org.janelia.saalfeldlab.n5.zarr.v3

Class ZarrV3KeyValueWriter

java.lang.Object

org.janelia.saalfeldlab.n5.N5KeyValueReader

org.janelia.saalfeldlab.n5.zarr.v3.ZarrV3KeyValueReader

org.janelia.saalfeldlab.n5.zarr.v3.ZarrV3KeyValueWriter

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 ZarrV3KeyValueWriter
extends ZarrV3KeyValueReader
implements org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

Zarr v3 N5Writer implementation.

Nested Class Summary

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.v3.ZarrV3KeyValueReader

datasetAttributesMap, DEFAULT_DIMENSION_SEPARATOR, dimensionSeparator, VERSION, ZARR_KEY

Fields inherited from class org.janelia.saalfeldlab.n5.N5KeyValueReader

ATTRIBUTES_JSON, cacheMeta, gson, keyValueAccess, uri

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

NO_VERSION, VERSION, VERSION_KEY

Constructor Summary

Constructors

Constructor and Description
ZarrV3KeyValueWriter(org.janelia.saalfeldlab.n5.KeyValueAccess keyValueAccess, String basePath, com.google.gson.GsonBuilder gsonBuilder, boolean cacheAttributes) Opens an ZarrV3KeyValueWriter at a given base path with a custom GsonBuilder to support custom attributes.

Method Summary

Modifier and Type	Method and Description
ZarrV3DatasetAttributes	createDataset(String datasetPath, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
ZarrV3DatasetAttributes	createDataset(String datasetPath, long[] dimensions, int[] blockSize, org.janelia.saalfeldlab.n5.DataType dataType, org.janelia.saalfeldlab.n5.Compression compression)
void	createGroup(String path)
ZarrV3DatasetAttributes	getConvertedDatasetAttributes(org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
<T> T	removeAttribute(String pathName, String key, Class<T> cls)
<T> void	setAttribute(String groupPath, String attributePath, T attribute)
void	setAttributes(String path, com.google.gson.JsonElement attributes)
void	setAttributes(String path, Map<String,?> attributes)
void	setDatasetAttributes(String datasetPath, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
<T> void	setRawAttribute(String groupPath, String attributePath, T attribute)
void	setRawAttributes(String path, com.google.gson.JsonElement attributes)
void	setRawAttributes(String path, Map<String,?> attributes)
void	setVersion(String path)
void	writeAttributes(String normalGroupPath, Map<String,?> attributes)

Methods inherited from class org.janelia.saalfeldlab.n5.zarr.v3.ZarrV3KeyValueReader

addTypeAdapters, createDatasetAttributes, exists, getAttribute, getAttribute, getAttributes, getAttributesKey, getDimensionSeparator, getRawAttribute, getRawAttributes, getVersion, getVersion, getVersion, isAttributes, isDatasetFromAttributes, isGroupFromAttributes, isGroupFromContainer, mapAttributeKey, setDimensionSeparator, toString

Methods inherited from class org.janelia.saalfeldlab.n5.N5KeyValueReader

cacheMeta, getCache, getGson, getKeyValueAccess, getURI, registerGson

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.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, removeAttribute, removeAttributes, writeBlock, writeChunk, writeChunks, writeRegion, writeRegion

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

deleteBlock, deleteChunk, remove, setVersion, writeSerializedBlock

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

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

close, deepList, deepList, deepList, deepList, deepList, deepListDatasets, deepListDatasets, deepListDatasets, deepListDatasets, deepListHelper, getGroupSeparator, getURI, getVersion, groupPath, readSerializedBlock

Constructor Detail

ZarrV3KeyValueWriter

public ZarrV3KeyValueWriter(org.janelia.saalfeldlab.n5.KeyValueAccess keyValueAccess,
                            String basePath,
                            com.google.gson.GsonBuilder gsonBuilder,
                            boolean cacheAttributes)
                     throws org.janelia.saalfeldlab.n5.N5Exception

Opens an ZarrV3KeyValueWriter at a given base path with a custom GsonBuilder to support custom attributes.

Parameters:

keyValueAccess -

basePath - N5 base path

gsonBuilder -

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 will not be tracked.

Throws:

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

Method Detail

setVersion

public void setVersion(String path)
                throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

setVersion in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

Specified by:

setVersion in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

createGroup

public void createGroup(String path)

Specified by:

createGroup in interface org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Writer

Specified by:

createGroup in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Specified by:

createGroup in interface org.janelia.saalfeldlab.n5.N5Writer

setDatasetAttributes

public void setDatasetAttributes(String datasetPath,
                                 org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
                          throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

setDatasetAttributes in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

createDataset

public ZarrV3DatasetAttributes createDataset(String datasetPath,
                                             long[] dimensions,
                                             int[] blockSize,
                                             org.janelia.saalfeldlab.n5.DataType dataType,
                                             org.janelia.saalfeldlab.n5.Compression compression)

Specified by:

createDataset in interface org.janelia.saalfeldlab.n5.N5Writer

createDataset

public ZarrV3DatasetAttributes createDataset(String datasetPath,
                                             org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)
                                      throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

createDataset in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

getConvertedDatasetAttributes

public ZarrV3DatasetAttributes getConvertedDatasetAttributes(org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes)

Specified by:

getConvertedDatasetAttributes in interface org.janelia.saalfeldlab.n5.N5Reader

Overrides:

getConvertedDatasetAttributes in class ZarrV3KeyValueReader

setRawAttribute

public <T> void setRawAttribute(String groupPath,
                                String attributePath,
                                T attribute)
                         throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setAttribute

public <T> void setAttribute(String groupPath,
                             String attributePath,
                             T attribute)
                      throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

setAttribute in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setRawAttributes

public void setRawAttributes(String path,
                             Map<String,?> attributes)
                      throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setRawAttributes

public void setRawAttributes(String path,
                             com.google.gson.JsonElement attributes)
                      throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setAttributes

public void setAttributes(String path,
                          Map<String,?> attributes)
                   throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

setAttributes in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Specified by:

setAttributes in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

setAttributes

public void setAttributes(String path,
                          com.google.gson.JsonElement attributes)
                   throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

setAttributes in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Specified by:

setAttributes in interface org.janelia.saalfeldlab.n5.GsonN5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

removeAttribute

public <T> T removeAttribute(String pathName,
                             String key,
                             Class<T> cls)
                      throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

removeAttribute in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Specified by:

removeAttribute in interface org.janelia.saalfeldlab.n5.N5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeAttributes

public void writeAttributes(String normalGroupPath,
                            Map<String,?> attributes)
                     throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

writeAttributes in interface org.janelia.saalfeldlab.n5.GsonKeyValueN5Writer

Throws:

org.janelia.saalfeldlab.n5.N5Exception