Package dev.zarr.zarrjava.core

Class Array

java.lang.Object

dev.zarr.zarrjava.core.AbstractNode

dev.zarr.zarrjava.core.Array

All Implemented Interfaces:

Node

Direct Known Subclasses:

Array, Array

public abstract class Array
extends AbstractNode

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	Array.ArrayAccessor

Field Summary

Fields

Modifier and Type	Field	Description
protected CodecPipeline	codecPipeline

Fields inherited from class dev.zarr.zarrjava.core.AbstractNode

storeHandle

Fields inherited from interface dev.zarr.zarrjava.core.Node

ZARR_JSON, ZARRAY, ZGROUP

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	Array(StoreHandle storeHandle)

Method Summary

Modifier and Type	Method	Description
Array.ArrayAccessor	access()
abstract ArrayMetadata	metadata()
static Array	open(StoreHandle storeHandle)	Opens an existing Zarr array at a specified storage location.
static Array	open(String path)	Opens an existing Zarr array at a specified storage location.
static Array	open(Path path)	Opens an existing Zarr array at a specified storage location.
ucar.ma2.Array	read()	Reads the entire Zarr array into an ucar.ma2.Array.
ucar.ma2.Array	read(boolean parallel)	Reads the entire Zarr array into an ucar.ma2.Array.
ucar.ma2.Array	read(long[] offset, int[] shape)	Reads a part of the Zarr array based on a requested offset and shape into an ucar.ma2.Array.
ucar.ma2.Array	read(long[] offset, int[] shape, boolean parallel)	Reads a part of the Zarr array based on a requested offset and shape into an ucar.ma2.Array.
ucar.ma2.Array	readChunk(long[] chunkCoords)	Reads one chunk of the Zarr array as specified by the chunk coordinates into an ucar.ma2.Array.
void	write(long[] offset, ucar.ma2.Array array)	Writes a ucar.ma2.Array into the Zarr array at a specified offset.
void	write(long[] offset, ucar.ma2.Array array, boolean parallel)	Writes a ucar.ma2.Array into the Zarr array at a specified offset.
void	write(ucar.ma2.Array array)	Writes a ucar.ma2.Array into the Zarr array at the beginning of the Zarr array.
void	write(ucar.ma2.Array array, boolean parallel)	Writes a ucar.ma2.Array into the Zarr array at the beginning of the Zarr array.
void	writeChunk(long[] chunkCoords, ucar.ma2.Array chunkArray)	Writes one chunk into the Zarr array as specified by the chunk coordinates.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

codecPipeline

protected CodecPipeline codecPipeline

Constructor Details

Array

protected Array(StoreHandle storeHandle)
         throws ZarrException

Throws:

ZarrException

Method Details

metadata

public abstract ArrayMetadata metadata()

open

public static Array open(StoreHandle storeHandle)
                  throws IOException,
ZarrException

Opens an existing Zarr array at a specified storage location. Automatically detects the Zarr version.

Parameters:

storeHandle - the storage location of the Zarr array

Throws:

IOException - throws IOException if the metadata cannot be read

ZarrException - throws ZarrException if the Zarr array cannot be opened

open

public static Array open(Path path)
                  throws IOException,
ZarrException

Opens an existing Zarr array at a specified storage location. Automatically detects the Zarr version.

Parameters:

path - the storage location of the Zarr array

Throws:

IOException - throws IOException if the metadata cannot be read

ZarrException - throws ZarrException if the Zarr array cannot be opened

open

public static Array open(String path)
                  throws IOException,
ZarrException

Opens an existing Zarr array at a specified storage location. Automatically detects the Zarr version.

Parameters:

path - the storage location of the Zarr array

Throws:

IOException - throws IOException if the metadata cannot be read

ZarrException - throws ZarrException if the Zarr array cannot be opened

write

public void write(long[] offset,
 ucar.ma2.Array array,
 boolean 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.

Parameters:

offset - the offset where to write the data

array - the data to write

parallel - utilizes parallelism if true

writeChunk

public void writeChunk(long[] chunkCoords,
 ucar.ma2.Array chunkArray)
                throws ZarrException

Writes one chunk into the Zarr array as specified by the chunk coordinates. The shape of the Zarr array needs to be large enough to write.

Parameters:

chunkCoords - The coordinates of the chunk as computed by the offset of the chunk divided by the chunk shape.

chunkArray - The data to write into the chunk

Throws:

ZarrException - throws ZarrException if the write fails

readChunk

@Nonnull
public ucar.ma2.Array readChunk(long[] chunkCoords)
                         throws ZarrException

Reads one chunk of the Zarr array as specified by the chunk coordinates into an ucar.ma2.Array.

Parameters:

chunkCoords - The coordinates of the chunk as computed by the offset of the chunk divided by the chunk shape.

Throws:

ZarrException - throws ZarrException if the requested chunk is outside the array's domain or if the read fails

write

public void write(ucar.ma2.Array array)

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.

Parameters:

array - the data to write

write

public void write(long[] offset,
 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.

Parameters:

offset - the offset where to write the data

array - the data to write

write

public void write(ucar.ma2.Array array,
 boolean parallel)

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.

Parameters:

array - the data to write

parallel - utilizes parallelism if true

read

@Nonnull
public ucar.ma2.Array read()
                    throws ZarrException

Reads the entire Zarr array into an ucar.ma2.Array. Utilizes no parallelism.

Throws:

ZarrException - throws ZarrException if the read fails

read

@Nonnull
public ucar.ma2.Array read(long[] offset,
 int[] shape)
                    throws ZarrException

Reads a part of the Zarr array based on a requested offset and shape into an ucar.ma2.Array. Utilizes no parallelism.

Parameters:

offset - the offset where to start reading

shape - the shape of the data to read

Throws:

ZarrException - throws ZarrException if the requested data is outside the array's domain or if the read fails

read

@Nonnull
public ucar.ma2.Array read(boolean parallel)
                    throws ZarrException

Reads the entire Zarr array into an ucar.ma2.Array.

Parameters:

parallel - utilizes parallelism if true

Throws:

ZarrException - throws ZarrException if the requested data is outside the array's domain or if the read fails

read

@Nonnull
public ucar.ma2.Array read(long[] offset,
 int[] shape,
 boolean parallel)
                    throws ZarrException

Reads a part of the Zarr array based on a requested offset and shape into an ucar.ma2.Array.

Parameters:

offset - the offset where to start reading

shape - the shape of the data to read

parallel - utilizes parallelism if true

Throws:

ZarrException - throws ZarrException if the requested data is outside the array's domain or if the read fails

access

public Array.ArrayAccessor access()