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Merged
merged 3 commits into from
Apr 10, 2025
Merged

Concurrent Read and Write #14

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950cc74
parallelize
brokkoli71 Apr 9, 2025
fab5bb6
Merge branch 'main' into parallel-streams
brokkoli71 Apr 9, 2025
7c6f6ed
correct test
brokkoli71 Apr 9, 2025
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191 changes: 125 additions & 66 deletions src/main/java/dev/zarr/zarrjava/v3/Array.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
import java.util.Map;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import ucar.ma2.InvalidRangeException;
Expand Down Expand Up @@ -119,6 +120,7 @@ public static ArrayMetadataBuilder metadataBuilder(ArrayMetadata existingMetadat

/**
* Reads the entire Zarr array into an ucar.ma2.Array.
* Utilizes no parallelism.
*
* @throws ZarrException
*/
Expand All @@ -129,13 +131,38 @@ public ucar.ma2.Array read() throws ZarrException {

/**
* Reads a part of the Zarr array based on a requested offset and shape into an ucar.ma2.Array.
* Utilizes no parallelism.
*
* @param offset
* @param shape
* @throws ZarrException
*/
@Nonnull
public ucar.ma2.Array read(final long[] offset, final int[] shape) throws ZarrException {
return read(offset, shape, false);
}

/**
* Reads the entire Zarr array into an ucar.ma2.Array.
*
* @param parallel
* @throws ZarrException
*/
@Nonnull
public ucar.ma2.Array read(final boolean parallel) throws ZarrException {
return read(new long[metadata.ndim()], Utils.toIntArray(metadata.shape), parallel);
}

/**
* Reads a part of the Zarr array based on a requested offset and shape into an ucar.ma2.Array.
*
* @param offset
* @param shape
* @param parallel
* @throws ZarrException
*/
@Nonnull
public ucar.ma2.Array read(final long[] offset, final int[] shape, final boolean parallel) throws ZarrException {
if (offset.length != metadata.ndim()) {
throw new IllegalArgumentException("'offset' needs to have rank '" + metadata.ndim() + "'.");
}
Expand All @@ -155,43 +182,46 @@ public ucar.ma2.Array read(final long[] offset, final int[] shape) throws ZarrEx

final ucar.ma2.Array outputArray = ucar.ma2.Array.factory(metadata.dataType.getMA2DataType(),
shape);
Arrays.stream(IndexingUtils.computeChunkCoords(metadata.shape, chunkShape, offset, shape))
.forEach(
chunkCoords -> {
try {
final IndexingUtils.ChunkProjection chunkProjection =
IndexingUtils.computeProjection(chunkCoords, metadata.shape, chunkShape, offset,
shape
);

if (chunkIsInArray(chunkCoords)) {
MultiArrayUtils.copyRegion(metadata.allocateFillValueChunk(),
chunkProjection.chunkOffset, outputArray, chunkProjection.outOffset,
chunkProjection.shape
);
}

final String[] chunkKeys = metadata.chunkKeyEncoding.encodeChunkKey(chunkCoords);
final StoreHandle chunkHandle = storeHandle.resolve(chunkKeys);
if (!chunkHandle.exists()) {
return;
}
if (codecPipeline.supportsPartialDecode()) {
final ucar.ma2.Array chunkArray = codecPipeline.decodePartial(chunkHandle,
Utils.toLongArray(chunkProjection.chunkOffset), chunkProjection.shape);
MultiArrayUtils.copyRegion(chunkArray, new int[metadata.ndim()], outputArray,
chunkProjection.outOffset, chunkProjection.shape
);
} else {
MultiArrayUtils.copyRegion(readChunk(chunkCoords), chunkProjection.chunkOffset,
outputArray, chunkProjection.outOffset, chunkProjection.shape
);
}

} catch (ZarrException e) {
throw new RuntimeException(e);
}
});
Stream<long[]> chunkStream = Arrays.stream(IndexingUtils.computeChunkCoords(metadata.shape, chunkShape, offset, shape));
if (parallel) {
chunkStream = chunkStream.parallel();
}
chunkStream.forEach(
chunkCoords -> {
try {
final IndexingUtils.ChunkProjection chunkProjection =
IndexingUtils.computeProjection(chunkCoords, metadata.shape, chunkShape, offset,
shape
);

if (chunkIsInArray(chunkCoords)) {
MultiArrayUtils.copyRegion(metadata.allocateFillValueChunk(),
chunkProjection.chunkOffset, outputArray, chunkProjection.outOffset,
chunkProjection.shape
);
}

final String[] chunkKeys = metadata.chunkKeyEncoding.encodeChunkKey(chunkCoords);
final StoreHandle chunkHandle = storeHandle.resolve(chunkKeys);
if (!chunkHandle.exists()) {
return;
}
if (codecPipeline.supportsPartialDecode()) {
final ucar.ma2.Array chunkArray = codecPipeline.decodePartial(chunkHandle,
Utils.toLongArray(chunkProjection.chunkOffset), chunkProjection.shape);
MultiArrayUtils.copyRegion(chunkArray, new int[metadata.ndim()], outputArray,
chunkProjection.outOffset, chunkProjection.shape
);
} else {
MultiArrayUtils.copyRegion(readChunk(chunkCoords), chunkProjection.chunkOffset,
outputArray, chunkProjection.outOffset, chunkProjection.shape
);
}

} catch (ZarrException e) {
throw new RuntimeException(e);
}
});
return outputArray;
}

Expand Down Expand Up @@ -235,6 +265,7 @@ public ucar.ma2.Array readChunk(long[] chunkCoords)
/**
* Writes a ucar.ma2.Array into the Zarr array at the beginning of the Zarr array. The shape of
* the Zarr array needs be large enough for the write.
* Utilizes no parallelism.
*
* @param array
*/
Expand All @@ -245,11 +276,37 @@ public void write(ucar.ma2.Array array) {
/**
* Writes a ucar.ma2.Array into the Zarr array at a specified offset. The shape of the Zarr array
* needs be large enough for the write.
* Utilizes no parallelism.
*
* @param offset
* @param array
*/
public void write(long[] offset, ucar.ma2.Array array) {
write(offset, array, false);
}

/**
* Writes a ucar.ma2.Array into the Zarr array at the beginning of the Zarr array. The shape of
* the Zarr array needs be large enough for the write.
*
* @param array
* @param parallel
*/
public void write(ucar.ma2.Array array, boolean parallel) {
write(new long[metadata.ndim()], array, parallel);
}



/**
* Writes a ucar.ma2.Array into the Zarr array at a specified offset. The shape of the Zarr array
* needs be large enough for the write.
*
* @param offset
* @param array
* @param parallel
*/
public void write(long[] offset, ucar.ma2.Array array, boolean parallel) {
if (offset.length != metadata.ndim()) {
throw new IllegalArgumentException("'offset' needs to have rank '" + metadata.ndim() + "'.");
}
Expand All @@ -260,34 +317,37 @@ public void write(long[] offset, ucar.ma2.Array array) {
int[] shape = array.getShape();

final int[] chunkShape = metadata.chunkShape();
Arrays.stream(IndexingUtils.computeChunkCoords(metadata.shape, chunkShape, offset, shape))
.forEach(
chunkCoords -> {
try {
final IndexingUtils.ChunkProjection chunkProjection =
IndexingUtils.computeProjection(chunkCoords, metadata.shape, chunkShape, offset,
shape
);

ucar.ma2.Array chunkArray;
if (IndexingUtils.isFullChunk(chunkProjection.chunkOffset, chunkProjection.shape,
chunkShape
)) {
chunkArray = array.sectionNoReduce(chunkProjection.outOffset,
chunkProjection.shape,
null
);
} else {
chunkArray = readChunk(chunkCoords);
MultiArrayUtils.copyRegion(array, chunkProjection.outOffset, chunkArray,
chunkProjection.chunkOffset, chunkProjection.shape
);
}
writeChunk(chunkCoords, chunkArray);
} catch (ZarrException | InvalidRangeException e) {
throw new RuntimeException(e);
}
});
Stream<long[]> chunkStream = Arrays.stream(IndexingUtils.computeChunkCoords(metadata.shape, chunkShape, offset, shape));
if(parallel) {
chunkStream = chunkStream.parallel();
}
chunkStream.forEach(
chunkCoords -> {
try {
final IndexingUtils.ChunkProjection chunkProjection =
IndexingUtils.computeProjection(chunkCoords, metadata.shape, chunkShape, offset,
shape
);

ucar.ma2.Array chunkArray;
if (IndexingUtils.isFullChunk(chunkProjection.chunkOffset, chunkProjection.shape,
chunkShape
)) {
chunkArray = array.sectionNoReduce(chunkProjection.outOffset,
chunkProjection.shape,
null
);
} else {
chunkArray = readChunk(chunkCoords);
MultiArrayUtils.copyRegion(array, chunkProjection.outOffset, chunkArray,
chunkProjection.chunkOffset, chunkProjection.shape
);
}
writeChunk(chunkCoords, chunkArray);
} catch (ZarrException | InvalidRangeException e) {
throw new RuntimeException(e);
}
});
}

/**
Expand Down Expand Up @@ -434,6 +494,5 @@ public void write(@Nonnull ucar.ma2.Array content) throws ZarrException {
}
array.write(offset, content);
}

}
}
24 changes: 24 additions & 0 deletions src/test/java/dev/zarr/zarrjava/ZarrTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -631,4 +631,28 @@ public void testReadL4Sample(String mag) throws IOException, ZarrException {

assert MultiArrayUtils.allValuesEqual(httpData2, localData2);
}

@ParameterizedTest
@ValueSource(booleans = {false,true})
public void testParallel(boolean useParallel) throws IOException, ZarrException {
int[] testData = new int[512 * 512 * 512];
Arrays.setAll(testData, p -> p);

StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("testParallelRead");
ArrayMetadata metadata = Array.metadataBuilder()
.withShape(512, 512, 512)
.withDataType(DataType.UINT32)
.withChunkShape(100, 100, 100)
.withFillValue(0)
.build();
Array writeArray = Array.create(storeHandle, metadata);
writeArray.write(ucar.ma2.Array.factory(ucar.ma2.DataType.UINT, new int[]{512, 512, 512}, testData), useParallel);

Array readArray = Array.open(storeHandle);
ucar.ma2.Array result = readArray.read(useParallel);

Assertions.assertArrayEquals(testData, (int[]) result.get1DJavaArray(ucar.ma2.DataType.INT));
clearTestoutputFolder();
}
}