A B C D E F G H I J K L M N O P R S T U V W X Z

A

absolute(int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

Get the absolute grid position at level.

absoluteAttributesPath(String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

Constructs the absolute path (in terms of this store) for the attributes file of a group or dataset.

absoluteGroupPath(String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

Constructs the absolute path (in terms of this store) for the group or dataset.

absolutePath(long...) - Method in class org.janelia.saalfeldlab.n5.shard.PositionValueAccess.KvaPositionValueAccess

Constructs the absolute path for a DataBlock at a given grid position.

absolutePosition(long[], int, long[], int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Computes the absolute targetPos grid position at targetLevel for the given sourcePos grid position at sourceLevel.

absolutePosition(long[], int, int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Get the absolute grid position at targetLevel for the given sourcePos grid position at sourceLevel.

absolutePosition(long[], int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Get the absolute grid position at targetLevel for the given sourcePos chunk grid position (level 0).

AbstractDataBlock<T> - Class in org.janelia.saalfeldlab.n5

Abstract base class for DataBlock implementations.

AbstractDataBlock(int[], long[], T, ToIntFunction<T>) - Constructor for class org.janelia.saalfeldlab.n5.AbstractDataBlock

ACCEPT_RANGE - Static variable in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

actualData - Variable in class org.janelia.saalfeldlab.n5.StringDataBlock

addChild(String, String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

Adds child to the parent's children list, only if the parent has been cached, creating a children list if it does not already exist.

addChildIfPresent(String, String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

Adds child to the parent's children list, only if the parent has been cached, and its children list already exists.

addNewCacheInfo(String, String, JsonElement) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

aggregate(Collection<? extends Range>) - Static method in interface org.janelia.saalfeldlab.n5.readdata.Range

Returns a potentially new collection of Ranges such that adjacent or overlapping Ranges are combined.

AggregatingPrefetchLazyRead - Class in org.janelia.saalfeldlab.n5.readdata.prefetch

A SliceTrackingLazyRead that implements AggregatingPrefetchLazyRead.prefetch(java.util.Collection<? extends org.janelia.saalfeldlab.n5.readdata.Range>) to aggregate overlapping / adjacent ranges and then materialize each aggregated range.

AggregatingPrefetchLazyRead(LazyRead) - Constructor for class org.janelia.saalfeldlab.n5.readdata.prefetch.AggregatingPrefetchLazyRead

allBytes() - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Return the contained data as a byte[] array.

allElementsNull() - Method in class org.janelia.saalfeldlab.n5.shard.ShardIndex.NDArray

apply(OutputStream) - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData.OutputStreamOperator

ARRAY_INDEX - Static variable in class org.janelia.saalfeldlab.n5.N5URI

ArrayAttributeToken(int) - Constructor for class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ArrayAttributeToken

asMap() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

at(long, long) - Static method in interface org.janelia.saalfeldlab.n5.readdata.Range

Atomic() - Constructor for class org.janelia.saalfeldlab.n5.FsIoPolicy.Atomic

ATTRIBUTES_JSON - Static variable in class org.janelia.saalfeldlab.n5.N5KeyValueReader

attributesCache - Variable in class org.janelia.saalfeldlab.n5.cache.N5JsonCache.N5CacheInfo

B

BLOCK_SIZE_KEY - Static variable in class org.janelia.saalfeldlab.n5.DatasetAttributes

BlockCodec<T> - Interface in org.janelia.saalfeldlab.n5.codec

De/serialize DataBlock from/to ReadData.

BlockCodecInfo - Interface in org.janelia.saalfeldlab.n5.codec

Metadata and factory for a particular family of BlockCodec.

blockCodecInfo - Variable in class org.janelia.saalfeldlab.n5.codec.CodecParser

blockExists(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

blockExists(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Checks if a block exists at the given grid position without reading the data.

blockSize(int[]) - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes.Builder

build() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes.Builder

builder(long[], DataType) - Static method in class org.janelia.saalfeldlab.n5.DatasetAttributes

builder(DatasetAttributes) - Static method in class org.janelia.saalfeldlab.n5.DatasetAttributes

Builder(long[], DataType) - Constructor for class org.janelia.saalfeldlab.n5.DatasetAttributes.Builder

Builder(DatasetAttributes) - Constructor for class org.janelia.saalfeldlab.n5.DatasetAttributes.Builder

BYTE - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

BYTE - Static variable in interface org.janelia.saalfeldlab.n5.util.MemCopy

ByteArrayDataBlock - Class in org.janelia.saalfeldlab.n5

ByteArrayDataBlock(int[], long[], byte[]) - Constructor for class org.janelia.saalfeldlab.n5.ByteArrayDataBlock

byteOrderAdapter - Static variable in class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo

ByteOrderAdapter() - Constructor for class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo.ByteOrderAdapter

BYTES - Static variable in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

bytesPerElement() - Method in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

Bzip2Compression - Class in org.janelia.saalfeldlab.n5

Bzip2Compression(int) - Constructor for class org.janelia.saalfeldlab.n5.Bzip2Compression

Bzip2Compression() - Constructor for class org.janelia.saalfeldlab.n5.Bzip2Compression

C

CachedGsonKeyValueN5Reader - Interface in org.janelia.saalfeldlab.n5

N5Reader implementation through KeyValueAccess with JSON attributes parsed with Gson.

CachedGsonKeyValueN5Writer - Interface in org.janelia.saalfeldlab.n5

Cached default implementation of N5Writer with JSON attributes parsed with Gson.

cacheMeta() - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

cacheMeta - Variable in class org.janelia.saalfeldlab.n5.N5KeyValueReader

cacheMeta() - Method in class org.janelia.saalfeldlab.n5.N5KeyValueReader

ChecksumCodec - Class in org.janelia.saalfeldlab.n5.codec.checksum

A CodecInfo that appends a checksum to data when encoding and can validate against that checksum when decoding.

ChecksumCodec(Supplier<Checksum>, int) - Constructor for class org.janelia.saalfeldlab.n5.codec.checksum.ChecksumCodec

ChecksumException - Exception in org.janelia.saalfeldlab.n5.codec.checksum

ChecksumException(String) - Constructor for exception org.janelia.saalfeldlab.n5.codec.checksum.ChecksumException

children - Variable in class org.janelia.saalfeldlab.n5.cache.N5JsonCache.N5CacheInfo

childToken - Variable in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

The token representing the subsequent path element.

classForJsonPrimitive(JsonPrimitive) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

Return a reasonable class for a JsonPrimitive.

close() - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Default implementation of AutoCloseable.close() for all implementations that do not hold any closable resources.

close() - Method in class org.janelia.saalfeldlab.n5.readdata.prefetch.SliceTrackingLazyRead

close() - Method in interface org.janelia.saalfeldlab.n5.readdata.VolatileReadData

CODEC_KEY - Static variable in class org.janelia.saalfeldlab.n5.DatasetAttributes

CodecInfo - Interface in org.janelia.saalfeldlab.n5.codec

CodecInfos are an untyped semantic layer for BlockCodecs, DataCodecs, and DatasetCodecs.

CodecParser - Class in org.janelia.saalfeldlab.n5.codec

CodecParser(CodecInfo[]) - Constructor for class org.janelia.saalfeldlab.n5.codec.CodecParser

COMPARATOR - Static variable in interface org.janelia.saalfeldlab.n5.readdata.Range

Order Ranges by Range.offset().

compareTo(Nesting.NestedPosition) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

components(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

components(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Split a path string into its components.

compose(String...) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

compose(URI, String...) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

compose(URI, String...) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Compose a path from a base uri and subsequent components.

compose(String...) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Deprecated.

Compression - Interface in org.janelia.saalfeldlab.n5

This interface is used to indicate that a DataCodec can be serialized as a "compression" for the N5 format (using the N5 API).

compression(Compression) - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes.Builder

Sets the compression codec.

Compression.CompressionParameter - Annotation Type in org.janelia.saalfeldlab.n5

Annotation for runtime discovery of compression schemes.

Compression.CompressionType - Annotation Type in org.janelia.saalfeldlab.n5

Annotation for runtime discovery of compression schemes.

COMPRESSION_KEY - Static variable in class org.janelia.saalfeldlab.n5.DatasetAttributes

CompressionAdapter - Class in org.janelia.saalfeldlab.n5

Compression adapter, auto-discovers annotated compression implementations in the classpath.

CompressionAdapter() - Constructor for class org.janelia.saalfeldlab.n5.CompressionAdapter

compressionTypeKey - Static variable in class org.janelia.saalfeldlab.n5.DatasetAttributes

computeChecksum(ReadData) - Method in class org.janelia.saalfeldlab.n5.codec.checksum.ChecksumCodec

concatenate(DataCodec...) - Static method in interface org.janelia.saalfeldlab.n5.codec.DataCodec

Create a DataCodec that sequentially applies codecs in the given order for encoding, and in reverse order for decoding.

concatenate(DatasetCodec<S, T>, BlockCodec<T>) - Static method in interface org.janelia.saalfeldlab.n5.codec.DatasetCodec

Create a BlockCodec that, for encoding, first applies datasetCodec and then blockCodec (and does the same in reverse order for decoding).

concatenate(DeterministicSizeDataCodec...) - Static method in interface org.janelia.saalfeldlab.n5.codec.DeterministicSizeDataCodec

Create a DeterministicSizeDataCodec that sequentially applies codecs in the given order for encoding, and in reverse order for decoding.

concatenate(TransposeCodecInfo[]) - Static method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodecInfo

concatenate(List<SegmentedReadData>) - Static method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

Return a SegmentedReadData representing the concatenation of the given readDatas.

concatenatePermutations(int[], int[]) - Static method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodec

Composes two permutations: result[i] = first[second[i]].

conjugateWithReverse(int[]) - Static method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodec

Conjugates a permutation with the reversal permutation: rev * p * rev^-1, where rev is the permutation that reverses the elements.

container - Variable in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

containsKey(String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache.N5CacheInfo

copy(Object, int[], int[], Object, int[], int[], int[]) - Static method in interface org.janelia.saalfeldlab.n5.util.SubArrayCopy

Copy a nD region from src to dest, where src and dest are flattened nD array of dimensions srcSize and destSize, respectively.

copyNDRangeRecursive(int, T, int[], int, T, int[], int, int[]) - Static method in interface org.janelia.saalfeldlab.n5.util.SubArrayCopy

Recursively copy a (d+1) dimensional region from src to dest, where src and dest are flattened nD array with strides srcStrides and destStrides, respectively.

copyStrided(T, int, T, int, int, int) - Method in interface org.janelia.saalfeldlab.n5.util.MemCopy

Copy length components from the src array to the dest array.

copyStrided(byte[], int, byte[], int, int, int) - Method in class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyByte

copyStrided(double[], int, double[], int, int, int) - Method in class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyDouble

copyStrided(float[], int, float[], int, int, int) - Method in class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyFloat

copyStrided(int[], int, int[], int, int, int) - Method in class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyInt

copyStrided(long[], int, long[], int, int, int) - Method in class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyLong

copyStrided(short[], int, short[], int, int, int) - Method in class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyShort

Crc32cChecksumCodec - Class in org.janelia.saalfeldlab.n5.codec.checksum

Crc32cChecksumCodec() - Constructor for class org.janelia.saalfeldlab.n5.codec.checksum.Crc32cChecksumCodec

create(DataType, int[], DataCodecInfo...) - Method in interface org.janelia.saalfeldlab.n5.codec.BlockCodecInfo

create(DatasetAttributes, DataCodecInfo...) - Method in interface org.janelia.saalfeldlab.n5.codec.BlockCodecInfo

create() - Method in class org.janelia.saalfeldlab.n5.codec.checksum.Crc32cChecksumCodec

create(DataCodecInfo...) - Static method in interface org.janelia.saalfeldlab.n5.codec.DataCodec

create() - Method in interface org.janelia.saalfeldlab.n5.codec.DataCodecInfo

create(DatasetAttributes) - Method in interface org.janelia.saalfeldlab.n5.codec.DatasetCodecInfo

create() - Method in class org.janelia.saalfeldlab.n5.codec.IdentityCodec

create(CodecInfo...) - Static method in class org.janelia.saalfeldlab.n5.codec.IndexCodecAdapter

create(DataType, int[], DataCodecInfo...) - Method in class org.janelia.saalfeldlab.n5.codec.N5BlockCodecInfo

create(DataType, DataCodec) - Static method in class org.janelia.saalfeldlab.n5.codec.N5BlockCodecs

create(DataType, int[], DataCodecInfo...) - Method in class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo

create(DataType, ByteOrder, int[], DataCodec) - Static method in class org.janelia.saalfeldlab.n5.codec.RawBlockCodecs

create(DatasetAttributes) - Method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodecInfo

create() - Method in interface org.janelia.saalfeldlab.n5.Compression

create(int[], DataCodecInfo...) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

create(DataType, int[], DataCodecInfo...) - Method in interface org.janelia.saalfeldlab.n5.shard.ShardCodecInfo

create(int[], DataCodecInfo...) - Method in interface org.janelia.saalfeldlab.n5.shard.ShardCodecInfo

createAllocationSteps(int[], int[]) - Static method in interface org.janelia.saalfeldlab.n5.util.SubArrayCopy

Create allocation step array from the dimensions of an N-dimensional array.

createAllocationSteps(int[]) - Static method in interface org.janelia.saalfeldlab.n5.util.SubArrayCopy

createAndCheckIsDirectory(Path, FileAttribute<?>...) - Static method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

This is a copy of a previous Files#createAndCheckIsDirectory(Path, FileAttribute...) method that follows symlinks.

createDataBlock(int[], long[], T) - Method in interface org.janelia.saalfeldlab.n5.DataBlock.DataBlockFactory

Create a new DataBlock with the given blockSize, gridPosition, and data content.

createDataBlock(int[], long[], int) - Method in enum org.janelia.saalfeldlab.n5.DataType

Factory for DataBlocks.

createDataBlock(int[], long[]) - Method in enum org.janelia.saalfeldlab.n5.DataType

Factory for DataBlocks with one data element for each block element (e.g. pixel image).

createDataset(String, DatasetAttributes) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Creates a dataset.

createDataset(String, long[], int[], DataType, Compression) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Creates a dataset.

createDatasetAttributes(JsonElement) - Method in interface org.janelia.saalfeldlab.n5.GsonN5Reader

createDirectories(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

createDirectories(Path, FileAttribute<?>...) - Static method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

This is a copy of Files.createDirectories(Path, FileAttribute...)

createDirectories(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

createDirectories(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Create a directory and all parent paths along the way.

createGroup(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

createGroup(String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

createGroup(String) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Creates a group (directory)

createReadData(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

createReadData(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

createReadData(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Create a VolatileReadData through which data at the normal key can be read.

D

data - Variable in class org.janelia.saalfeldlab.n5.AbstractDataBlock

data() - Method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData.SegmentsAndData

DATA_TYPE_KEY - Static variable in class org.janelia.saalfeldlab.n5.DatasetAttributes

DataBlock<T> - Interface in org.janelia.saalfeldlab.n5

Interface for data blocks.

DataBlock.DataBlockFactory<T> - Interface in org.janelia.saalfeldlab.n5

Factory for creating DataBlock<T>.

DataCodec - Interface in org.janelia.saalfeldlab.n5.codec

DataCodecs transform one ReadData into another, for example, compressing it.

DataCodecInfo - Interface in org.janelia.saalfeldlab.n5.codec

Used to create DataCodecs, which transform one ReadData into another, for example, applying compression.

dataCodecInfos - Variable in class org.janelia.saalfeldlab.n5.codec.CodecParser

DatasetAccess<T> - Interface in org.janelia.saalfeldlab.n5.shard

Wrap an instantiated DataBlock/block codec hierarchy to implement (single and batch) DataBlock read/write methods.

DatasetAttributes - Class in org.janelia.saalfeldlab.n5

Mandatory dataset attributes: long[] : dimensions int[] : blockSize DataType : dataType CodecInfo... : encode/decode routines

DatasetAttributes(long[], int[], DataType, JsonElement, BlockCodecInfo, DatasetCodecInfo[], DataCodecInfo...) - Constructor for class org.janelia.saalfeldlab.n5.DatasetAttributes

DatasetAttributes(long[], int[], DataType, BlockCodecInfo, DatasetCodecInfo[], DataCodecInfo...) - Constructor for class org.janelia.saalfeldlab.n5.DatasetAttributes

DatasetAttributes(long[], int[], DataType, BlockCodecInfo, DataCodecInfo...) - Constructor for class org.janelia.saalfeldlab.n5.DatasetAttributes

DatasetAttributes(long[], int[], DataType, DataCodecInfo...) - Constructor for class org.janelia.saalfeldlab.n5.DatasetAttributes

Constructs a DatasetAttributes instance with specified dimensions, block size, data type, and single compressor with default codec.

DatasetAttributes(long[], int[], DataType) - Constructor for class org.janelia.saalfeldlab.n5.DatasetAttributes

Constructs a DatasetAttributes instance with specified dimensions, block size, data type, and default codecs

DatasetAttributes.Builder - Class in org.janelia.saalfeldlab.n5

DatasetAttributes.DatasetAttributesAdapter - Class in org.janelia.saalfeldlab.n5

DatasetAttributesAdapter() - Constructor for class org.janelia.saalfeldlab.n5.DatasetAttributes.DatasetAttributesAdapter

DatasetCodec<S,T> - Interface in org.janelia.saalfeldlab.n5.codec

A Codec that transforms the contents of a DataBlock.

DatasetCodecInfo - Interface in org.janelia.saalfeldlab.n5.codec

Used to create typed DatasetCodecs, which transform one DataBlock into another, for example, by applying a transposition (@link TransposeCodec.

datasetCodecInfos - Variable in class org.janelia.saalfeldlab.n5.codec.CodecParser

datasetExists(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

datasetExists(String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

datasetExists(String) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Test whether a dataset exists at a given path.

DataType - Enum in org.janelia.saalfeldlab.n5

Enumerates available data types.

DataType.JsonAdapter - Class in org.janelia.saalfeldlab.n5

decode(ReadData) - Method in class org.janelia.saalfeldlab.n5.Bzip2Compression

decode(ReadData, long[]) - Method in interface org.janelia.saalfeldlab.n5.codec.BlockCodec

Deserializes a DataBlock from its ReadData representation.

decode(ReadData) - Method in class org.janelia.saalfeldlab.n5.codec.checksum.ChecksumCodec

decode(ReadData) - Method in interface org.janelia.saalfeldlab.n5.codec.DataCodec

Decode the given ReadData.

decode(DataBlock<T>) - Method in interface org.janelia.saalfeldlab.n5.codec.DatasetCodec

decode(ReadData, int) - Method in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

decode(ReadData) - Method in class org.janelia.saalfeldlab.n5.codec.IdentityCodec

decode(DataBlock<T>) - Method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodec

decode(ReadData) - Method in class org.janelia.saalfeldlab.n5.GzipCompression

decode(ReadData) - Method in class org.janelia.saalfeldlab.n5.Lz4Compression

decode(ReadData) - Method in class org.janelia.saalfeldlab.n5.RawCompression

decode(ReadData, long[]) - Method in class org.janelia.saalfeldlab.n5.shard.RawShardCodec

decode(ReadData) - Method in class org.janelia.saalfeldlab.n5.XzCompression

decodedSize(long) - Method in interface org.janelia.saalfeldlab.n5.codec.BlockCodecInfo

decodedSize(long) - Method in interface org.janelia.saalfeldlab.n5.codec.DeterministicSizeCodecInfo

deepCopy() - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache.EmptyJson

deepList(String, Predicate<String>) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Recursively list all groups and datasets in the given path.

deepList(String) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Recursively list all groups and datasets in the given path.

deepList(N5Reader, String, boolean, Predicate<String>) - Static method in interface org.janelia.saalfeldlab.n5.N5Reader

Helper method to recursively list all groups and datasets.

deepList(String, Predicate<String>, ExecutorService) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Recursively list all groups (including datasets) in the given group, in parallel, using the given ExecutorService.

deepList(String, ExecutorService) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Recursively list all groups (including datasets) in the given group, in parallel, using the given ExecutorService.

deepListDatasets(String, Predicate<String>) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Recursively list all datasets in the given path.

deepListDatasets(String) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Recursively list all including datasets in the given path.

deepListDatasets(String, Predicate<String>, ExecutorService) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Recursively list all datasets in the given group, in parallel, using the given ExecutorService.

deepListDatasets(String, ExecutorService) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Recursively list all datasets in the given group, in parallel, using the given ExecutorService.

deepListHelper(N5Reader, String, boolean, Predicate<String>, ExecutorService, LinkedBlockingQueue<Future<String>>) - Static method in interface org.janelia.saalfeldlab.n5.N5Reader

Helper method for parallel deep listing.

defaultBlockCodecInfo() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

defaultBlockSize(long[]) - Static method in class org.janelia.saalfeldlab.n5.DatasetAttributes

DefaultDatasetAccess<T> - Class in org.janelia.saalfeldlab.n5.shard

DefaultDatasetAccess(Nesting.NestedGrid, BlockCodec<?>[]) - Constructor for class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

defaultDirectoryListParser() - Static method in interface org.janelia.saalfeldlab.n5.http.ListResponseParser

defaultListParser() - Static method in interface org.janelia.saalfeldlab.n5.http.ListResponseParser

DefaultShardCodecInfo - Class in org.janelia.saalfeldlab.n5.shard

Default (and probably only) implementation of ShardCodecInfo.

DefaultShardCodecInfo(int[], DatasetCodecInfo[], BlockCodecInfo, DataCodecInfo[], BlockCodecInfo, DataCodecInfo[], ShardIndex.IndexLocation) - Constructor for class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

DefaultShardCodecInfo(int[], BlockCodecInfo, DataCodecInfo[], BlockCodecInfo, DataCodecInfo[], ShardIndex.IndexLocation) - Constructor for class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

delete(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

delete(String) - Method in class org.janelia.saalfeldlab.n5.FsIoPolicy.Atomic

delete(String) - Method in class org.janelia.saalfeldlab.n5.FsIoPolicy.Unsafe

delete(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

delete(String) - Method in interface org.janelia.saalfeldlab.n5.IoPolicy

delete(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Delete a path.

deleteBlock(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

deleteBlock(String, long...) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Deletes the block at gridPosition.

deleteBlock(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Deletes the block at gridPosition.

deleteChunk(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

deleteChunk(String, long...) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Deletes the chunk at gridPosition.

deleteChunk(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Deletes the chunk at gridPosition.

deleteChunk(PositionValueAccess, long[]) - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

Deletes the chunk at gridPosition.

deleteChunk(PositionValueAccess, long[]) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

deleteChunks(String, DatasetAttributes, List<long[]>) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

deleteChunks(String, DatasetAttributes, List<long[]>) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Deletes the chunks at the given gridPositions.

deleteChunks(PositionValueAccess, List<long[]>) - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

Deletes the chunks at the given positions.

deleteChunks(PositionValueAccess, List<long[]>) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo.ByteOrderAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.CompressionAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes.DatasetAttributesAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.DataType.JsonAdapter

deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class org.janelia.saalfeldlab.n5.NameConfigAdapter

deserialize(byte[]) - Method in class org.janelia.saalfeldlab.n5.StringDataBlock

DeterministicSizeCodecInfo - Interface in org.janelia.saalfeldlab.n5.codec

A CodecInfo that can deterministically determine the size of encoded data from the size of the raw data and vice versa from the data length alone (i.e. encoding is data independent).

DeterministicSizeDataCodec - Interface in org.janelia.saalfeldlab.n5.codec

A DataCodec that can deterministically determine the size of encoded data from the size of the raw data (i.e. encoding is data independent).

DIMENSIONS_KEY - Static variable in class org.janelia.saalfeldlab.n5.DatasetAttributes

DOUBLE(ByteOrder) - Static method in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

DOUBLE - Static variable in interface org.janelia.saalfeldlab.n5.util.MemCopy

DOUBLE_BIG_ENDIAN - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

DOUBLE_LITTLE_ENDIAN - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

DoubleArrayDataBlock - Class in org.janelia.saalfeldlab.n5

DoubleArrayDataBlock(int[], long[], double[]) - Constructor for class org.janelia.saalfeldlab.n5.DoubleArrayDataBlock

E

empty() - Static method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Returns an empty ReadData.

emptyCacheInfo - Static variable in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

emptyJson - Static variable in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

EmptyJson() - Constructor for class org.janelia.saalfeldlab.n5.cache.N5JsonCache.EmptyJson

EnclosingPrefetchLazyRead - Class in org.janelia.saalfeldlab.n5.readdata.prefetch

A SliceTrackingLazyRead that implements EnclosingPrefetchLazyRead.prefetch(java.util.Collection<? extends org.janelia.saalfeldlab.n5.readdata.Range>) to materialize the bounding range of all requested ranges.

EnclosingPrefetchLazyRead(LazyRead) - Constructor for class org.janelia.saalfeldlab.n5.readdata.prefetch.EnclosingPrefetchLazyRead

encode(ReadData) - Method in class org.janelia.saalfeldlab.n5.Bzip2Compression

encode(DataBlock<T>) - Method in interface org.janelia.saalfeldlab.n5.codec.BlockCodec

Serializes a DataBlock into a ReadData representation for storage.

encode(ReadData) - Method in class org.janelia.saalfeldlab.n5.codec.checksum.ChecksumCodec

encode(ReadData) - Method in interface org.janelia.saalfeldlab.n5.codec.DataCodec

Encode the given ReadData.

encode(DataBlock<S>) - Method in interface org.janelia.saalfeldlab.n5.codec.DatasetCodec

encode(T) - Method in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

encode(ReadData) - Method in class org.janelia.saalfeldlab.n5.codec.IdentityCodec

encode(DataBlock<T>) - Method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodec

encode(ReadData) - Method in class org.janelia.saalfeldlab.n5.GzipCompression

encode(ReadData) - Method in class org.janelia.saalfeldlab.n5.Lz4Compression

encode(ReadData) - Method in class org.janelia.saalfeldlab.n5.RawCompression

encode(ReadData.OutputStreamOperator) - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Returns a new ReadData that uses the given OutputStreamOperator to encode this ReadData.

encode(DataBlock<RawShard>) - Method in class org.janelia.saalfeldlab.n5.shard.RawShardCodec

encode(ReadData) - Method in class org.janelia.saalfeldlab.n5.XzCompression

encodeAsUri(String) - Static method in class org.janelia.saalfeldlab.n5.N5URI

Encode the inpurt uri so that illegal characters are properly escaped prior to generating the resulting URI.

encodeAsUriPath(String) - Static method in class org.janelia.saalfeldlab.n5.N5URI

encodeDouble(double) - Static method in class org.janelia.saalfeldlab.n5.util.FloatValueParser

Encodes a double value to a hex string.

encodedSize(int[]) - Method in interface org.janelia.saalfeldlab.n5.codec.BlockCodec

Given the blockSize of a DataBlock<T> return the size of the encoded block in bytes.

encodedSize(long) - Method in interface org.janelia.saalfeldlab.n5.codec.BlockCodecInfo

encodedSize(long) - Method in class org.janelia.saalfeldlab.n5.codec.checksum.ChecksumCodec

encodedSize(long) - Method in interface org.janelia.saalfeldlab.n5.codec.DeterministicSizeCodecInfo

encodedSize(long) - Method in interface org.janelia.saalfeldlab.n5.codec.DeterministicSizeDataCodec

Given size bytes of raw data, how many bytes will the encoded data have.

encodedSize(long) - Method in class org.janelia.saalfeldlab.n5.codec.IdentityCodec

encodedSize(long) - Method in class org.janelia.saalfeldlab.n5.codec.IndexCodecAdapter

encodedSize(long) - Method in class org.janelia.saalfeldlab.n5.codec.N5BlockCodecInfo

encodedSize(long) - Method in class org.janelia.saalfeldlab.n5.RawCompression

encodeFloat(float) - Static method in class org.janelia.saalfeldlab.n5.util.FloatValueParser

Encodes a float value to a hex string.

ENCODING - Static variable in class org.janelia.saalfeldlab.n5.StringDataBlock

end() - Method in interface org.janelia.saalfeldlab.n5.readdata.Range

ensureValidByteOrder(DataType, ByteOrder) - Static method in class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo

equals(Object) - Method in class org.janelia.saalfeldlab.n5.Bzip2Compression

equals(Object) - Method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodecInfo

equals(Object) - Method in class org.janelia.saalfeldlab.n5.GzipCompression

equals(Object) - Method in class org.janelia.saalfeldlab.n5.Lz4Compression

equals(Object) - Method in class org.janelia.saalfeldlab.n5.N5Reader.Version

equals(Object) - Method in class org.janelia.saalfeldlab.n5.RawCompression

equals(Range, Range) - Static method in interface org.janelia.saalfeldlab.n5.readdata.Range

equals(Object) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

equals(Object) - Method in class org.janelia.saalfeldlab.n5.XzCompression

exists(String, String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

Returns true if a resource exists.

exists(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

exists(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

exists(String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

exists(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

Test whether the normalPath exists.

exists(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Test whether the path exists.

exists(String) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Test whether a group or dataset exists at a given path.

exists(long[]) - Method in interface org.janelia.saalfeldlab.n5.shard.PositionValueAccess

exists(long[]) - Method in class org.janelia.saalfeldlab.n5.shard.PositionValueAccess.KvaPositionValueAccess

existsFromContainer(String, String) - Method in interface org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer

Query whether a resource exists in this container.

existsFromContainer(String, String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

F

FileSystemKeyValueAccess - Class in org.janelia.saalfeldlab.n5

Filesystem KeyValueAccess.

FileSystemKeyValueAccess() - Constructor for class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

FlatArrayCodec<T> - Class in org.janelia.saalfeldlab.n5.codec

De/serialize the data contained in a DataBlock<T> from/to a sequence of bytes.

FLOAT(ByteOrder) - Static method in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

FLOAT - Static variable in interface org.janelia.saalfeldlab.n5.util.MemCopy

FLOAT_BIG_ENDIAN - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

FLOAT_LITTLE_ENDIAN - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

FloatArrayDataBlock - Class in org.janelia.saalfeldlab.n5

FloatArrayDataBlock(int[], long[], float[]) - Constructor for class org.janelia.saalfeldlab.n5.FloatArrayDataBlock

FloatValueParser - Class in org.janelia.saalfeldlab.n5.util

Parses Float and Double values from JSON hex strings.

FloatValueParser() - Constructor for class org.janelia.saalfeldlab.n5.util.FloatValueParser

forDataType(DataType) - Static method in interface org.janelia.saalfeldlab.n5.util.MemCopy

from(String, String, String) - Static method in class org.janelia.saalfeldlab.n5.N5URI

Generate an N5URI from a container, group, and attribute

from(InputStream, int) - Static method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Create a new ReadData that loads lazily from inputStream and reports the given length.

from(InputStream) - Static method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Create a new ReadData that loads lazily from inputStream and reports length() == -1 (i.e., unknown length).

from(byte[], int, int) - Static method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Create a new ReadData that wraps the specified portion of a byte[] array.

from(byte[]) - Static method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Create a new ReadData that wraps the given byte[] array.

from(ByteBuffer) - Static method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Create a new ReadData that wraps the given ByteBuffer.

from(ReadData.Generator) - Static method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Create a new ReadData that is lazily generated by the given ReadData.Generator.

from(LazyRead) - Static method in interface org.janelia.saalfeldlab.n5.readdata.VolatileReadData

Create a new VolatileReadData that loads (lazily) from lazyRead.

fromKva(KeyValueAccess, URI, String, DatasetAttributes) - Static method in interface org.janelia.saalfeldlab.n5.shard.PositionValueAccess

fromString(String) - Static method in enum org.janelia.saalfeldlab.n5.DataType

FsIoPolicy - Class in org.janelia.saalfeldlab.n5

FsIoPolicy() - Constructor for class org.janelia.saalfeldlab.n5.FsIoPolicy

FsIoPolicy.Atomic - Class in org.janelia.saalfeldlab.n5

FsIoPolicy.Unsafe - Class in org.janelia.saalfeldlab.n5

fullyContains(Nesting.NestedPosition) - Method in class org.janelia.saalfeldlab.n5.shard.Region

Check whether the shard or chunk corresponding to the given position is fully contained inside the region.

G

GET - Static variable in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

get(long[], DataBlock<T>) - Method in interface org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier

get(long[]) - Method in interface org.janelia.saalfeldlab.n5.shard.PositionValueAccess

Gets the VolatileReadData for the DataBlock at the given position in the block grid.

get(long[]) - Method in class org.janelia.saalfeldlab.n5.shard.PositionValueAccess.KvaPositionValueAccess

getAsUri(String) - Static method in class org.janelia.saalfeldlab.n5.N5URI

If uri is a valid URI, just return it as a URI.

getAttribute(String, String, Class<T>) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

getAttribute(String, String, Type) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

getAttribute(String, String, Class<T>) - Method in interface org.janelia.saalfeldlab.n5.GsonN5Reader

getAttribute(String, String, Type) - Method in interface org.janelia.saalfeldlab.n5.GsonN5Reader

getAttribute(JsonElement, String) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

Return the attribute at normalizedAttributePath as a JsonElement.

getAttribute(String, String, Class<T>) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Reads an attribute.

getAttribute(String, String, Type) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Reads an attribute.

getAttributePath() - Method in class org.janelia.saalfeldlab.n5.N5URI

getAttributePathTokens() - Method in class org.janelia.saalfeldlab.n5.N5URI

Parse this N5URI as a LinkedAttributePathToken.

getAttributePathTokens(String) - Static method in class org.janelia.saalfeldlab.n5.N5URI

Parses the normalizedAttributePath to a list of LinkedAttributePathToken.

getAttributes(String, String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

getAttributes(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

Reads or creates the attributes map of a group or dataset.

getAttributes(String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

Reads or creates the attributes map of a group or dataset.

getAttributes(String) - Method in interface org.janelia.saalfeldlab.n5.GsonN5Reader

Reads or the attributes of a group or dataset.

getAttributesFromContainer(String, String) - Method in interface org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer

Returns a JsonElement containing attributes at a given path, for a given cache key.

getAttributesFromContainer(String, String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

getAttributesKey() - Method in interface org.janelia.saalfeldlab.n5.GsonN5Reader

Get the key for the KeyValueAccess, that is used for storing attributes.

getAttributesKey() - Method in class org.janelia.saalfeldlab.n5.N5KeyValueReader

getBlockCodecInfo() - Method in class org.janelia.saalfeldlab.n5.codec.IndexCodecAdapter

getBlockCodecInfo() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

getBlockSize() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

getBlockSize(int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Get the block size in pixels at the given level.

getByteOrder() - Method in class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo

getCache(String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache.N5CacheInfo

getCache() - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

getCache() - Method in class org.janelia.saalfeldlab.n5.N5KeyValueReader

getCacheInfo(String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

getChecksum() - Method in class org.janelia.saalfeldlab.n5.codec.checksum.ChecksumCodec

Returns a new Checksum instance.

getChecksumValue(Checksum) - Method in class org.janelia.saalfeldlab.n5.codec.checksum.ChecksumCodec

Return the value of the checksum as a ByteBuffer to be serialized.

getChecksumValue(Checksum) - Method in class org.janelia.saalfeldlab.n5.codec.checksum.Crc32cChecksumCodec

getChildElement() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ArrayAttributeToken

getChildElement() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

getChildElement() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ObjectAttributeToken

getChunkSize() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

getCodecs() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

getCompression() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

Deprecated.

getContainerPath() - Method in class org.janelia.saalfeldlab.n5.N5URI

getConvertedDatasetAttributes(DatasetAttributes) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Some implementations may need to convert arbitrary DatasetAttributes to their specific equivalent variant.

getData() - Method in class org.janelia.saalfeldlab.n5.AbstractDataBlock

getData() - Method in interface org.janelia.saalfeldlab.n5.DataBlock

Returns the data object held by this data block.

getData() - Method in class org.janelia.saalfeldlab.n5.shard.RawShardDataBlock

getData() - Method in class org.janelia.saalfeldlab.n5.StringDataBlock

getDataCodecInfos() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

getDataCodecs() - Method in class org.janelia.saalfeldlab.n5.codec.IndexCodecAdapter

getDatasetAccess() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

Get the DatasetAccess for this dataset.

getDatasetAttributes(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

getDatasetAttributes(String) - Method in interface org.janelia.saalfeldlab.n5.GsonN5Reader

getDatasetAttributes(String) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Get mandatory dataset attributes.

getDatasetCodecInfos() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

getDatasetSize() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Get the size of the dataset in pixels.

getDatasetSizeInChunks() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Get the size of the dataset in units of chunks.

getDataType() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

getDefaultValue() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

getDimensions() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

getElementData(long[]) - Method in class org.janelia.saalfeldlab.n5.shard.RawShard

getGrid() - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

getGrid() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

getGridPosition() - Method in class org.janelia.saalfeldlab.n5.AbstractDataBlock

getGridPosition() - Method in interface org.janelia.saalfeldlab.n5.DataBlock

Returns the position of this data block on the block grid relative to dataset.

getGridPosition() - Method in class org.janelia.saalfeldlab.n5.shard.RawShardDataBlock

getGroupPath() - Method in class org.janelia.saalfeldlab.n5.N5URI

getGroupSeparator() - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Returns the symbol that is used to separate nodes in a group path.

getGson() - Method in interface org.janelia.saalfeldlab.n5.GsonN5Reader

getGson() - Method in class org.janelia.saalfeldlab.n5.N5KeyValueReader

getIndex() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ArrayAttributeToken

getIndexBlockCodecInfo() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

getIndexBlockCodecInfo() - Method in interface org.janelia.saalfeldlab.n5.shard.ShardCodecInfo

BlockCodec for shard index

getIndexCodecs() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

getIndexDataCodecInfos() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

getIndexDataCodecInfos() - Method in interface org.janelia.saalfeldlab.n5.shard.ShardCodecInfo

Deterministic-size DataCodecs for index BlockCodec

getIndexLocation() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

getIndexLocation() - Method in interface org.janelia.saalfeldlab.n5.shard.ShardCodecInfo

getInnerBlockCodecInfo() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

getInnerBlockCodecInfo() - Method in interface org.janelia.saalfeldlab.n5.shard.ShardCodecInfo

BlockCodecInfo for shard elements (either nested shard or DataBlock)

getInnerBlockSize() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

getInnerBlockSize() - Method in interface org.janelia.saalfeldlab.n5.shard.ShardCodecInfo

Size in pixels of each shard element (either nested shard or chunk)

getInnerDataCodecInfos() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

getInnerDataCodecInfos() - Method in interface org.janelia.saalfeldlab.n5.shard.ShardCodecInfo

getInnerDatasetCodecInfos() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

getInnerDatasetCodecInfos() - Method in interface org.janelia.saalfeldlab.n5.shard.ShardCodecInfo

getJsonAdapter() - Static method in class org.janelia.saalfeldlab.n5.CompressionAdapter

getJsonAdapter() - Static method in class org.janelia.saalfeldlab.n5.DatasetAttributes

getJsonAdapter(Class<T>) - Static method in class org.janelia.saalfeldlab.n5.NameConfigAdapter

getJsonAsArray(Gson, JsonArray, Class<T>) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

getJsonAsArray(Gson, JsonArray, Type) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

getJsonType() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ArrayAttributeToken

getJsonType() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

getJsonType() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ObjectAttributeToken

getKey() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ObjectAttributeToken

getKeyPositionForBlock(DatasetAttributes, DataBlock<?>) - Method in interface org.janelia.saalfeldlab.n5.codec.BlockCodecInfo

getKeyPositionForBlock(DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.codec.BlockCodecInfo

getKeyPositionForBlock(DatasetAttributes, DataBlock<?>) - Method in class org.janelia.saalfeldlab.n5.codec.N5BlockCodecInfo

getKeyPositionForBlock(DatasetAttributes, long...) - Method in class org.janelia.saalfeldlab.n5.codec.N5BlockCodecInfo

getKeyValueAccess() - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

getKeyValueAccess() - Method in class org.janelia.saalfeldlab.n5.N5KeyValueReader

getMajor() - Method in class org.janelia.saalfeldlab.n5.N5Reader.Version

getMinor() - Method in class org.janelia.saalfeldlab.n5.N5Reader.Version

getNestedBlockGrid() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

Returns the NestedGrid for this dataset, from which block and shard sizes are accessible.

getNumDimensions() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

getNumElements() - Method in class org.janelia.saalfeldlab.n5.AbstractDataBlock

getNumElements() - Method in interface org.janelia.saalfeldlab.n5.DataBlock

Returns the number of elements in this DataBlock.

getNumElements(int[]) - Static method in interface org.janelia.saalfeldlab.n5.DataBlock

Returns the number of elements in a box of given size.

getNumElements() - Method in class org.janelia.saalfeldlab.n5.shard.RawShardDataBlock

getNumElements() - Method in class org.janelia.saalfeldlab.n5.StringDataBlock

getOrCreateChildElement() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ArrayAttributeToken

getOrCreateChildElement() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

This method will return the child element, if the LinkedAttributePathToken.parentJson contains a child that is valid for this token.

getOrCreateChildElement() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ObjectAttributeToken

getOrder() - Method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodecInfo

getOrMakeCacheInfo(String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

getPatch() - Method in class org.janelia.saalfeldlab.n5.N5Reader.Version

getSize() - Method in class org.janelia.saalfeldlab.n5.AbstractDataBlock

getSize() - Method in interface org.janelia.saalfeldlab.n5.DataBlock

Returns the size of this data block.

getSize() - Method in class org.janelia.saalfeldlab.n5.shard.RawShardDataBlock

getSuffix() - Method in class org.janelia.saalfeldlab.n5.N5Reader.Version

getType() - Method in class org.janelia.saalfeldlab.n5.codec.checksum.Crc32cChecksumCodec

getType() - Method in interface org.janelia.saalfeldlab.n5.codec.CodecInfo

getType() - Method in class org.janelia.saalfeldlab.n5.codec.IdentityCodec

getType() - Method in class org.janelia.saalfeldlab.n5.codec.N5BlockCodecInfo

getType() - Method in class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo

getType() - Method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodecInfo

getType() - Method in interface org.janelia.saalfeldlab.n5.Compression

getType() - Method in interface org.janelia.saalfeldlab.n5.serialization.NameConfig

Returns the serialization type name for this instance.

getType() - Method in class org.janelia.saalfeldlab.n5.shard.DefaultShardCodecInfo

getURI() - Method in class org.janelia.saalfeldlab.n5.N5KeyValueReader

getURI() - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Returns the URI of the container's root.

getURI() - Method in class org.janelia.saalfeldlab.n5.N5URI

getVersion() - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Get the SemVer version of this container as specified in the 'version' attribute of the root group.

gridPosition - Variable in class org.janelia.saalfeldlab.n5.AbstractDataBlock

gridPositions(long[], long[]) - Static method in class org.janelia.saalfeldlab.n5.shard.Region

groupExists(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

groupExists(String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

groupPath(String...) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Creates a group path by concatenating all nodes with the node separator defined by N5Reader.getGroupSeparator().

gson - Variable in class org.janelia.saalfeldlab.n5.N5KeyValueReader

GsonKeyValueN5Reader - Interface in org.janelia.saalfeldlab.n5

N5Reader implementation through KeyValueAccess with JSON attributes parsed with Gson.

GsonKeyValueN5Writer - Interface in org.janelia.saalfeldlab.n5

Default implementation of N5Writer with JSON attributes parsed with Gson.

GsonN5Reader - Interface in org.janelia.saalfeldlab.n5

N5Reader with JSON attributes parsed with Gson.

GsonN5Writer - Interface in org.janelia.saalfeldlab.n5

N5Writer with JSON attributes parsed with Gson.

GsonUtils - Interface in org.janelia.saalfeldlab.n5

Utility class for working with JSON.

GzipCompression - Class in org.janelia.saalfeldlab.n5

GzipCompression() - Constructor for class org.janelia.saalfeldlab.n5.GzipCompression

GzipCompression(int) - Constructor for class org.janelia.saalfeldlab.n5.GzipCompression

GzipCompression(int, boolean) - Constructor for class org.janelia.saalfeldlab.n5.GzipCompression

H

hasDatasetAttributes(JsonElement) - Static method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

Check for attributes that are required for a group to be a dataset.

hashCode() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

hasNext() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

HEAD - Static variable in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

HttpKeyValueAccess - Class in org.janelia.saalfeldlab.n5

A read-only KeyValueAccess implementation using HTTP.

HttpKeyValueAccess() - Constructor for class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

Opens an HttpKeyValueAccess

I

IdentityCodec - Class in org.janelia.saalfeldlab.n5.codec

IdentityCodec() - Constructor for class org.janelia.saalfeldlab.n5.codec.IdentityCodec

index() - Method in class org.janelia.saalfeldlab.n5.shard.RawShard

Maps grid position of shard elements to Segments that give the byte range for the blocks in this shard.

IndexCodecAdapter - Class in org.janelia.saalfeldlab.n5.codec

IndexCodecAdapter(BlockCodecInfo, DeterministicSizeCodecInfo...) - Constructor for class org.janelia.saalfeldlab.n5.codec.IndexCodecAdapter

initializeContainer(KeyValueAccess, String) - Static method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

initializeNonemptyCache(String, String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

inputStream() - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Open a InputStream on this data.

insertAttribute(JsonElement, String, T, Gson) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

insertAttributes(JsonElement, Map<String, ?>, Gson) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

INT(ByteOrder) - Static method in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

INT - Static variable in interface org.janelia.saalfeldlab.n5.util.MemCopy

INT_BIG_ENDIAN - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

INT_LITTLE_ENDIAN - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

IntArrayDataBlock - Class in org.janelia.saalfeldlab.n5

IntArrayDataBlock(int[], long[], int[]) - Constructor for class org.janelia.saalfeldlab.n5.IntArrayDataBlock

invertPermutation(int[]) - Static method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodec

IoPolicy - Interface in org.janelia.saalfeldlab.n5

isAbsolute() - Method in class org.janelia.saalfeldlab.n5.N5URI

N5URI is always considered absolute if a scheme is provided.

isCompatible(N5Reader.Version) - Method in class org.janelia.saalfeldlab.n5.N5Reader.Version

Returns true if this implementation is compatible with a given version.

isCovered(Range) - Method in class org.janelia.saalfeldlab.n5.readdata.prefetch.SliceTrackingLazyRead

isDataset(String, String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

isDataset - Variable in class org.janelia.saalfeldlab.n5.cache.N5JsonCache.N5CacheInfo

isDataset() - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache.N5CacheInfo

isDatasetFromAttributes(String, JsonElement) - Method in interface org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer

Returns true if a path is a dataset, given that the the given attributes exist for the given cache key.

isDatasetFromAttributes(String, JsonElement) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

isDatasetFromContainer(String) - Method in interface org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer

Query whether a path in this container is a dataset.

isDatasetFromContainer(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

isDirectory(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

isDirectory(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

Test whether the path is a directory.

isDirectory(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Test whether the path is a directory.

isEmpty() - Method in class org.janelia.saalfeldlab.n5.shard.RawShard

isFile(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

isFile(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

Test whether the path is a file.

isFile(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Test whether the path is a file.

isGroup(String, String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

isGroup - Variable in class org.janelia.saalfeldlab.n5.cache.N5JsonCache.N5CacheInfo

isGroup() - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache.N5CacheInfo

isGroupFromAttributes(String, JsonElement) - Method in interface org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer

Returns true if a path is a group, given that the the given attributes exist for the given cache key.

isGroupFromAttributes(String, JsonElement) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

isGroupFromContainer(String) - Method in interface org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer

Query whether a path in this container is a group.

isGroupFromContainer(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

isIdentity(int[]) - Static method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodec

isReversal(int[]) - Static method in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodec

isSharded() - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

J

JsonAdapter() - Constructor for class org.janelia.saalfeldlab.n5.DataType.JsonAdapter

JsonArrayUtils - Class in org.janelia.saalfeldlab.n5.serialization

JsonArrayUtils() - Constructor for class org.janelia.saalfeldlab.n5.serialization.JsonArrayUtils

jsonCompatible(JsonElement) - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

Check if the provided json is compatible with this token.

K

key() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

KeyValueAccess - Interface in org.janelia.saalfeldlab.n5

Key value read primitives used by N5KeyValueReader implementations.

keyValueAccess - Variable in class org.janelia.saalfeldlab.n5.N5KeyValueReader

L

LazyRead - Interface in org.janelia.saalfeldlab.n5.readdata

A lazy reading strategy for lazy, partial reading of data from some source.

length() - Method in class org.janelia.saalfeldlab.n5.readdata.prefetch.SliceTrackingLazyRead.Slice

length() - Method in interface org.janelia.saalfeldlab.n5.readdata.Range

length() - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Returns number of bytes in this ReadData, if known.

level() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

Get the nesting level of this position.

limit(long) - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Returns a ReadData whose length is limited to the given value.

limit(long) - Method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

LinkedAttributePathToken<T extends com.google.gson.JsonElement> - Class in org.janelia.saalfeldlab.n5

LinkedAttributePathToken() - Constructor for class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

LinkedAttributePathToken.ArrayAttributeToken - Class in org.janelia.saalfeldlab.n5

LinkedAttributePathToken.ObjectAttributeToken - Class in org.janelia.saalfeldlab.n5

list(String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

list(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

list(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

list(String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

list(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

List all children of a path.

list(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

List all children of a path.

list(String) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

List all groups (including datasets) in a group.

listAttributes(String) - Method in interface org.janelia.saalfeldlab.n5.GsonN5Reader

listAttributes(JsonElement) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

Best effort implementation of N5Reader.listAttributes(String) with limited type resolution.

listAttributes(String) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

List all attributes and their class of a group.

listDirectories(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

listDirectories(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

List all 'directory'-like children of a path.

listDirectories(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

List all 'directory'-like children of a path.

listFromContainer(String) - Method in interface org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer

List the children of a path for this container.

listFromContainer(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

ListResponseParser - Interface in org.janelia.saalfeldlab.n5.http

location(Segment) - Method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

Returns the location of segment in this ReadData.

LockedChannel - Interface in org.janelia.saalfeldlab.n5

A lock on a path that can create a Reader, Writer, InputStream, or OutputStream.

lockForReading(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

lockForReading(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Deprecated.

migrate to KeyValueAccess.createReadData(String)

lockForWriting(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

lockForWriting(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Deprecated.

migrate to KeyValueAccess.write(String, ReadData)

LockingPolicy - Enum in org.janelia.saalfeldlab.n5

File locking policy.

LONG(ByteOrder) - Static method in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

LONG - Static variable in interface org.janelia.saalfeldlab.n5.util.MemCopy

LONG_BIG_ENDIAN - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

LONG_LITTLE_ENDIAN - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

LongArrayDataBlock - Class in org.janelia.saalfeldlab.n5

LongArrayDataBlock(int[], long[], long[]) - Constructor for class org.janelia.saalfeldlab.n5.LongArrayDataBlock

Lz4Compression - Class in org.janelia.saalfeldlab.n5

Lz4Compression(int) - Constructor for class org.janelia.saalfeldlab.n5.Lz4Compression

Lz4Compression() - Constructor for class org.janelia.saalfeldlab.n5.Lz4Compression

M

materialize(long, long) - Method in interface org.janelia.saalfeldlab.n5.readdata.LazyRead

Materializes a portion of the data into a concrete ReadData instance.

materialize(long, long) - Method in class org.janelia.saalfeldlab.n5.readdata.prefetch.SliceTrackingLazyRead

materialize() - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Read the underlying data into a byte[] array, and return it as a ReadData.

materialize() - Method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

maxPixelPosition(long[], int, long[]) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Get the maximum pixel position in the block (chunk/shard) at the given sourcePos grid position at sourceLevel.

maxPixelPosition(long[], int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Get the maximum pixel position in the block (chunk/shard) at the given sourcePos grid position at sourceLevel.

maxPixelPosition() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

maxPos() - Method in class org.janelia.saalfeldlab.n5.shard.Region

Get the NestedPosition of the maximum chunk touched by the region.

MemCopy<T> - Interface in org.janelia.saalfeldlab.n5.util

Low-level range copying methods between source and target primitve array (type T, e.g., double[]).

MemCopy.MemCopyByte - Class in org.janelia.saalfeldlab.n5.util

MemCopy.MemCopyDouble - Class in org.janelia.saalfeldlab.n5.util

MemCopy.MemCopyFloat - Class in org.janelia.saalfeldlab.n5.util

MemCopy.MemCopyInt - Class in org.janelia.saalfeldlab.n5.util

MemCopy.MemCopyLong - Class in org.janelia.saalfeldlab.n5.util

MemCopy.MemCopyShort - Class in org.janelia.saalfeldlab.n5.util

MemCopyByte() - Constructor for class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyByte

MemCopyDouble() - Constructor for class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyDouble

MemCopyFloat() - Constructor for class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyFloat

MemCopyInt() - Constructor for class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyInt

MemCopyLong() - Constructor for class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyLong

MemCopyShort() - Constructor for class org.janelia.saalfeldlab.n5.util.MemCopy.MemCopyShort

minPos() - Method in class org.janelia.saalfeldlab.n5.shard.Region

Get the NestedPosition of the minimum chunk touched by the region.

N

N5_DATASET_ATTRIBUTES - Static variable in class org.janelia.saalfeldlab.n5.DatasetAttributes

N5Annotations - Interface in org.janelia.saalfeldlab.n5.serialization

Provides specialized annotations for N5 serialization behaviors.

N5Annotations.ReverseArray - Annotation Type in org.janelia.saalfeldlab.n5.serialization

Indicates that an array field should be reversed during serialization/deserialization.

N5BlockCodecInfo - Class in org.janelia.saalfeldlab.n5.codec

N5BlockCodecInfo() - Constructor for class org.janelia.saalfeldlab.n5.codec.N5BlockCodecInfo

N5BlockCodecs - Class in org.janelia.saalfeldlab.n5.codec

N5CacheInfo() - Constructor for class org.janelia.saalfeldlab.n5.cache.N5JsonCache.N5CacheInfo

N5ClassCastException(Class<?>) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5ClassCastException

N5ClassCastException(String) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5ClassCastException

N5ClassCastException(String, Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5ClassCastException

N5ClassCastException(Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5ClassCastException

N5ClassCastException(String, Throwable, boolean, boolean) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5ClassCastException

N5ConcurrentModificationException(String) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5ConcurrentModificationException

N5ConcurrentModificationException(String, Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5ConcurrentModificationException

N5ConcurrentModificationException(Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5ConcurrentModificationException

N5ConcurrentModificationException(String, Throwable, boolean, boolean) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5ConcurrentModificationException

N5Exception - Exception in org.janelia.saalfeldlab.n5

N5Exception() - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception

N5Exception(String) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception

N5Exception(String, Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception

N5Exception(Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception

N5Exception(String, Throwable, boolean, boolean) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception

N5Exception.N5ClassCastException - Exception in org.janelia.saalfeldlab.n5

This excpetion represents the situation when an attribute is requested by key as a specific Class, that attribute key does exist, but is not parseable as the desired Class

N5Exception.N5ConcurrentModificationException - Exception in org.janelia.saalfeldlab.n5

N5Exception.N5IOException - Exception in org.janelia.saalfeldlab.n5

N5Exception.N5JsonParseException - Exception in org.janelia.saalfeldlab.n5

Exception to represent an error when attempting to parse json attributes

N5Exception.N5NoSuchKeyException - Exception in org.janelia.saalfeldlab.n5

N5FSReader - Class in org.janelia.saalfeldlab.n5

N5Reader implementation through KeyValueAccess with JSON attributes parsed with Gson.

N5FSReader(String, GsonBuilder, boolean) - Constructor for class org.janelia.saalfeldlab.n5.N5FSReader

Opens an N5FSReader at a given base path with a custom GsonBuilder to support custom attributes.

N5FSReader(String, boolean) - Constructor for class org.janelia.saalfeldlab.n5.N5FSReader

Opens an N5FSReader at a given base path.

N5FSReader(String, GsonBuilder) - Constructor for class org.janelia.saalfeldlab.n5.N5FSReader

Opens an N5FSReader at a given base path with a custom GsonBuilder to support custom attributes.

N5FSReader(String) - Constructor for class org.janelia.saalfeldlab.n5.N5FSReader

Opens an N5FSReader at a given base path.

N5FSWriter - Class in org.janelia.saalfeldlab.n5

Filesystem N5Writer implementation with version compatibility check.

N5FSWriter(String, GsonBuilder, boolean) - Constructor for class org.janelia.saalfeldlab.n5.N5FSWriter

Opens an N5FSWriter at a given base path with a custom GsonBuilder to support custom attributes.

N5FSWriter(String, boolean) - Constructor for class org.janelia.saalfeldlab.n5.N5FSWriter

Opens an N5FSWriter at a given base path.

N5FSWriter(String, GsonBuilder) - Constructor for class org.janelia.saalfeldlab.n5.N5FSWriter

Opens an N5FSWriter at a given base path with a custom GsonBuilder to support custom attributes.

N5FSWriter(String) - Constructor for class org.janelia.saalfeldlab.n5.N5FSWriter

Opens an N5FSWriter at a given base path.

N5IOException(String) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5IOException

N5IOException(String, Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5IOException

N5IOException(Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5IOException

N5IOException(String, Throwable, boolean, boolean) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5IOException

N5JsonCache - Class in org.janelia.saalfeldlab.n5.cache

N5JsonCache(N5JsonCacheableContainer) - Constructor for class org.janelia.saalfeldlab.n5.cache.N5JsonCache

N5JsonCache.EmptyJson - Class in org.janelia.saalfeldlab.n5.cache

N5JsonCache.N5CacheInfo - Class in org.janelia.saalfeldlab.n5.cache

Data object for caching meta data.

N5JsonCacheableContainer - Interface in org.janelia.saalfeldlab.n5.cache

An N5 container whose structure and attributes can be cached.

N5JsonParseException(String) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5JsonParseException

N5JsonParseException(String, Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5JsonParseException

N5JsonParseException(Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5JsonParseException

N5JsonParseException(String, Throwable, boolean, boolean) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5JsonParseException

N5KeyValueReader - Class in org.janelia.saalfeldlab.n5

N5Reader implementation through KeyValueAccess with JSON attributes parsed with Gson.

N5KeyValueReader(KeyValueAccess, String, GsonBuilder, boolean) - Constructor for class org.janelia.saalfeldlab.n5.N5KeyValueReader

Opens an N5KeyValueReader at a given base path with a custom GsonBuilder to support custom attributes.

N5KeyValueReader(boolean, KeyValueAccess, String, GsonBuilder, boolean, boolean) - Constructor for class org.janelia.saalfeldlab.n5.N5KeyValueReader

Opens an N5KeyValueReader at a given base path with a custom GsonBuilder to support custom attributes.

N5KeyValueWriter - Class in org.janelia.saalfeldlab.n5

Filesystem N5Writer implementation with version compatibility check.

N5KeyValueWriter(KeyValueAccess, String, GsonBuilder, boolean) - Constructor for class org.janelia.saalfeldlab.n5.N5KeyValueWriter

Opens an N5KeyValueWriter at a given base path with a custom GsonBuilder to support custom attributes.

N5NoSuchKeyException(String) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5NoSuchKeyException

N5NoSuchKeyException(String, Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5NoSuchKeyException

N5NoSuchKeyException(Throwable) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5NoSuchKeyException

N5NoSuchKeyException(String, Throwable, boolean, boolean) - Constructor for exception org.janelia.saalfeldlab.n5.N5Exception.N5NoSuchKeyException

N5Reader - Interface in org.janelia.saalfeldlab.n5

A simple structured container for hierarchies of chunked n-dimensional datasets and attributes.

N5Reader.Version - Class in org.janelia.saalfeldlab.n5

N5URI - Class in org.janelia.saalfeldlab.n5

A URI for N5 containers, groups, datasets, and attributes.

N5URI(String) - Constructor for class org.janelia.saalfeldlab.n5.N5URI

N5URI(URI) - Constructor for class org.janelia.saalfeldlab.n5.N5URI

N5Writer - Interface in org.janelia.saalfeldlab.n5

A simple structured container API for hierarchies of chunked n-dimensional datasets and attributes.

N5Writer.DataBlockSupplier<T> - Interface in org.janelia.saalfeldlab.n5

NameConfig - Interface in org.janelia.saalfeldlab.n5.serialization

Configuration interface for N5 serialization naming and parameter annotations.

NameConfig.Name - Annotation Type in org.janelia.saalfeldlab.n5.serialization

Specifies the serialization type name for a class.

NameConfig.Parameter - Annotation Type in org.janelia.saalfeldlab.n5.serialization

Marks a field as a parameter to be serialized.

NameConfig.Prefix - Annotation Type in org.janelia.saalfeldlab.n5.serialization

Defines a namespace prefix for serialization.

NameConfig.Serialize - Annotation Type in org.janelia.saalfeldlab.n5.serialization

Controls whether a class should be serializable as a NameConfig.

NameConfigAdapter<T> - Class in org.janelia.saalfeldlab.n5

T adapter, auto-discovers annotated T implementations in the classpath.

NameConfigAdapter(Class<T>) - Constructor for class org.janelia.saalfeldlab.n5.NameConfigAdapter

NestedGrid(int[][], long[]) - Constructor for class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

blockSizes[l][d] is the block size at level l in dimension d.

NestedGrid(int[][]) - Constructor for class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

nestedPosition(long[], int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Create a NestedPosition at the specified nesting level grid position.

nestedPosition(long[]) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Create a NestedPosition at the specified chunk grid position (that is, at nesting level 0).

NestedPosition(Nesting.NestedGrid, long[], int) - Constructor for class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

Nesting - Class in org.janelia.saalfeldlab.n5.shard

Container for classes that coordinate hierarchical grid structures for sharded N5 datasets.

Nesting() - Constructor for class org.janelia.saalfeldlab.n5.shard.Nesting

Nesting.NestedGrid - Class in org.janelia.saalfeldlab.n5.shard

A nested grid of blocks used to coordinate the relationships of shards and the blocks (chunks / sub-shards) they contain.

Nesting.NestedPosition - Class in org.janelia.saalfeldlab.n5.shard

Represents the position of a block at a particular level of a nested hierarchy, where the hierarchy is defined by a given Nesting.NestedGrid.

newArray(int) - Method in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

newCache() - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

newCacheInfo() - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

newInputStream() - Method in interface org.janelia.saalfeldlab.n5.LockedChannel

Create a new InputStream.

newOutputStream() - Method in interface org.janelia.saalfeldlab.n5.LockedChannel

Create a new OutputStream.

newReader() - Method in interface org.janelia.saalfeldlab.n5.LockedChannel

Create a UTF-8 Reader.

newWriter() - Method in interface org.janelia.saalfeldlab.n5.LockedChannel

Create a new UTF-8 Writer.

next() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

NO_VERSION - Static variable in interface org.janelia.saalfeldlab.n5.N5Reader

SemVer version of this N5 spec.

normalGetDatasetAttributes(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

normalize(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

Returns a normalized path.

normalize(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

normalize(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Normalize a path to canonical form.

normalizeAttributePath() - Method in class org.janelia.saalfeldlab.n5.N5URI

normalizeAttributePath(String) - Static method in class org.janelia.saalfeldlab.n5.N5URI

Normalize the attributePath.

normalizeGroupPath() - Method in class org.janelia.saalfeldlab.n5.N5URI

normalizeGroupPath(String) - Static method in class org.janelia.saalfeldlab.n5.N5URI

Normalize a group path relative to a container's root, resulting in removal of redundant "/", "./", resolution of relative "../", and removal of leading slashes.

NULLCHAR - Static variable in class org.janelia.saalfeldlab.n5.StringDataBlock

numChecksumBytes() - Method in class org.janelia.saalfeldlab.n5.codec.checksum.ChecksumCodec

numDimensions() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

numDimensions() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

numElements() - Method in class org.janelia.saalfeldlab.n5.shard.ShardIndex.NDArray

numLevels() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

O

OBJECT - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

ObjectAttributeToken(String) - Constructor for class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ObjectAttributeToken

offset() - Method in class org.janelia.saalfeldlab.n5.readdata.prefetch.SliceTrackingLazyRead.Slice

offset() - Method in interface org.janelia.saalfeldlab.n5.readdata.Range

org.janelia.saalfeldlab.n5 - package org.janelia.saalfeldlab.n5

org.janelia.saalfeldlab.n5.cache - package org.janelia.saalfeldlab.n5.cache

org.janelia.saalfeldlab.n5.codec - package org.janelia.saalfeldlab.n5.codec

org.janelia.saalfeldlab.n5.codec.checksum - package org.janelia.saalfeldlab.n5.codec.checksum

org.janelia.saalfeldlab.n5.codec.transpose - package org.janelia.saalfeldlab.n5.codec.transpose

org.janelia.saalfeldlab.n5.http - package org.janelia.saalfeldlab.n5.http

org.janelia.saalfeldlab.n5.readdata - package org.janelia.saalfeldlab.n5.readdata

org.janelia.saalfeldlab.n5.readdata.prefetch - package org.janelia.saalfeldlab.n5.readdata.prefetch

org.janelia.saalfeldlab.n5.readdata.segment - package org.janelia.saalfeldlab.n5.readdata.segment

org.janelia.saalfeldlab.n5.serialization - package org.janelia.saalfeldlab.n5.serialization

org.janelia.saalfeldlab.n5.shard - package org.janelia.saalfeldlab.n5.shard

org.janelia.saalfeldlab.n5.util - package org.janelia.saalfeldlab.n5.util

P

parent(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

parent(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Get the parent of a path string.

parentJson - Variable in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

The JsonElement which contains the mapping that this token represents.

parseAttributeElement(JsonElement, Gson, Type) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

Deserialize the attribute as type T.

parseBytes(String) - Static method in class org.janelia.saalfeldlab.n5.util.FloatValueParser

Parses a hex string to a byte array.

parseDouble(String) - Static method in class org.janelia.saalfeldlab.n5.util.FloatValueParser

Parses a hex string to a double value.

parseFloat(String) - Static method in class org.janelia.saalfeldlab.n5.util.FloatValueParser

Parses a hex string to a float value.

parseListResponse(String) - Method in interface org.janelia.saalfeldlab.n5.http.ListResponseParser

Parse a String response for a list call, and return the results as a String array.

pixelPosition(long[], int, long[]) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Computes the pixel position for the given sourcePos grid position at sourceLevel.

pixelPosition(long[], int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Get the pixel position for the given sourcePos grid position at sourceLevel.

pixelPosition() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

positionToIndex(int[], int[]) - Static method in interface org.janelia.saalfeldlab.n5.util.SubArrayCopy

PositionValueAccess - Interface in org.janelia.saalfeldlab.n5.shard

Wrap a KeyValueAccess and a dataset URI to be able to get/set values (ReadData) by long[] key indicating the position of a top-level DataBlock (a top-level shard for sharded datasets, a chunk for non-sharded datasets).

PositionValueAccess.KvaPositionValueAccess - Class in org.janelia.saalfeldlab.n5.shard

prefetch(Collection<? extends Range>) - Method in interface org.janelia.saalfeldlab.n5.readdata.LazyRead

Indicates that the given slices will be subsequently read.

prefetch(Collection<? extends Range>) - Method in class org.janelia.saalfeldlab.n5.readdata.prefetch.AggregatingPrefetchLazyRead

Indicates that the given slices will be subsequently read.

prefetch(Collection<? extends Range>) - Method in class org.janelia.saalfeldlab.n5.readdata.prefetch.EnclosingPrefetchLazyRead

Indicates that the given slices will be subsequently read.

prefetch(Collection<? extends Range>) - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Indicates that the given slices will be subsequently read.

prefetch(List<long[]>) - Method in class org.janelia.saalfeldlab.n5.shard.RawShard

R

RANGE - Static variable in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

Range - Interface in org.janelia.saalfeldlab.n5.readdata

A range specified as a Range.offset(), Range.length() pair.

RawBlockCodecInfo - Class in org.janelia.saalfeldlab.n5.codec

RawBlockCodecInfo() - Constructor for class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo

RawBlockCodecInfo(ByteOrder) - Constructor for class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo

RawBlockCodecInfo.ByteOrderAdapter - Class in org.janelia.saalfeldlab.n5.codec

RawBlockCodecs - Class in org.janelia.saalfeldlab.n5.codec

RawCompression - Class in org.janelia.saalfeldlab.n5

RawCompression() - Constructor for class org.janelia.saalfeldlab.n5.RawCompression

RawShard - Class in org.janelia.saalfeldlab.n5.shard

RawShardCodec - Class in org.janelia.saalfeldlab.n5.shard

RawShardDataBlock - Class in org.janelia.saalfeldlab.n5.shard

Wrap a RawShard as a DataBlock.

read(String) - Method in class org.janelia.saalfeldlab.n5.FsIoPolicy.Atomic

read(String) - Method in class org.janelia.saalfeldlab.n5.FsIoPolicy.Unsafe

read(String) - Method in interface org.janelia.saalfeldlab.n5.IoPolicy

readAttribute(JsonElement, String, Class<T>, Gson) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

readAttribute(JsonElement, String, Type, Gson) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

readAttributes(Reader, Gson) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

Reads the attributes json from a given Reader.

readBlock(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

readBlock(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Reads a block, returning a DataBlock.

readBlock(PositionValueAccess, long[], int) - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

Read a block at shardGridPosition at the given nesting level.

readBlock(PositionValueAccess, long[], int) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

readChecksum(ReadData) - Method in class org.janelia.saalfeldlab.n5.codec.checksum.ChecksumCodec

readChunk(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

readChunk(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Reads a chunk as a DataBlock.

readChunk(PositionValueAccess, long[]) - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

Read the chunk at the given gridPosition.

readChunk(PositionValueAccess, long[]) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

readChunks(String, DatasetAttributes, List<long[]>) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

readChunks(String, DatasetAttributes, List<long[]>) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Reads multiple chunks as DataBlocks.

readChunks(PositionValueAccess, List<long[]>) - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

Read the chunks at the given gridPositions.

readChunks(PositionValueAccess, List<long[]>) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

ReadData - Interface in org.janelia.saalfeldlab.n5.readdata

An abstraction over byte[] data.

readData(ByteBuffer) - Method in class org.janelia.saalfeldlab.n5.StringDataBlock

ReadData.Generator - Interface in org.janelia.saalfeldlab.n5.readdata

Generator supplies the content of a ReadData by writing it to an OutputStream on demand.

ReadData.OutputStreamOperator - Interface in org.janelia.saalfeldlab.n5.readdata

OutputStreamOperator is applied to an OutputStream to transform it into another(e.g., compressed) OutputStream.

readSerializedBlock(String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.N5Reader

Load a DataBlock as a Serializable.

Region - Class in org.janelia.saalfeldlab.n5.shard

Bounds, in pixel coordinates, of a region in a dataset.

Region(long[], long[], Nesting.NestedGrid) - Constructor for class org.janelia.saalfeldlab.n5.shard.Region

registerGson(GsonBuilder) - Method in class org.janelia.saalfeldlab.n5.N5KeyValueReader

relative(int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

Get the relative grid position at level, that is, relative offset within containing the (level+1) element.

relative() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

Get the relative grid position at this positions Nesting.NestedPosition.level(), that is, relative offset within containing the (level+1) element.

relativeBlockPath(long...) - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes

relativeBlockSize(int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Get size of a block at the given level relative to level-1 (that is, in units of level-1 blocks).

relativePosition(long[], int, long[], int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Computes the targetPos grid position at targetLevel for the given sourcePos grid position at sourceLevel, relative to the containing element at targetLevel+1.

relativePosition(long[], int, int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

relativeToBaseBlockSize(int) - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedGrid

Get size of a block at the given level relative to level 0 (that is, in units of chunks).

relativize(String, String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

relativize(String, String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Relativize path relative to base.

remove(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

remove(String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

remove(String) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Removes a group or dataset (directory and all contained files).

remove() - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Removes the N5 container.

remove(long[]) - Method in class org.janelia.saalfeldlab.n5.shard.PositionValueAccess.KvaPositionValueAccess

remove(long[]) - Method in interface org.janelia.saalfeldlab.n5.shard.PositionValueAccess

removeAttribute(String, String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

removeAttribute(String, String, Class<T>) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

removeAttribute(Writer, JsonElement, String, Class<T>, Gson) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

If there is an attribute in root such that it can be parsed and deserialized as T, then remove it from root, write root to the writer, and return the removed attribute.

removeAttribute(Writer, JsonElement, String, Gson) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

If there is an attribute in root at location normalizedAttributePath then remove it from root..

removeAttribute(JsonElement, String, Class<T>, Gson) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

If there is an attribute in root such that it can be parsed and desrialized as T, then remove it from root and return the removed attribute.

removeAttribute(JsonElement, String) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

Remove and return the attribute at normalizedAttributePath as a JsonElement.

removeAttribute(String, String) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Remove the attribute from group pathName with key key.

removeAttribute(String, String, Class<T>) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Remove the attribute from group pathName with key key and type T.

removeAttributes(String, List<String>) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

removeAttributes(String, List<String>) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Remove attributes as provided by attributes.

removeCache(String, String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

requireLength() - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Returns number of bytes in this ReadData.

resolve(N5URI) - Method in class org.janelia.saalfeldlab.n5.N5URI

Generate a new N5URI which is the result of resolving relativeN5Url to this N5URI.

resolve(URI) - Method in class org.janelia.saalfeldlab.n5.N5URI

Generate a new N5URI which is the result of resolving relativeUri to this N5URI.

resolve(String) - Method in class org.janelia.saalfeldlab.n5.N5URI

Generate a new N5URI which is the result of resolving relativeString to this N5URI If relativeString is not relative to this N5URI, then the resulting N5URI is equivalent to relativeString.

reverse(JsonArray) - Static method in class org.janelia.saalfeldlab.n5.serialization.JsonArrayUtils

Reverses the order of elements in a JSON array in-place.

S

Segment - Interface in org.janelia.saalfeldlab.n5.readdata.segment

A particular segment in a source SegmentedReadData.

SegmentedReadData - Interface in org.janelia.saalfeldlab.n5.readdata.segment

A ReadData which keeps track of contained Segments.

SegmentedReadData.SegmentsAndData - Interface in org.janelia.saalfeldlab.n5.readdata.segment

segments() - Method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

Return all segments (fully) contained in this ReadData, ordered by location (that is, sorted by Range.COMPARATOR).

segments() - Method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData.SegmentsAndData

serialize(ByteOrder, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo.ByteOrderAdapter

serialize(Compression, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.CompressionAdapter

serialize(DatasetAttributes, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.DatasetAttributes.DatasetAttributesAdapter

serialize(DataType, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.DataType.JsonAdapter

serialize(T, Type, JsonSerializationContext) - Method in class org.janelia.saalfeldlab.n5.NameConfigAdapter

serialize(String[]) - Method in class org.janelia.saalfeldlab.n5.StringDataBlock

serializedData - Variable in class org.janelia.saalfeldlab.n5.StringDataBlock

set(long[], ReadData) - Method in class org.janelia.saalfeldlab.n5.shard.PositionValueAccess.KvaPositionValueAccess

set(long[], ReadData) - Method in interface org.janelia.saalfeldlab.n5.shard.PositionValueAccess

Write the data for a DataBlock to the given position in the block grid.

setAndCreateParentElement(JsonElement) - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

If json is compatible with the type or token that we are, then set LinkedAttributePathToken.parentJson to json.

setAttribute(String, String, T) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Sets an attribute.

setAttributes(String, String, JsonElement) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

setAttributes(String, JsonElement) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

setAttributes(String, Map<String, ?>) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

setAttributes(String, JsonElement) - Method in interface org.janelia.saalfeldlab.n5.GsonN5Writer

Set the attributes of a group.

setAttributes(String, Map<String, ?>) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Sets a map of attributes.

setConnectionTimeout(int) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

setDatasetAttributes(String, DatasetAttributes) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Sets mandatory dataset attributes.

setElementData(ReadData, long[]) - Method in class org.janelia.saalfeldlab.n5.shard.RawShard

setListDirectoryParser(ListResponseParser) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

setListParser(ListResponseParser) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

setReadTimeout(int) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

setVersion(String) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

setVersion(String) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

TODO This overrides the version even if incompatible, check if this is the desired behavior or if it is always overridden, e.g. as by the caching version.

setVersion() - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Set the SemVer version of this container as specified in the N5Reader.VERSION_KEY attribute of the root group.

SHARD_SIZE_KEY - Static variable in class org.janelia.saalfeldlab.n5.DatasetAttributes

ShardCodecInfo - Interface in org.janelia.saalfeldlab.n5.shard

ShardIndex - Class in org.janelia.saalfeldlab.n5.shard

ShardIndex.IndexLocation - Enum in org.janelia.saalfeldlab.n5.shard

ShardIndex.NDArray<T> - Class in org.janelia.saalfeldlab.n5.shard

Access flat T[] array as n-dimensional array.

SHORT(ByteOrder) - Static method in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

SHORT - Static variable in interface org.janelia.saalfeldlab.n5.util.MemCopy

SHORT_BIG_ENDIAN - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

SHORT_LITTLE_ENDIAN - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

ShortArrayDataBlock - Class in org.janelia.saalfeldlab.n5

ShortArrayDataBlock(int[], long[], short[]) - Constructor for class org.janelia.saalfeldlab.n5.ShortArrayDataBlock

size - Variable in class org.janelia.saalfeldlab.n5.AbstractDataBlock

size(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

size(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

size(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Returns the size in bytes of the object at the given normalPath if it exists.

size() - Method in interface org.janelia.saalfeldlab.n5.readdata.LazyRead

Returns the total size of the data source in bytes.

size() - Method in class org.janelia.saalfeldlab.n5.readdata.prefetch.SliceTrackingLazyRead

size() - Method in class org.janelia.saalfeldlab.n5.shard.ShardIndex.NDArray

slice(long, long) - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Returns a new ReadData representing a slice, or subset of this ReadData.

slice(Range) - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Returns a new ReadData representing a slice, or subset of this ReadData.

slice(Segment) - Method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

Return a SegmentedReadData wrapping a slice containing exactly the given segment.

slice(long, long) - Method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

Returns a new SegmentedReadData representing a slice, or subset of this ReadData.

slice(Range) - Method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

Returns a new SegmentedReadData representing a slice, or subset of this ReadData.

slices - Variable in class org.janelia.saalfeldlab.n5.readdata.prefetch.SliceTrackingLazyRead

SliceTrackingLazyRead - Class in org.janelia.saalfeldlab.n5.readdata.prefetch

A LazyRead that wraps a delegate LazyRead and keeps track of all slices that have been materialized.

SliceTrackingLazyRead(LazyRead) - Constructor for class org.janelia.saalfeldlab.n5.readdata.prefetch.SliceTrackingLazyRead

SliceTrackingLazyRead.Slice - Class in org.janelia.saalfeldlab.n5.readdata.prefetch

source() - Method in interface org.janelia.saalfeldlab.n5.readdata.segment.Segment

Returns the SegmentedReadData on which this segment is originally defined.

sourceData() - Method in class org.janelia.saalfeldlab.n5.shard.RawShard

The ReadData from which the shard was constructed, or null for a new empty shard.

STRING - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

StringDataBlock - Class in org.janelia.saalfeldlab.n5

StringDataBlock(int[], long[], String[]) - Constructor for class org.janelia.saalfeldlab.n5.StringDataBlock

StringDataBlock(int[], long[], byte[]) - Constructor for class org.janelia.saalfeldlab.n5.StringDataBlock

SubArrayCopy - Interface in org.janelia.saalfeldlab.n5.util

Copy sub-region between flattened arrays (of different sizes).

T

toByteBuffer() - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Return the contained data as a ByteBuffer.

toString() - Method in enum org.janelia.saalfeldlab.n5.DataType

toString() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ArrayAttributeToken

toString() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ObjectAttributeToken

toString() - Method in class org.janelia.saalfeldlab.n5.N5Reader.Version

toString() - Method in class org.janelia.saalfeldlab.n5.N5URI

toString() - Method in class org.janelia.saalfeldlab.n5.readdata.prefetch.SliceTrackingLazyRead.Slice

toString() - Method in class org.janelia.saalfeldlab.n5.shard.Nesting.NestedPosition

TransposeCodec<T> - Class in org.janelia.saalfeldlab.n5.codec.transpose

TransposeCodec(DataType, int[]) - Constructor for class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodec

TransposeCodecInfo - Class in org.janelia.saalfeldlab.n5.codec.transpose

Describes a permutation of the dimensions of a block.

TransposeCodecInfo() - Constructor for class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodecInfo

TransposeCodecInfo(int[]) - Constructor for class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodecInfo

tryDelete(Path) - Static method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

TYPE - Static variable in class org.janelia.saalfeldlab.n5.codec.checksum.Crc32cChecksumCodec

TYPE - Static variable in class org.janelia.saalfeldlab.n5.codec.IdentityCodec

TYPE - Static variable in class org.janelia.saalfeldlab.n5.codec.N5BlockCodecInfo

TYPE - Static variable in class org.janelia.saalfeldlab.n5.codec.RawBlockCodecInfo

TYPE - Static variable in class org.janelia.saalfeldlab.n5.codec.transpose.TransposeCodecInfo

U

Unsafe() - Constructor for class org.janelia.saalfeldlab.n5.FsIoPolicy.Unsafe

update(boolean) - Static method in class org.janelia.saalfeldlab.n5.CompressionAdapter

update() - Static method in class org.janelia.saalfeldlab.n5.CompressionAdapter

update(NameConfigAdapter<T>) - Static method in class org.janelia.saalfeldlab.n5.NameConfigAdapter

updateCache(String, N5JsonCache.N5CacheInfo) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

updateCacheAttributes(N5JsonCache.N5CacheInfo, String, JsonElement) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

updateCacheInfo(String, String) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

Updates the cache attributes for the given normalPathKey adding the appropriate node to the cache if necessary.

updateCacheInfo(String, String, JsonElement) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

Updates the cache attributes for the given normalPathKey and normalCacheKey, adding the appropriate node to the cache if necessary.

updateCacheIsDataset(N5JsonCache.N5CacheInfo, boolean) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

updateCacheIsGroup(N5JsonCache.N5CacheInfo, boolean) - Method in class org.janelia.saalfeldlab.n5.cache.N5JsonCache

uri(String) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

uri(String) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

uri(String) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Get the absolute (including scheme) URI of the given path

uri - Variable in class org.janelia.saalfeldlab.n5.N5KeyValueReader

V

valueOf(String) - Static method in enum org.janelia.saalfeldlab.n5.DataType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.janelia.saalfeldlab.n5.LockingPolicy

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.janelia.saalfeldlab.n5.shard.ShardIndex.IndexLocation

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.janelia.saalfeldlab.n5.DataType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.janelia.saalfeldlab.n5.LockingPolicy

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.janelia.saalfeldlab.n5.shard.ShardIndex.IndexLocation

Returns an array containing the constants of this enum type, in the order they are declared.

VERSION - Static variable in interface org.janelia.saalfeldlab.n5.N5Reader

SemVer version of this N5 spec.

Version(int, int, int, String) - Constructor for class org.janelia.saalfeldlab.n5.N5Reader.Version

Version(int, int, int) - Constructor for class org.janelia.saalfeldlab.n5.N5Reader.Version

Version(String) - Constructor for class org.janelia.saalfeldlab.n5.N5Reader.Version

Creates a version from a SemVer compatible version string.

VERSION_KEY - Static variable in interface org.janelia.saalfeldlab.n5.N5Reader

Version attribute key.

VolatileReadData - Interface in org.janelia.saalfeldlab.n5.readdata

During its life-time, the content of a VolatileReadData should not be mutated.

W

withFallback(IoPolicy, IoPolicy) - Static method in interface org.janelia.saalfeldlab.n5.IoPolicy

wrap(ReadData) - Static method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

Wrap a ReadData and create one segment comprising the entire readData.

wrap(ReadData, Range...) - Static method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

Wrap readData and create segments at the given locations.

wrap(ReadData, List<Range>) - Static method in interface org.janelia.saalfeldlab.n5.readdata.segment.SegmentedReadData

Wrap readData and create segments at the given locations.

write(String, ReadData) - Method in class org.janelia.saalfeldlab.n5.FileSystemKeyValueAccess

write(String, ReadData) - Method in class org.janelia.saalfeldlab.n5.FsIoPolicy.Atomic

write(String, ReadData) - Method in class org.janelia.saalfeldlab.n5.FsIoPolicy.Unsafe

write(String, ReadData) - Method in class org.janelia.saalfeldlab.n5.HttpKeyValueAccess

write(String, ReadData) - Method in interface org.janelia.saalfeldlab.n5.IoPolicy

write(String, ReadData) - Method in interface org.janelia.saalfeldlab.n5.KeyValueAccess

Write data to the given normalPath.

writeAndCacheAttributes(String, JsonElement) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

writeAttribute(Writer, JsonElement, String, T, Gson) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

Inserts attribute into root at location normalizedAttributePath and write the resulting root.

writeAttributes(String, JsonElement) - Method in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

writeAttributes(String, JsonElement) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Helper method that writes an attributes tree into the store TODO This method is not part of the public API and should be protected in Java versions greater than 8

writeAttributes(String, Map<String, ?>) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Helper method that reads the existing map of attributes, JSON encodes, inserts and overrides the provided attributes, and writes them back into the attributes store.

writeAttributes(Writer, JsonElement, Gson) - Static method in interface org.janelia.saalfeldlab.n5.GsonUtils

Writes the attributes JsonElement to a given Writer.

writeBlock(String, DatasetAttributes, DataBlock<T>) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

writeBlock(String, DatasetAttributes, DataBlock<T>) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Writes a block stored as a DataBlock.

writeBlock(PositionValueAccess, DataBlock<T>, int) - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

Write a full block at the given nesting level.

writeBlock(PositionValueAccess, DataBlock<T>, int) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

writeChecksum(Checksum, OutputStream) - Method in class org.janelia.saalfeldlab.n5.codec.checksum.ChecksumCodec

writeChild(Gson, Object) - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

This method will write into LinkedAttributePathToken.parentJson the subsequent JsonElement.

writeChildElement() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ArrayAttributeToken

writeChildElement() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ObjectAttributeToken

writeChildElement() - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

Write the JsonElement the corresponds to LinkedAttributePathToken.childToken into LinkedAttributePathToken.parentJson.

writeChunk(String, DatasetAttributes, DataBlock<T>) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

writeChunk(String, DatasetAttributes, DataBlock<T>) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Writes a chunk represented by a DataBlock.

writeChunk(PositionValueAccess, DataBlock<T>) - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

Writes a chunk to the grid position specified by chunk.

writeChunk(PositionValueAccess, DataBlock<T>) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

writeChunks(String, DatasetAttributes, DataBlock<T>...) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

writeChunks(String, DatasetAttributes, DataBlock<T>...) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Write multiple chunks represented by DataBlocks, useful for aggregation.

writeChunks(PositionValueAccess, List<DataBlock<T>>) - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

Writes multiple chunks to the grid positions specified by the respective chunks.

writeChunks(PositionValueAccess, List<DataBlock<T>>) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

writeRegion(String, DatasetAttributes, long[], long[], N5Writer.DataBlockSupplier<T>, boolean) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

writeRegion(String, DatasetAttributes, long[], long[], N5Writer.DataBlockSupplier<T>, boolean, ExecutorService) - Method in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

writeRegion(String, DatasetAttributes, long[], long[], N5Writer.DataBlockSupplier<T>, boolean) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

writeRegion(String, DatasetAttributes, long[], long[], N5Writer.DataBlockSupplier<T>, boolean, ExecutorService) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

writeRegion(PositionValueAccess, long[], long[], N5Writer.DataBlockSupplier<T>, boolean) - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

writeRegion(PositionValueAccess, long[], long[], N5Writer.DataBlockSupplier<T>, boolean, ExecutorService) - Method in interface org.janelia.saalfeldlab.n5.shard.DatasetAccess

writeRegion(PositionValueAccess, long[], long[], N5Writer.DataBlockSupplier<T>, boolean) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

writeRegion(PositionValueAccess, long[], long[], N5Writer.DataBlockSupplier<T>, boolean, ExecutorService) - Method in class org.janelia.saalfeldlab.n5.shard.DefaultDatasetAccess

writeSerializedBlock(Serializable, String, DatasetAttributes, long...) - Method in interface org.janelia.saalfeldlab.n5.N5Writer

Save a Serializable as an N5 DataBlock at a given offset.

writeTo(OutputStream) - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData.Generator

writeTo(OutputStream) - Method in interface org.janelia.saalfeldlab.n5.readdata.ReadData

Write the contained data into an OutputStream.

writeValue(Gson, Object) - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ArrayAttributeToken

writeValue(Gson, Object) - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken.ObjectAttributeToken

writeValue(Gson, Object) - Method in class org.janelia.saalfeldlab.n5.LinkedAttributePathToken

Write value into LinkedAttributePathToken.parentJson.

X

XzCompression - Class in org.janelia.saalfeldlab.n5

XzCompression(int) - Constructor for class org.janelia.saalfeldlab.n5.XzCompression

XzCompression() - Constructor for class org.janelia.saalfeldlab.n5.XzCompression

Z

ZARR_STRING - Static variable in class org.janelia.saalfeldlab.n5.codec.FlatArrayCodec

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