From b87cfc4025c569b36779d0bab3a1a35b136f118e Mon Sep 17 00:00:00 2001
From: John Bogovic <bogovicj@janelia.hhmi.org>
Date: Mon, 23 Mar 2026 14:43:58 -0400
Subject: [PATCH] fix: add writeRegion

* bump n5 dependency (no longer has default implementation)
* add generic type to readBlock
---
 pom.xml                                       |  2 +-
 .../saalfeldlab/n5/hdf5/N5HDF5Reader.java     |  7 +--
 .../saalfeldlab/n5/hdf5/N5HDF5Writer.java     | 49 +++++++++++++++++++
 3 files changed, 54 insertions(+), 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index 1933a63..fbbd19b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -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-SNAPSHOT</n5.version>
 	</properties>
 
 	<dependencies>
diff --git a/src/main/java/org/janelia/saalfeldlab/n5/hdf5/N5HDF5Reader.java b/src/main/java/org/janelia/saalfeldlab/n5/hdf5/N5HDF5Reader.java
index e19a23e..84ff01e 100644
--- a/src/main/java/org/janelia/saalfeldlab/n5/hdf5/N5HDF5Reader.java
+++ b/src/main/java/org/janelia/saalfeldlab/n5/hdf5/N5HDF5Reader.java
@@ -688,8 +688,9 @@ public DatasetAttributes getDatasetAttributes(String pathName) {
 				new RawCompression());
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
-	public DataBlock<?> readBlock(
+	public <T> DataBlock<T> readBlock(
 			String pathName,
 			final DatasetAttributes datasetAttributes,
 			final long... gridPosition) throws N5Exception {
@@ -713,7 +714,7 @@ 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();
@@ -733,7 +734,7 @@ public DataBlock<?> readBlock(
 			H5Sclose(fileSpaceId);
 			H5Sclose(memorySpaceId);
 		}
-		return block;
+		return (DataBlock<T>)block;
 	}
 
 	@Override
diff --git a/src/main/java/org/janelia/saalfeldlab/n5/hdf5/N5HDF5Writer.java b/src/main/java/org/janelia/saalfeldlab/n5/hdf5/N5HDF5Writer.java
index 9997ccc..148ef5b 100644
--- a/src/main/java/org/janelia/saalfeldlab/n5/hdf5/N5HDF5Writer.java
+++ b/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.Region;
+import org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid;
+import org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition;
 
 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;
@@ -564,6 +569,50 @@ public <T> void writeShard(
 		writeBlock(pathName, datasetAttributes, dataBlock);
 	}
 
+	@Override
+	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 deleteBlock(String pathName, final long... gridPosition) throws N5Exception {