Support NGFF using n5-universe

pom.xml

@@ -63,7 +63,7 @@
 			<groupId>cisd</groupId>
 			<artifactId>jhdf5</artifactId>
 		</dependency>
-		
+
 		<!-- ImgLib2 dependencies -->
 		<dependency>
 			<groupId>org.scijava</groupId>
@@ -77,7 +77,39 @@
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2-roi</artifactId>
 		</dependency>
-
+
+		<!-- N5 dependencies. -->
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-universe</artifactId>
+			<version>1.6.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-google-cloud</artifactId>
+			<version>4.1.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-aws-s3</artifactId>
+			<version>4.2.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-viewer_fiji</artifactId>
+			<version>6.1.1</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-ij</artifactId>
+			<version>4.2.1</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-zarr</artifactId>
+			<version>1.3.4</version>
+		</dependency>
+
 		<!-- Misc dependencies. -->
 		<dependency>
 			<groupId>com.opencsv</groupId>
@@ -99,6 +131,12 @@
 			<artifactId>junit</artifactId>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>uk.org.webcompere</groupId>
+			<artifactId>system-stubs-junit4</artifactId>
+			<version>2.1.3</version>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>sc.fiji</groupId>
 			<artifactId>TrackMate</artifactId>
@@ -109,7 +147,6 @@
 			<artifactId>MaMuT</artifactId>
 			<scope>test</scope>
 		</dependency>
-
 
 	</dependencies>
 

src/main/java/org/mastodon/mamut/io/img/cache/MastodonSimpleCacheArrayLoader.java

@@ -0,0 +1,118 @@
+/*-
+ * #%L
+ * Mastodon
+ * %%
+ * Copyright (C) 2014 - 2024 Mastodon developers
+ * %%
+ * 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 org.mastodon.mamut.io.img.cache;
+
+import java.io.IOException;
+
+import bdv.img.cache.CacheArrayLoader;
+import bdv.img.cache.CreateInvalidVolatileCell;
+import bdv.img.cache.DefaultEmptyArrayCreator;
+import bdv.img.cache.EmptyArrayCreator;
+import bdv.img.cache.SimpleCacheArrayLoader;
+import net.imglib2.img.basictypeaccess.DataAccess;
+import net.imglib2.img.basictypeaccess.volatiles.VolatileArrayDataAccess;
+import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileByteArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileCharArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileDoubleArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileFloatArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileIntArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileLongArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.DirtyVolatileShortArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.VolatileByteArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.VolatileCharArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.VolatileDoubleArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.VolatileFloatArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.VolatileIntArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.VolatileLongArray;
+import net.imglib2.img.basictypeaccess.volatiles.array.VolatileShortArray;
+import net.imglib2.img.cell.CellGrid;
+import net.imglib2.type.NativeType;
+
+public interface MastodonSimpleCacheArrayLoader< A extends DataAccess > extends SimpleCacheArrayLoader< A >
+{
+
+    /**
+     * Implementing classes must override this if {@code A} is not a standard
+     * {@link VolatileArrayDataAccess} type. The default implementation returns
+     * {@code null}, which will let
+     * {@link CreateInvalidVolatileCell#get(CellGrid, NativeType, boolean)
+     * CreateInvalidVolatileCell.get(...)} try to figure out the appropriate
+     * {@link DefaultEmptyArrayCreator}.
+     * <p>
+     * Default access types are
+     * </p>
+     * <ul>
+     * <li>{@link DirtyVolatileByteArray}</li>
+     * <li>{@link VolatileByteArray}</li>
+     * <li>{@link DirtyVolatileCharArray}</li>
+     * <li>{@link VolatileCharArray}</li>
+     * <li>{@link DirtyVolatileDoubleArray}</li>
+     * <li>{@link VolatileDoubleArray}</li>
+     * <li>{@link DirtyVolatileFloatArray}</li>
+     * <li>{@link VolatileFloatArray}</li>
+     * <li>{@link DirtyVolatileIntArray}</li>
+     * <li>{@link VolatileIntArray}</li>
+     * <li>{@link DirtyVolatileLongArray}</li>
+     * <li>{@link VolatileLongArray}</li>
+     * <li>{@link DirtyVolatileShortArray}</li>
+     * <li>{@link VolatileShortArray}</li>
+     * </ul>
+     *
+     * @return an {@link EmptyArrayCreator} for {@code A} or null.
+     */
+    default EmptyArrayCreator< A > getEmptyArrayCreator()
+    {
+        return null;
+    }
+
+    /**
+     * Load cell data into memory. This method blocks until data is successfully
+     * loaded. If it completes normally, the returned data is always valid. If
+     * anything goes wrong, an {@link IOException} is thrown.
+     * <p>
+     * {@code SimpleCacheArrayLoader} is supposed to load data one specific
+     * image. {@code loadArray()} will not get information about which
+     * timepoint, resolution level, etc a requested block belongs to.
+     * <p>
+     * This is in contrast to
+     * {@link CacheArrayLoader#loadArray(int, int, int, int[], long[])}, where
+     * all information to identify a particular block in a whole dataset is
+     * provided.
+     *
+     * @param gridPosition
+     *            the coordinate of the cell in the cell grid.
+     * @param cellDimensions
+     *            the dimensions of the cell.
+     * @param timepoint
+     *            the timepoint.
+     *
+     * @return loaded cell data.
+     */
+    A loadArrayAtTimepoint( long[] gridPosition, int[] cellDimensions, int timepoint ) throws IOException;
+}