org.janelia.saalfeldlab.n5.zarr

Class N5ZarrWriter

java.lang.Object

org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader

org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueWriter

org.janelia.saalfeldlab.n5.zarr.N5ZarrWriter

All Implemented Interfaces:

AutoCloseable, org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer, org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader, org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer, org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader, org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer, org.janelia.saalfeldlab.n5.GsonN5Reader, org.janelia.saalfeldlab.n5.GsonN5Writer, org.janelia.saalfeldlab.n5.N5Reader, org.janelia.saalfeldlab.n5.N5Writer

public class N5ZarrWriter
extends ZarrKeyValueWriter
implements org.janelia.saalfeldlab.n5.N5Writer

Author:

Stephan Saalfeld

Nested Class Summary

Nested classes/interfaces inherited from class org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueWriter

ZarrKeyValueWriter.ZarrJsonElements

Nested classes/interfaces inherited from interface org.janelia.saalfeldlab.n5.N5Writer

org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier<T>

Nested classes/interfaces inherited from interface org.janelia.saalfeldlab.n5.N5Reader

org.janelia.saalfeldlab.n5.N5Reader.Version

Field Summary

Fields inherited from class org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader

cache, cacheMeta, dimensionSeparator, gson, keyValueAccess, mapN5DatasetAttributes, mergeAttributes, uri, VERSION, VERSION_ZERO, ZARR_FORMAT_KEY, ZARRAY_FILE, ZATTRS_FILE, ZGROUP_FILE

Fields inherited from interface org.janelia.saalfeldlab.n5.N5Reader

NO_VERSION, VERSION, VERSION_KEY

Constructor Summary

Constructors

Constructor and Description
N5ZarrWriter(String basePath) Opens an N5ZarrWriter at a given base path.
N5ZarrWriter(String basePath, boolean cacheAttributes) Opens an N5ZarrWriter at a given base path.
N5ZarrWriter(String basePath, com.google.gson.GsonBuilder gsonBuilder) Opens an N5ZarrWriter at a given base path with a custom GsonBuilder to support custom attributes.
N5ZarrWriter(String basePath, com.google.gson.GsonBuilder gsonBuilder, boolean cacheAttributes) Opens an N5ZarrWriter at a given base path with a custom GsonBuilder to support custom attributes.
N5ZarrWriter(String basePath, com.google.gson.GsonBuilder gsonBuilder, String dimensionSeparator, boolean mapN5DatasetAttributes, boolean cacheAttributes) Opens an N5ZarrWriter at a given base path with a custom GsonBuilder to support custom attributes.
N5ZarrWriter(String basePath, String dimensionSeparator, boolean cacheAttributes) Opens an N5ZarrWriter at a given base path.

Method Summary

Methods inherited from class org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueWriter

build, build, createDataset, createGroup, deleteJsonResource, hasRequiredArrayKeys, initializeGroup, isCompatible, move, padCrop, redirectCompression, redirectDatasetAttribute, redirectDatasetAttribute, redirectDatasetAttribute, redirectDataType, redirectGroupDatasetAttribute, removeAttribute, removeAttribute, setAttributes, setDatasetAttributes, setVersion, setVersion, setZArrayAttributes, setZGroup, writeJson, writeJsonResource, writeZArray, writeZAttrs, writeZGroup

Methods inherited from class org.janelia.saalfeldlab.n5.zarr.ZarrKeyValueReader

addTypeAdapters, cacheMeta, combine, combineAll, createDatasetAttributes, datasetExists, exists, existsFromContainer, getAttribute, getAttribute, getAttributes, getAttributesFromContainer, getAttributesKey, getAttributesUnmapped, getCache, getConvertedDatasetAttributes, getDatasetAttributes, getGson, getJsonResource, getKeyValueAccess, getURI, getVersion, getVersion, getZArray, getZArrayAttributes, getZArrayAttributes, getZAttributes, getZGroup, groupExists, isDatasetFromAttributes, isDatasetFromContainer, isGroupFromAttributes, isGroupFromContainer, n5ToZarrDatasetAttributes, newCache, reverseAttrsWhenCOrder, toString, zarrToN5DatasetAttributes

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.janelia.saalfeldlab.n5.N5Writer

createDataset, createDataset, createGroup, deleteBlock, deleteBlock, deleteChunk, deleteChunk, deleteChunks, remove, remove, removeAttribute, removeAttribute, removeAttributes, setAttribute, setAttributes, setDatasetAttributes, setVersion, writeBlock, writeChunk, writeChunks, writeRegion, writeRegion, writeSerializedBlock

Methods inherited from interface org.janelia.saalfeldlab.n5.N5Reader

blockExists, close, datasetExists, deepList, deepList, deepList, deepList, deepList, deepListDatasets, deepListDatasets, deepListDatasets, deepListDatasets, deepListHelper, exists, getAttribute, getAttribute, getConvertedDatasetAttributes, getDatasetAttributes, getGroupSeparator, getURI, getVersion, groupPath, list, listAttributes, readBlock, readChunk, readChunks, readSerializedBlock

Methods inherited from interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

remove, writeAndCacheAttributes, writeAttributes

Methods inherited from interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader

cacheMeta, datasetExists, exists, existsFromContainer, getAttribute, getAttribute, getAttributes, getAttributesFromContainer, getCache, getDatasetAttributes, groupExists, hasDatasetAttributes, isDatasetFromAttributes, isDatasetFromContainer, isGroupFromAttributes, isGroupFromContainer, list, listFromContainer, newCache, normalGetDatasetAttributes

Methods inherited from interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

deleteBlock, deleteChunk, deleteChunks, initializeContainer, removeAttributes, setAttributes, writeAttributes, writeBlock, writeChunk, writeChunks, writeRegion, writeRegion

Methods inherited from interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader

absoluteAttributesPath, absoluteGroupPath, blockExists, getKeyValueAccess, readBlock, readChunk, readChunks

Methods inherited from interface org.janelia.saalfeldlab.n5.GsonN5Reader

createDatasetAttributes, getAttributesKey, getGson, listAttributes

Constructor Detail

N5ZarrWriter

public N5ZarrWriter(String basePath,
                    com.google.gson.GsonBuilder gsonBuilder,
                    String dimensionSeparator,
                    boolean mapN5DatasetAttributes,
                    boolean cacheAttributes)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrWriter at a given base path with a custom GsonBuilder to support custom attributes. If the base path does not exist, it will be created. If the base path exists and if the N5 version of the container is compatible with this implementation, the N5 version of this container will be set to the current N5 version of this implementation.

Parameters:

basePath - n5 base path

gsonBuilder -

dimensionSeparator -

cacheAttributes - cache attributes and meta data Setting this to true avoids frequent reading and parsing of JSON encoded attributes and other meta data that requires accessing the store. This is most interesting for high latency backends. Changes of cached attributes and meta data by an independent writer on the same container will not be tracked.

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be written to or cannot be created, if the N5 version of the container is not compatible with this implementation.

N5ZarrWriter

public N5ZarrWriter(String basePath,
                    String dimensionSeparator,
                    boolean cacheAttributes)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrWriter at a given base path. If the base path does not exist, it will be created. If the base path exists and if the N5 version of the container is compatible with this implementation, the N5 version of this container will be set to the current N5 version of this implementation.

Parameters:

basePath - n5 base path

dimensionSeparator -

cacheAttributes - cache attributes and meta data Setting this to true avoids frequent reading and parsing of JSON encoded attributes and other meta data that requires accessing the store. This is most interesting for high latency backends. Changes of cached attributes and meta data by an independent writer on the same container will not be tracked.

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be written to or cannot be created, if the N5 version of the container is not compatible with this implementation.

N5ZarrWriter

public N5ZarrWriter(String basePath,
                    boolean cacheAttributes)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrWriter at a given base path. If the base path does not exist, it will be created. If the base path exists and if the N5 version of the container is compatible with this implementation, the N5 version of this container will be set to the current N5 version of this implementation.

Parameters:

basePath - n5 base path

cacheAttributes - cache attributes and meta data Setting this to true avoids frequent reading and parsing of JSON encoded attributes and other meta data that requires accessing the store. This is most interesting for high latency backends. Changes of cached attributes and meta data by an independent writer on the same container will not be tracked.

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be written to or cannot be created, if the N5 version of the container is not compatible with this implementation.

N5ZarrWriter

public N5ZarrWriter(String basePath,
                    com.google.gson.GsonBuilder gsonBuilder,
                    boolean cacheAttributes)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrWriter at a given base path with a custom GsonBuilder to support custom attributes.

If the base path does not exist, it will be created.

If the base path exists and if the N5 version of the container is compatible with this implementation, the N5 version of this container will be set to the current N5 version of this implementation.

Parameters:

basePath - n5 base path

gsonBuilder -

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be written to or cannot be created, if the N5 version of the container is not compatible with this implementation.

N5ZarrWriter

public N5ZarrWriter(String basePath,
                    com.google.gson.GsonBuilder gsonBuilder)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrWriter at a given base path with a custom GsonBuilder to support custom attributes.

If the base path does not exist, it will be created.

If the base path exists and if the N5 version of the container is compatible with this implementation, the N5 version of this container will be set to the current N5 version of this implementation.

Parameters:

basePath - n5 base path

gsonBuilder -

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be written to or cannot be created, if the N5 version of the container is not compatible with this implementation.

N5ZarrWriter

public N5ZarrWriter(String basePath)
             throws org.janelia.saalfeldlab.n5.N5Exception

Opens an N5ZarrWriter at a given base path.

If the base path does not exist, it will be created.

If the base path exists and if the N5 version of the container is compatible with this implementation, the N5 version of this container will be set to the current N5 version of this implementation.

Parameters:

basePath - n5 base path

Throws:

org.janelia.saalfeldlab.n5.N5Exception - if the base path cannot be written to or cannot be created, if the N5 version of the container is not compatible with this implementation.