Development

.github/workflows/build-main.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Java
-        uses: actions/setup-java@v4
+        uses: actions/setup-java@v5
         with:
           java-version: '8'
           distribution: 'zulu'

.github/workflows/build-pr.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Java
-        uses: actions/setup-java@v4
+        uses: actions/setup-java@v5
         with:
           java-version: '8'
           distribution: 'zulu'

.github/workflows/platform-test.yml

@@ -21,7 +21,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Java
-        uses: actions/setup-java@v4
+        uses: actions/setup-java@v5
         with:
           java-version: '8'
           distribution: 'zulu'

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>40.0.0</version>
+		<version>43.0.0</version>
 		<relativePath />
 	</parent>
 
@@ -139,7 +139,7 @@
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
-		<n5.version>4.0.0-alpha-9</n5.version>
+		<n5.version>4.0.0-alpha-12</n5.version>
 	</properties>
 
 	<dependencies>

src/main/java/org/janelia/saalfeldlab/n5/hdf5/N5HDF5Reader.java

@@ -689,7 +689,7 @@ public DatasetAttributes getDatasetAttributes(String pathName) {
 	}
 
 	@Override
-	public DataBlock<?> readBlock(
+	public <T> DataBlock<T> readChunk(
 			String pathName,
 			final DatasetAttributes datasetAttributes,
 			final long... gridPosition) throws N5Exception {
@@ -713,7 +713,7 @@ public DataBlock<?> readBlock(
 		if (datasetAttributes.getDataType() == DataType.STRING) {
 			final int[] intHdf5CroppedBlockSize = Arrays.stream(hdf5CroppedBlockSize).mapToInt(i -> (int)i).toArray();
 			MDArray<String> data = reader.string().readMDArrayBlockWithOffset(normalizedPathName, intHdf5CroppedBlockSize, hdf5Offset);
-			return new StringDataBlock(croppedBlockSize, gridPosition, data.getAsFlatArray());
+			return (DataBlock<T>)new StringDataBlock(croppedBlockSize, gridPosition, data.getAsFlatArray());
 		}
 
 		final DataType dataType = datasetAttributes.getDataType();
@@ -733,21 +733,21 @@ public DataBlock<?> readBlock(
 			H5Sclose(fileSpaceId);
 			H5Sclose(memorySpaceId);
 		}
-		return block;
+		return (DataBlock<T>)block;
 	}
 
 	@Override
-	public DataBlock<?> readShard(
+	public <T> DataBlock<T> readBlock(
 			final String pathName,
 			final DatasetAttributes datasetAttributes,
 			final long... gridPosition) throws N5Exception {
 
-		// HDF5 does not support sharding, so readShard is always equivalent to readBlock
-		return readBlock(pathName, datasetAttributes, gridPosition);
+		// HDF5 does not support sharding, so readBlock is always equivalent to readChunk
+		return (DataBlock<T>)readChunk(pathName, datasetAttributes, gridPosition);
 	}
 
 	@Override
-	public boolean shardExists(String pathName, DatasetAttributes datasetAttributes, long... gridPosition) throws N5Exception {
+	public boolean blockExists(String pathName, DatasetAttributes datasetAttributes, long... gridPosition) throws N5Exception {
 
 		return true;
 	}

src/main/java/org/janelia/saalfeldlab/n5/hdf5/N5HDF5Writer.java

@@ -47,6 +47,9 @@
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.n5.RawCompression;
 import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Util.OpenDataSetCache.OpenDataSet;
+import org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid;
+import org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition;
+import org.janelia.saalfeldlab.n5.shard.Region;
 
 import java.io.File;
 import java.io.IOException;
@@ -55,6 +58,8 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
 
 import static hdf.hdf5lib.H5.H5Dget_space;
 import static hdf.hdf5lib.H5.H5Dwrite;
@@ -527,7 +532,7 @@ public boolean removeAttributes(
 	}
 
 	@Override
-	public <T> void writeBlock(
+	public <T> void writeChunk(
 			String pathName,
 			final DatasetAttributes datasetAttributes,
 			final DataBlock<T> dataBlock) throws N5Exception {
@@ -555,29 +560,74 @@ public <T> void writeBlock(
 		}
 	}
 
-	public <T> void writeShard(
+	@Override
+	public <T> void writeBlock(
 			final String pathName,
 			final DatasetAttributes datasetAttributes,
 			final DataBlock<T> dataBlock) throws N5Exception {
 
-		// HDF5 does not support sharding, so readShard is always equivalent to readBlock
-		writeBlock(pathName, datasetAttributes, dataBlock);
+		// HDF5 does not support sharding, so writeBlock is always equivalent to writeChunk
+		writeChunk(pathName, datasetAttributes, dataBlock);
 	}
 
 	@Override
-	public boolean deleteBlock(String pathName, final long... gridPosition) throws N5Exception {
+	public <T> void writeRegion(
+			String datasetPath,
+			DatasetAttributes datasetAttributes,
+			long[] min,
+			long[] size,
+			DataBlockSupplier<T> dataBlocks,
+			boolean writeFully) throws N5Exception {
+
+		final NestedGrid grid = datasetAttributes.getNestedBlockGrid();
+		final Region region = new Region(min, size, grid);
+		for (long[] key : Region.gridPositions(region.minPos().key(), region.maxPos().key())) {
+			final NestedPosition pos = grid.nestedPosition(key, 0); // HDF5 is never nested, get level 0
+			final long[] gridPosition = pos.absolute(0);
+			final DataBlock<T> existingDataBlock = writeFully || region.fullyContains(pos)
+					? null
+					: readBlock(datasetPath, datasetAttributes, gridPosition);
+			final DataBlock<T> dataBlock = dataBlocks.get(gridPosition, existingDataBlock);
+			// null blocks may be provided when they contain only the fill value
+			// and only non-empty blocks should be written, for example
+			if (dataBlock == null) {
+				deleteBlock(datasetPath, datasetAttributes, gridPosition);
+			} else {
+				writeBlock(datasetPath, datasetAttributes, dataBlock);
+			}
+		}
+
+	}
+
+	public <T> void writeRegion(
+			String datasetPath,
+	DatasetAttributes datasetAttributes,
+			long[] min,
+			long[] size,
+			DataBlockSupplier<T> dataBlocks,
+			boolean writeFully,
+			ExecutorService exec) throws N5Exception, InterruptedException, ExecutionException {
+
+		// block until the write is complete
+		exec.submit(() ->  {
+			writeRegion(datasetPath, datasetAttributes, min, size, dataBlocks, writeFully);
+		}).get();
+	}
+
+	@Override
+	public boolean deleteChunk(String pathName, final long... gridPosition) throws N5Exception {
 
 		if (pathName.equals(""))
 			pathName = "/";
 
 		final DatasetAttributes datasetAttributes = getDatasetAttributes(pathName);
-		return deleteBlock(pathName, datasetAttributes, gridPosition);
+		return deleteChunk(pathName, datasetAttributes, gridPosition);
 	}
 
 	@Override
-	public boolean deleteBlock(String datasetPath, DatasetAttributes datasetAttributes, long... gridPosition) throws N5Exception {
+	public boolean deleteChunk(String datasetPath, DatasetAttributes datasetAttributes, long... gridPosition) throws N5Exception {
 
-		// deletion is not supported in HDF5, so the block is overwritten with zeros instead
+		// deletion is not supported in HDF5, so the chunk is overwritten with zeros instead
 		// Consider using defaultValue instead of zero?
 
 		if (datasetPath.equals(""))
@@ -597,13 +647,27 @@ public boolean deleteBlock(String datasetPath, DatasetAttributes datasetAttribut
 			case FLOAT32:
 			case FLOAT64:
 				final DataBlock<?> empty = dataType.createDataBlock(datasetAttributes.getBlockSize(), gridPosition);
-				writeBlock(datasetPath, datasetAttributes, empty);
+				writeChunk(datasetPath, datasetAttributes, empty);
 				return true;
 			default:
 				return false;
 		}
 	}
 
+	@Override
+	public boolean deleteBlock(String pathName, final long... gridPosition) throws N5Exception {
+
+		// HDF5 does not support sharding, so deleteBlock is always equivalent to deleteChunk
+		return deleteChunk(pathName, gridPosition);
+	}
+
+	@Override
+	public boolean deleteBlock(String datasetPath, DatasetAttributes datasetAttributes, long... gridPosition) throws N5Exception {
+
+		// HDF5 does not support sharding, so deleteBlock is always equivalent to deleteChunk
+		return deleteChunk(datasetPath, datasetAttributes, gridPosition);
+	}
+
 	@Override
 	public boolean remove() {
 

src/test/java/org/janelia/saalfeldlab/n5/hdf5/N5HDF5Test.java

@@ -190,6 +190,12 @@ public void testMode1WriteReadByteBlock() {
 	public void testWriteReadSerializableBlock() {
 	}
 
+	@Override
+	@Test
+	@Ignore("HDF5 does not support modifying dataset attributes after creating the dataset.")
+	public void testDatasetAttributes() {
+	}
+
 	@Override
 	@Test
 	@Ignore("Writing blocks larger than the dimensions of the dataset is invalid for HDF5.")
@@ -522,30 +528,30 @@ public void testDelete() {
 			final long[] position1 = {0, 0, 0};
 			final long[] position2 = {0, 1, 2};
 
-			// non-existant block should be zeros
-			final DataBlock<?> emptyBlock = n5.readBlock(datasetName, attributes, position1);
+			// non-existant chunk should be zeros
+			final DataBlock<?> emptyBlock = n5.readChunk(datasetName, attributes, position1);
 			assertTrue(emptyBlock instanceof ByteArrayDataBlock);
 			final byte[] zeros = new byte[byteBlock.length];
 			assertArrayEquals(zeros, ((ByteArrayDataBlock)emptyBlock).getData());
 
 			final ByteArrayDataBlock dataBlock = new ByteArrayDataBlock(blockSize, position1, byteBlock);
-			n5.writeBlock(datasetName, attributes, dataBlock);
+			n5.writeChunk(datasetName, attributes, dataBlock);
 
-			// block should exist at position1 but not at position2
-			final DataBlock<?> readBlock = n5.readBlock(datasetName, attributes, position1);
+			// chunk should exist at position1 but not at position2
+			final DataBlock<?> readBlock = n5.readChunk(datasetName, attributes, position1);
 			assertNotNull(readBlock);
 			assertTrue(readBlock instanceof ByteArrayDataBlock);
 			assertArrayEquals(byteBlock, ((ByteArrayDataBlock)readBlock).getData());
 
-			assertTrue("deleting existing block should return true", n5.deleteBlock(datasetName, position1));
-			assertTrue("hdf5 returns true even on non-existent blocks, since they can only be zeroed out", n5.deleteBlock(datasetName, position1));
-			assertTrue("hdf5 returns true even on non-existent blocks, since they can only be zeroed out", n5.deleteBlock(datasetName, position2));
+			assertTrue("deleting existing chunk should return true", n5.deleteChunk(datasetName, position1));
+			assertTrue("hdf5 returns true even on non-existent chunks, since they can only be zeroed out", n5.deleteChunk(datasetName, position1));
+			assertTrue("hdf5 returns true even on non-existent chunks, since they can only be zeroed out", n5.deleteChunk(datasetName, position2));
 
-			// no block should exist anymore
-			final DataBlock<?> pos1EmptyBlock = n5.readBlock(datasetName, attributes, position1);
+			// no chunk should exist anymore
+			final DataBlock<?> pos1EmptyBlock = n5.readChunk(datasetName, attributes, position1);
 			assertArrayEquals(zeros, ((ByteArrayDataBlock)pos1EmptyBlock).getData());
 
-			final DataBlock<?> pos2EmptyBlock = n5.readBlock(datasetName, attributes, position2);
+			final DataBlock<?> pos2EmptyBlock = n5.readChunk(datasetName, attributes, position2);
 			assertArrayEquals(zeros, ((ByteArrayDataBlock)pos2EmptyBlock).getData());
 		}
 	}