Feat/replace labels

pom.xml

@@ -5,12 +5,12 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>38.0.1</version>
+		<version>40.0.0</version>
 	</parent>
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>paintera</artifactId>
-	<version>1.8.1-SNAPSHOT</version>
+	<version>1.9.0-SNAPSHOT</version>
 
 	<name>Paintera</name>
 	<description>New Era Painting and annotation tool</description>
@@ -59,7 +59,6 @@
 		<!-- JavaFx Version-->
 		<javafx.version>22.0.1</javafx.version>
 		<saalfx.version>2.2.0</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>
@@ -68,7 +67,7 @@
 		<main-class>org.janelia.saalfeldlab.paintera.Paintera</main-class>
 		<app.name>Paintera</app.name>
 		<app.package>paintera</app.package>
-		<app.version>1.8.0</app.version>
+		<app.version>1.9.0</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>
@@ -77,13 +76,11 @@
 		<macos.sign.identity />
 
 		<!-- 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>0.15.1</imglib2-label-multisets.version>
-		<imglib2.version>6.1.0</imglib2.version>
-		<imglib2-realtransform.version>4.0.1</imglib2-realtransform.version>
+		<n5-universe.version>2.0.1</n5-universe.version>
+		<n5-google-cloud.version>4.1.2</n5-google-cloud.version>
+		<n5-aws-s3.version>4.2.2</n5-aws-s3.version>
+		<n5-zarr.version>1.4.0</n5-zarr.version>
+		<n5.version>3.3.1-SNAPSHOT</n5.version>
 
 		<maven-compiler-plugin.version>3.13.0</maven-compiler-plugin.version>
 		<enforcer.skip>true</enforcer.skip>
@@ -115,6 +112,12 @@
 			<groupId>org.janelia.saalfeldlab</groupId>
 			<artifactId>n5-universe</artifactId>
 			<version>${n5-universe.version}</version>
+			<exclusions>
+				<exclusion>
+					<groupId>junit</groupId>
+					<artifactId>junit</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 
 		<dependency>
@@ -488,46 +491,28 @@
 
 		<!--		Tests-->
 		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<version>${junit.version}</version>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-api</artifactId>
+			<version>${junit-jupiter.version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>org.jetbrains.kotlin</groupId>
-			<artifactId>kotlin-test-junit</artifactId>
-			<version>${kotlin.version}</version>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-engine</artifactId>
+			<version>${junit-jupiter.version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>org.testfx</groupId>
-			<artifactId>testfx-junit</artifactId>
-			<version>4.0.16-alpha</version>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-params</artifactId>
+			<version>${junit-jupiter.version}</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>org.testfx</groupId>
-			<artifactId>openjfx-monocle</artifactId>
-			<version>21.0.2</version>
+			<groupId>org.jetbrains.kotlin</groupId>
+			<artifactId>kotlin-test-junit5</artifactId>
+			<version>${kotlin.version}</version>
 			<scope>test</scope>
-			<exclusions>
-				<exclusion>
-					<groupId>org.openjfx</groupId>
-					<artifactId>javafx-base</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.openjfx</groupId>
-					<artifactId>javafx-controls</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.openjfx</groupId>
-					<artifactId>javafx-graphics</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.openjfx</groupId>
-					<artifactId>javafx-fxml</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.controlsfx</groupId>
@@ -680,19 +665,17 @@
 				<filtering>true</filtering>
 			</resource>
 		</resources>
-		<pluginManagement>
-			<plugins>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-surefire-plugin</artifactId>
-					<configuration>
-						<forkCount>1</forkCount>
-						<argLine>-Dtestfx.robot=glass -Dglass.platform=Monocle -Dmonocle.platform=Headless -Dprism.order=sw</argLine>
-					</configuration>
-				</plugin>
-			</plugins>
-		</pluginManagement>
 		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<configuration>
+					<excludes>
+						<exclude>**PainteraBaseViewTest**</exclude>
+						<exclude>**SplashScreenTest**</exclude>
+					</excludes>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
@@ -924,6 +907,20 @@
 		</plugins>
 	</build>
 	<profiles>
+		<profile>
+			<id>run-ui-tests</id>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-surefire-plugin</artifactId>
+						<configuration>
+							<excludes combine.self="override" />
+						</configuration>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
 		<profile>
 		<id>build-installer</id>
 			<properties>

src/main/java/org/janelia/saalfeldlab/bdv/fx/viewer/project/VolatileHierarchyProjector.java

@@ -32,7 +32,6 @@
 import io.github.oshai.kotlinlogging.KLogger;
 import io.github.oshai.kotlinlogging.KotlinLogging;
 import net.imglib2.FinalInterval;
-import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.Volatile;
@@ -114,12 +113,6 @@ public class VolatileHierarchyProjector<A extends Volatile<?>, B extends SetZero
 	 */
 	protected final FinalInterval sourceInterval;
 
-	/**
-	 * A reference to the target image as an iterable. Used for source-less
-	 * operations such as clearing its content.
-	 */
-	protected final IterableInterval<B> iterableTarget;
-
 	/**
 	 * Executor service to be used for rendering
 	 */
@@ -169,8 +162,6 @@ public VolatileHierarchyProjector(
 		numInvalidLevels = sources.size();
 		this.mask = mask;
 
-		this.iterableTarget = Views.iterable(target);
-
 		final int n = Math.max(2, sources.get(0).numDimensions());
 		final long[] min = new long[n];
 		final long[] max = new long[n];
@@ -248,16 +239,13 @@ private void clearUntouchedTargetPixels() {
 	public boolean map(final boolean clearUntouchedTargetPixels) {
 
 		canceled.set(false);
-
 		valid = false;
 
 		final StopWatch stopWatch = StopWatch.createAndStart();
 		final IoStatistics iostat = CacheIoTiming.getIoStatistics();
 		final long startTimeIo = iostat.getIoNanoTime();
 		final long startTimeIoCumulative = iostat.getCumulativeIoNanoTime();
 
-		valid = false;
-
 		int resolutionLevel;
 		/*
 		 * After the for loop, resolutionLevel is the highest (coarsest)

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

@@ -960,10 +960,8 @@ private static <T> void prefetch(
 				hints = new CacheHints(LoadingStrategy.VOLATILE, d.getQueuePriority(), false);
 			}
 			cellImg.setCacheHints(hints);
-			final int[] cellDimensions = new int[3];
-			cellImg.getCellGrid().cellDimensions(cellDimensions);
-			final long[] dimensions = new long[3];
-			cellImg.dimensions(dimensions);
+			final int[] cellDimensions = cellImg.getCellGrid().getCellDimensions();
+			final long[] dimensions = cellImg.dimensionsAsLongArray();
 			final RandomAccess<?> cellsRandomAccess = cellImg.getCells().randomAccess();
 
 			final AffineTransform3D sourceToScreen = viewerTransform.copy();

src/main/java/org/janelia/saalfeldlab/net/imglib2/FinalRealRandomAccessibleRealInterval.java

@@ -67,4 +67,9 @@ public RealRandomAccess<T> realRandomAccess(final RealInterval interval) {
 
 		return src.realRandomAccess(interval);
 	}
+
+	@Override public T getType() {
+
+		return src.getType();
+	}
 }

src/main/java/org/janelia/saalfeldlab/net/imglib2/converter/read/read/ConvertedRandomAccess.java

@@ -76,6 +76,6 @@ public B get() {
 	@Override
 	public ConvertedRandomAccess<A, B> copy() {
 
-		return new ConvertedRandomAccess<>(source.copyRandomAccess(), converter, supplier);
+		return new ConvertedRandomAccess<>(source.copy(), converter, supplier);
 	}
 }

src/main/java/org/janelia/saalfeldlab/net/imglib2/outofbounds/AbstractOutOfBoundsValue.java

@@ -61,7 +61,7 @@ public abstract class AbstractOutOfBoundsValue<T> extends AbstractLocalizable im
 	protected AbstractOutOfBoundsValue(final AbstractOutOfBoundsValue<T> outOfBounds) {
 
 		super(outOfBounds.numDimensions());
-		this.sampler = outOfBounds.sampler.copyRandomAccess();
+		this.sampler = outOfBounds.sampler.copy();
 		dimension = new long[n];
 		min = new long[n];
 		max = new long[n];

src/main/java/org/janelia/saalfeldlab/net/imglib2/outofbounds/AbstractRealOutOfBoundsValue.java

@@ -321,10 +321,4 @@ public long getLongPosition(final int d) {
 
 		return Math.round(position[d]);
 	}
-
-	@Override
-	public RealRandomAccess<T> copyRealRandomAccess() {
-
-		return sampler.copyRealRandomAccess();
-	}
 }

src/main/java/org/janelia/saalfeldlab/net/imglib2/outofbounds/OutOfBoundsConstantValue.java

@@ -58,8 +58,7 @@ protected OutOfBoundsConstantValue(final OutOfBoundsConstantValue<T> outOfBounds
 		this.value = outOfBounds.valueSupplier.get();
 	}
 
-	public <F extends Interval & RandomAccessible<T>> OutOfBoundsConstantValue(final F f, final Supplier<T>
-			valueSupplier) {
+	public <F extends Interval & RandomAccessible<T>> OutOfBoundsConstantValue(final F f, final Supplier<T> valueSupplier) {
 
 		super(f);
 		this.valueSupplier = valueSupplier;
@@ -69,7 +68,6 @@ public <F extends Interval & RandomAccessible<T>> OutOfBoundsConstantValue(final
 	/* Sampler */
 
 	@Override final public T get() {
-		// System.out.println( getLocationAsString() + " " + isOutOfBounds );
 		if (isOutOfBounds) {
 			return value;
 		}
@@ -81,10 +79,4 @@ public <F extends Interval & RandomAccessible<T>> OutOfBoundsConstantValue(final
 		return new OutOfBoundsConstantValue<>(this);
 	}
 
-	/* RandomAccess */
-
-	@Override final public OutOfBoundsConstantValue<T> copyRandomAccess() {
-
-		return copy();
-	}
 }