Add N5Writer.writeRegion methods

src/main/java/org/janelia/saalfeldlab/n5/GsonKeyValueN5Writer.java

@@ -35,6 +35,8 @@
 import java.util.Map;
 
 import com.google.gson.JsonSyntaxException;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
 import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
 import org.janelia.saalfeldlab.n5.shard.PositionValueAccess;
 
@@ -210,6 +212,41 @@ default boolean removeAttributes(final String pathName, final List<String> attri
 		return removed;
 	}
 
+	@Override
+	default <T> void writeRegion(
+			final String datasetPath,
+			final DatasetAttributes datasetAttributes,
+			final long[] min,
+			final long[] size,
+			final DataBlockSupplier<T> dataBlocks,
+			final boolean writeFully) throws N5Exception {
+		try {
+			final PositionValueAccess posKva = PositionValueAccess.fromKva(getKeyValueAccess(), getURI(), N5URI.normalizeGroupPath(datasetPath), datasetAttributes);
+			datasetAttributes.<T>getDatasetAccess().writeRegion(posKva, min, size, dataBlocks, datasetAttributes.getDimensions(), writeFully);
+		} catch (final UncheckedIOException e) {
+			throw new N5IOException(
+					"Failed to write blocks into dataset " + datasetPath, e);
+		}
+	}
+
+	@Override
+	default <T> void writeRegion(
+			final String datasetPath,
+			final DatasetAttributes datasetAttributes,
+			final long[] min,
+			final long[] size,
+			final DataBlockSupplier<T> dataBlocks,
+			final boolean writeFully,
+			final ExecutorService exec) throws N5Exception, InterruptedException, ExecutionException {
+		try {
+			final PositionValueAccess posKva = PositionValueAccess.fromKva(getKeyValueAccess(), getURI(), N5URI.normalizeGroupPath(datasetPath), datasetAttributes);
+			datasetAttributes.<T>getDatasetAccess().writeRegion(posKva, min, size, dataBlocks, datasetAttributes.getDimensions(), writeFully, exec);
+		} catch (final UncheckedIOException e) {
+			throw new N5IOException(
+					"Failed to write blocks into dataset " + datasetPath, e);
+		}
+	}
+
 	@Override
 	default <T> void writeBlocks(
 			final String datasetPath,
@@ -239,7 +276,6 @@ default <T> void writeBlock(
 					"Failed to write block " + Arrays.toString(dataBlock.getGridPosition()) + " into dataset " + path,
 					e);
 		}
-
 	}
 
 	@Override

src/main/java/org/janelia/saalfeldlab/n5/N5Writer.java

@@ -28,9 +28,6 @@
  */
 package org.janelia.saalfeldlab.n5;
 
-import org.janelia.saalfeldlab.n5.codec.BlockCodecInfo;
-import org.janelia.saalfeldlab.n5.codec.DataCodecInfo;
-
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.ObjectOutputStream;
@@ -39,6 +36,8 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
 
 /**
  * A simple structured container API for hierarchies of chunked
@@ -265,6 +264,56 @@ default <T> void writeBlocks(
 			writeBlock(datasetPath, datasetAttributes, block);
 	}
 
+	@FunctionalInterface
+	interface DataBlockSupplier<T> {
+
+		/**
+		 *
+		 * @param gridPos
+		 * @param existingDataBlock
+		 * 		existing data to be merged into the new data block (maybe {@code null})
+		 *
+		 * @return data block at the given gridPos
+		 */
+		DataBlock<T> get(long[] gridPos, final DataBlock<T> existingDataBlock);
+	}
+
+	/**
+	 * @param datasetPath the dataset path
+	 * @param datasetAttributes the dataset attributes
+	 * @param min min pixel coordinate of region to write
+	 * @param size size in pixels of region to write
+	 * @param dataBlocks is asked to create blocks within the given region
+	 * @param writeFully if false, merge existing data in shards/blocks that overlap the region boundary. if true, override everything.
+	 * @throws N5Exception the exception
+	 */
+	<T> void writeRegion(
+			String datasetPath,
+			DatasetAttributes datasetAttributes,
+			long[] min,
+			long[] size,
+			DataBlockSupplier<T> dataBlocks,
+			boolean writeFully) throws N5Exception;
+
+	/**
+	 * @param datasetPath the dataset path
+	 * @param datasetAttributes the dataset attributes
+	 * @param min min pixel coordinate of region to write
+	 * @param size size in pixels of region to write
+	 * @param dataBlocks is asked to create blocks within the given region
+	 * @param writeFully if false, merge existing data in shards/blocks that overlap the region boundary. if true, override everything.
+	 * @param exec used to parallelize over blocks and shards
+	 * @throws N5Exception the exception
+	 */
+	<T> void writeRegion(
+			String datasetPath,
+			DatasetAttributes datasetAttributes,
+			long[] min,
+			long[] size,
+			DataBlockSupplier<T> dataBlocks,
+			boolean writeFully,
+			ExecutorService exec) throws N5Exception, InterruptedException, ExecutionException;
+
 	/**
 	 * Deletes the block at {@code gridPosition}.
 	 *
@@ -278,6 +327,24 @@ boolean deleteBlock(
 			final String datasetPath,
 			final long... gridPosition) throws N5Exception;
 
+	/**
+	 * Deletes the blocks at the given {@code gridPositions}.
+	 *
+	 * @param datasetPath dataset path
+	 * @param gridPositions a list of grid positions
+	 * @return {@code true} if any of the specified blocks existed and was deleted
+	 * @throws N5Exception if any of the block exists but could not be deleted
+	 */
+	default boolean deleteBlocks(
+			final String datasetPath,
+			final List<long[]> gridPositions) throws N5Exception {
+		boolean deleted = false;
+		for (long[] pos : gridPositions) {
+			deleted |= deleteBlock(datasetPath, pos);
+		}
+		return deleted;
+	}
+
 	/**
 	 * Save a {@link Serializable} as an N5 {@link DataBlock} at a given offset.
 	 * The

src/main/java/org/janelia/saalfeldlab/n5/shard/DatasetAccess.java

@@ -1,15 +1,18 @@
 package org.janelia.saalfeldlab.n5.shard;
 
-import org.janelia.saalfeldlab.n5.DataBlock;
-import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
-import org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid;
-import org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition;
-
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 import java.util.TreeMap;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import org.janelia.saalfeldlab.n5.DataBlock;
+import org.janelia.saalfeldlab.n5.N5Exception;
+import org.janelia.saalfeldlab.n5.N5Exception.N5IOException;
+import org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier;
+import org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid;
+import org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition;
 
 /**
  * Wrap an instantiated DataBlock/shard codec hierarchy to implement (single and
@@ -20,15 +23,73 @@
  */
 public interface DatasetAccess<T> {
 
-	DataBlock<T> readBlock(PositionValueAccess kva, long[] gridPosition) throws N5IOException;
+	DataBlock<T> readBlock(PositionValueAccess pva, long[] gridPosition) throws N5IOException;
+
+	void writeBlock(PositionValueAccess pva, DataBlock<T> dataBlock) throws N5IOException;
+
+	boolean deleteBlock(PositionValueAccess pva, long[] gridPosition) throws N5IOException;
 
-	void writeBlock(PositionValueAccess kva, DataBlock<T> dataBlock) throws N5IOException;
 
-	boolean deleteBlock(PositionValueAccess kva, long[] gridPosition) throws N5IOException;
+	List<DataBlock<T>> readBlocks(PositionValueAccess pva, List<long[]> positions) throws N5IOException;
 
-	List<DataBlock<T>> readBlocks(PositionValueAccess kva, List<long[]> positions);
+	void writeBlocks(PositionValueAccess pva, List<DataBlock<T>> blocks) throws N5IOException;
 
-	void writeBlocks(PositionValueAccess kva, List<DataBlock<T>> blocks);
+//	TODO:
+//	  boolean deleteBlocks(PositionValueAccess pva, List<long[]> positions) throws N5IOException;
+
+
+	/**
+	 *
+	 * @param pva
+	 * @param min
+	 * 		min pixel coordinate of region to write
+	 * @param size
+	 * 		size in pixels of region to write
+	 * @param blocks
+	 * 		is asked to create blocks within the given region
+	 * @param datasetDimensions
+	 * @param writeFully
+	 * 		if false, merge existing data in shards/blocks that overlap the region boundary. if true, override everything.
+	 *
+	 * @throws N5IOException
+	 */
+	void writeRegion(
+			PositionValueAccess pva,
+			long[] min,
+			long[] size,
+			DataBlockSupplier<T> blocks,
+			long[] datasetDimensions,
+			boolean writeFully
+	) throws N5IOException;
+
+	/**
+	 *
+	 * @param pva
+	 * @param min
+	 * 		min pixel coordinate of region to write
+	 * @param size
+	 * 		size in pixels of region to write
+	 * @param blocks
+	 * 		is asked to create blocks within the given region. must be thread-safe.
+	 * @param datasetDimensions
+	 * @param writeFully
+	 * 		if false, merge existing data in shards/blocks that overlap the region boundary. if true, override everything.
+	 * @param exec
+	 * 		used to parallelize over blocks and shards
+	 *
+	 * @throws N5Exception
+	 * @throws InterruptedException
+	 * @throws ExecutionException
+	 */
+	void writeRegion(
+			PositionValueAccess pva,
+			long[] min,
+			long[] size,
+			DataBlockSupplier<T> blocks,
+			long[] datasetDimensions,
+			boolean writeFully,
+			ExecutorService exec
+	) throws N5Exception, InterruptedException, ExecutionException;
 
 	NestedGrid getGrid();
 
@@ -42,6 +103,7 @@ public interface DatasetAccess<T> {
 	 * @param outerLevel of the outerLevel shard position to group by. must be in range {@code [1, NestedGrid.numLevels() - 1]}
 	 * @return map of outerLevel shard positions to inner level block positions
 	 */
+	// TODO: move to Nesting
 	static <T extends NestedPosition> Collection<List<T>> groupInnerPositions(final NestedGrid grid, final List<T> innerPositions, final int outerLevel)  {
 
 		if (outerLevel < 1 || outerLevel >= grid.numLevels())
@@ -56,7 +118,7 @@ static <T extends NestedPosition> Collection<List<T>> groupInnerPositions(final
 			if (nestedPosition.level() == outerLevel)
 				outerNestedPosition = nestedPosition;
 			else
-				outerNestedPosition = new NestedPosition(grid, nestedPosition.absolute(0), outerLevel);
+				outerNestedPosition = grid.nestedPosition(nestedPosition.absolute(outerLevel), outerLevel);
 
 
 			final List<T> blocks = blocksPerShard.computeIfAbsent(outerNestedPosition, it -> new ArrayList<>());