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fix: remove writeRegion default implementations #217

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Merged
tpietzsch merged 1 commit into from
Mar 25, 2026
Merged

fix: remove writeRegion default implementations #217

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62 changes: 9 additions & 53 deletions src/main/java/org/janelia/saalfeldlab/n5/N5Writer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,9 +39,6 @@
import java.util.Map;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid;
import org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition;
import org.janelia.saalfeldlab.n5.shard.Region;

/**
* A simple structured container API for hierarchies of chunked
Expand Down Expand Up @@ -320,33 +317,13 @@ interface DataBlockSupplier<T> {
* @param writeFully if false, merge existing data in shards/blocks that overlap the region boundary. if true, override everything.
* @throws N5Exception the exception
*/
default <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, grid.numLevels() - 1);
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);
}
}

}
<T> void writeRegion(
final String datasetPath,
final DatasetAttributes datasetAttributes,
final long[] min,
final long[] size,
final DataBlockSupplier<T> dataBlocks,
final boolean writeFully) throws N5Exception;

/**
* @param datasetPath the dataset path
Expand All @@ -358,35 +335,14 @@ default <T> void writeRegion(
* @param exec used to parallelize over blocks and shards
* @throws N5Exception the exception
*/
default <T> void writeRegion(
<T> void writeRegion(
String datasetPath,
DatasetAttributes datasetAttributes,
long[] min,
long[] size,
DataBlockSupplier<T> dataBlocks,
boolean writeFully,
ExecutorService exec) throws N5Exception, InterruptedException, ExecutionException {

final NestedGrid grid = datasetAttributes.getNestedBlockGrid();
final Region region = new Region(min, size, grid);
for (long[] key : Region.gridPositions(region.minPos().key(), region.maxPos().key())) {
exec.submit(() -> {
final NestedPosition pos = grid.nestedPosition(key, grid.numLevels() - 1);
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);
}
});
}
}
ExecutorService exec) throws N5Exception, InterruptedException, ExecutionException;

/**
* Deletes the block at {@code gridPosition}.
Expand Down
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