are

diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/ProjectDirectory.java b/src/main/java/org/janelia/saalfeldlab/paintera/ProjectDirectory.java
@@ -88,10 +88,14 @@ public void close() {
 	private File inferActualDirectory(final File directory) throws IOException {
 
 		return directory == null
-				? Files.createTempDirectory("paintera-project-").toFile()
+				? temporaryN5PainteraProjectDirectory()
 				: directory;
 	}
 
+	private File temporaryN5PainteraProjectDirectory() throws IOException {
+		return new File(Files.createTempDirectory("paintera-project-").toString() + ".n5");
+	}
+
 	private void stateChanged() {
 
 		this.listeners.forEach(l -> l.accept(this));

diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/control/navigation/ValueDisplayListener.java b/src/main/java/org/janelia/saalfeldlab/paintera/control/navigation/ValueDisplayListener.java
@@ -1,18 +1,19 @@
 package org.janelia.saalfeldlab.paintera.control.navigation;
 
-import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerPanelFX;
-import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerState;
 import bdv.viewer.Interpolation;
 import bdv.viewer.Source;
 import bdv.viewer.TransformListener;
+import javafx.application.Platform;
 import javafx.beans.value.ObservableValue;
-import javafx.concurrent.Task;
 import javafx.event.EventHandler;
 import javafx.scene.input.MouseEvent;
+import kotlinx.coroutines.Deferred;
 import net.imglib2.RealRandomAccess;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.realtransform.RealViews;
 import net.imglib2.view.composite.Composite;
+import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerPanelFX;
+import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerState;
 import org.janelia.saalfeldlab.fx.Tasks;
 import org.janelia.saalfeldlab.paintera.data.ChannelDataSource;
 import org.janelia.saalfeldlab.paintera.data.DataSource;
@@ -95,17 +96,17 @@ private static <D> D getVal(final RealRandomAccess<D> access, final ViewerPanelF
 		return access.get();
 	}
 
-	private final Map<DataSource<?, ?>, Task<?>> taskMap = new HashMap<>();
+	private final Map<DataSource<?, ?>, Deferred<?>> taskMap = new HashMap<>();
 
 	private final ExecutorService executor = Executors.newSingleThreadExecutor(new NamedThreadFactory("value-display-listener", true, 2));
 
 	private <D> void getInfo() {
 
 		final Optional<Source<?>> optionalSource = Optional.ofNullable(currentSource.getValue());
 		if (optionalSource.isPresent() && optionalSource.get() instanceof DataSource<?, ?>) {
-			final DataSource<D, ?> source = (DataSource<D, ?>) optionalSource.get();
+			final DataSource<D, ?> source = (DataSource<D, ?>)optionalSource.get();
 
-			final var taskObj = Tasks.<String>createTask(t -> {
+			final var job = Tasks.createTask(() -> {
 				final ViewerState state = viewer.getState();
 				final Interpolation interpolation = this.interpolation.apply(source);
 				final AffineTransform3D screenScaleTransform = new AffineTransform3D();
@@ -123,28 +124,29 @@ private <D> void getInfo() {
 				).realRandomAccess();
 				final var val = getVal(x, y, access, viewer);
 				return stringConverterFromSource(source).apply(val);
-			}).onSuccess((event, t) -> {
-				/* submit the value if the task is completed; remove from the map*/
-				submitValue.accept(t.getValue());
+			}).onSuccess(result -> {
+				Platform.runLater(() -> submitValue.accept(result));
 				taskMap.remove(source);
 			});
 
+
+
 			/* If we are creating a task for a source which has a running task, cancel the old task after removing. */
-			Optional.ofNullable(taskMap.put(source, taskObj)).ifPresent(Task::cancel);
+			Optional.ofNullable(taskMap.put(source, job)).ifPresent(it -> it.cancel(null));
 
-			taskObj.submit(executor);
+			job.start();
 
 		}
 	}
 
 	private static <D> Function<D, String> stringConverterFromSource(final DataSource<D, ?> source) {
 
 		if (source instanceof ChannelDataSource<?, ?>) {
-			final long numChannels = ((ChannelDataSource<?, ?>) source).numChannels();
+			final long numChannels = ((ChannelDataSource<?, ?>)source).numChannels();
 
 			// Cast not actually redundant
 			//noinspection unchecked,RedundantCast
-			return (Function<D, String>) (Function<? extends Composite<?>, String>) comp -> {
+			return (Function<D, String>)(Function<? extends Composite<?>, String>)comp -> {
 				StringBuilder sb = new StringBuilder("(");
 				if (numChannels > 0)
 					sb.append(comp.get(0).toString());