Adapts to changes related to https://forum.image.sc/t/updated-ngff-su…

…pport-in-fiji-hdf5-n5-zarr-ome-ngff/91705

SNAPSHOT parent pom - build will fail

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>37.0.0</version>
+		<version>37.1.0-SNAPSHOT</version>
 		<relativePath />
 	</parent>
 
@@ -162,11 +162,6 @@
 			<version>${bigvolumeviewer.version}</version>
 		</dependency>
 
-		<dependency>
-			<groupId>sc.fiji</groupId>
-			<artifactId>bigwarp_fiji</artifactId>
-		</dependency>
-
 		<dependency>
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2</artifactId>
@@ -186,6 +181,12 @@
 			<scope>test</scope>
 		</dependency>
 
+		<dependency>
+			<groupId>sc.fiji</groupId>
+			<artifactId>bigwarp_fiji</artifactId>
+			<version>9.1.0</version>
+		</dependency>
+
 		<dependency>
 			<groupId>net.imagej</groupId>
 			<artifactId>imagej</artifactId>

src/main/java/bdv/util/VolatileSource.java → src/main/java/bdv/util/WrapVolatileSource.java

@@ -55,7 +55,7 @@
 import java.util.concurrent.ConcurrentHashMap;
 
 /**
- * A {@link VolatileSource} simply wraps and cache volatileviews of a
+ * A {@link WrapVolatileSource} simply wraps and cache volatileviews of a
  * {@link Source} which can be made Volatile thanks to
  * {@link VolatileViews#wrapAsVolatile} That's not always possible! A
  * {@link SharedQueue} can be passed as an argument in the constructor to
@@ -66,7 +66,7 @@
  * @param <V> {@link Volatile} type
  */
 
-public class VolatileSource<T extends NumericType<T>, V extends Volatile<T> & NumericType<V>>
+public class WrapVolatileSource<T extends NumericType<T>, V extends Volatile<T> & NumericType<V>>
 	implements Source<V>
 {
 
@@ -80,12 +80,12 @@ public class VolatileSource<T extends NumericType<T>, V extends Volatile<T> & Nu
 	final ConcurrentHashMap<Integer, ConcurrentHashMap<Integer, RandomAccessibleInterval<V>>> cachedRAIs =
 		new ConcurrentHashMap<>();
 
-	public VolatileSource(final Source<T> source) {
+	public WrapVolatileSource(final Source<T> source) {
 		this.originSource = source;
 		queue = new SharedQueue(2);
 	}
 
-	public VolatileSource(final Source<T> originSource, final SharedQueue queue) {
+	public WrapVolatileSource(final Source<T> originSource, final SharedQueue queue) {
 		this.originSource = originSource;
 		this.queue = queue;
 	}

src/main/java/net/imglib2/realtransform/InvertibleWrapped2DTransformAs3DRealTransformRunTimeAdapter.java

@@ -0,0 +1,57 @@
+/*-
+ * #%L
+ * BigDataViewer-Playground
+ * %%
+ * Copyright (C) 2019 - 2023 Nicolas Chiaruttini, EPFL - Robert Haase, MPI CBG - Christian Tischer, EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package net.imglib2.realtransform;
+
+import org.scijava.plugin.Plugin;
+import sc.fiji.persist.IClassRuntimeAdapter;
+
+/**
+ * Adapter of an 2D transformed wrapped as 3D
+ */
+
+@Plugin(type = IClassRuntimeAdapter.class)
+public class InvertibleWrapped2DTransformAs3DRealTransformRunTimeAdapter implements
+		IClassRuntimeAdapter<RealTransform, InvertibleWrapped2DTransformAs3D>
+{
+	@Override
+	public Class<? extends RealTransform> getBaseClass() {
+		return RealTransform.class;
+	}
+
+	@Override
+	public Class<? extends InvertibleWrapped2DTransformAs3D> getRunTimeClass() {
+		return InvertibleWrapped2DTransformAs3D.class;
+	}
+
+	@Override
+	public boolean useCustomAdapter() {
+		return false;
+	}
+}

src/main/java/net/imglib2/realtransform/Wrapped2DTransformAs3DRealTransformAdapter.java

@@ -63,12 +63,11 @@ public Wrapped2DTransformAs3D deserialize(JsonElement jsonElement, Type type,
 			"wrappedTransform"), RealTransform.class);
 
 		if (!(rt instanceof InvertibleRealTransform)) {
-			logger.error(
-				"Wrapped transform not invertible -> deserialization impossible...");
-			return null;
+
+			return new Wrapped2DTransformAs3D(rt);
 		}
 
-		return new Wrapped2DTransformAs3D((InvertibleRealTransform) rt);
+		return new InvertibleWrapped2DTransformAs3D((InvertibleRealTransform) rt);
 	}
 
 	@Override

src/main/java/sc/fiji/bdvpg/sourceandconverter/register/BigWarpLauncher.java

@@ -35,6 +35,7 @@
 import bdv.util.ViewerPanelHandle;
 import bdv.viewer.SourceAndConverter;
 import bigwarp.BigWarp;
+import bigwarp.BigWarpData;
 import mpicbg.spim.data.SpimDataException;
 
 import java.util.ArrayList;
@@ -50,7 +51,7 @@
 
 public class BigWarpLauncher implements Runnable {
 
-	final BigWarp.BigWarpData<?> bwData;
+	final BigWarpData<?> bwData;
 
 	BigWarp<?> bigWarp;
 
@@ -116,7 +117,7 @@ public BigWarpLauncher(List<SourceAndConverter<?>> movingSources,
 		allConverterSetups.forEach(setup -> displaysettings.put(setup,
 			new double[] { setup.getDisplayRangeMin(), setup.getDisplayRangeMax() }));
 
-		bwData = new BigWarp.BigWarpData(allSources, allConverterSetups, null,
+		bwData = new BigWarpData(allSources, allConverterSetups, null,
 			mvSrcIndices, fxSrcIndices);
 
 	}

src/main/java/sc/fiji/bdvpg/sourceandconverter/transform/SourceResampler.java

@@ -30,7 +30,7 @@
 package sc.fiji.bdvpg.sourceandconverter.transform;
 
 import bdv.util.ResampledSource;
-import bdv.util.VolatileSource;
+import bdv.util.WrapVolatileSource;
 import bdv.viewer.Source;
 import bdv.viewer.SourceAndConverter;
 import net.imglib2.Volatile;
@@ -91,7 +91,7 @@ public SourceAndConverter<T> apply(SourceAndConverter<T> src) {
 			SourceAndConverter<? extends Volatile<T>> vsac;
 			Source<? extends Volatile<T>> vsrcResampled;
 			if (cache) {
-				vsrcResampled = new VolatileSource<>(srcRsampled);
+				vsrcResampled = new WrapVolatileSource<>(srcRsampled);
 			}
 			else {
 				vsrcResampled = new ResampledSource(src.asVolatile().getSpimSource(),