org.janelia.saalfeldlab.n5.zarr.v3

Class ZarrV3KeyValueReader

java.lang.Object

org.janelia.saalfeldlab.n5.N5KeyValueReader

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

All Implemented Interfaces:

AutoCloseable, org.janelia.saalfeldlab.n5.cache.N5JsonCacheableContainer, org.janelia.saalfeldlab.n5.CachedGsonKeyValueN5Reader, org.janelia.saalfeldlab.n5.GsonKeyValueN5Reader, org.janelia.saalfeldlab.n5.GsonN5Reader, org.janelia.saalfeldlab.n5.N5Reader

Direct Known Subclasses:

ZarrV3KeyValueWriter

public class ZarrV3KeyValueReader
extends org.janelia.saalfeldlab.n5.N5KeyValueReader

Nested Class Summary

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

org.janelia.saalfeldlab.n5.N5Reader.Version

Field Summary

Fields

Modifier and Type	Field and Description
protected HashMap<org.janelia.saalfeldlab.n5.DatasetAttributes,ZarrV3DatasetAttributes>	datasetAttributesMap
static String	DEFAULT_DIMENSION_SEPARATOR
protected String	dimensionSeparator
static org.janelia.saalfeldlab.n5.N5Reader.Version	VERSION
static String	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_KEY

Constructor Summary

Constructors

Modifier	Constructor and Description
	ZarrV3KeyValueReader(boolean checkVersion, org.janelia.saalfeldlab.n5.KeyValueAccess keyValueAccess, String basePath, com.google.gson.GsonBuilder gsonBuilder, boolean cacheMeta) Opens an ZarrV3KeyValueReader at a given base path with a custom GsonBuilder to support custom attributes.
protected	ZarrV3KeyValueReader(boolean checkVersion, org.janelia.saalfeldlab.n5.KeyValueAccess keyValueAccess, String basePath, com.google.gson.GsonBuilder gsonBuilder, boolean cacheMeta, boolean checkRootExists)
	ZarrV3KeyValueReader(org.janelia.saalfeldlab.n5.KeyValueAccess keyValueAccess, String basePath, com.google.gson.GsonBuilder gsonBuilder, boolean cacheMeta) Opens an ZarrV3KeyValueReader at a given base path with a custom GsonBuilder to support custom attributes.

Method Summary

Modifier and Type	Method and Description
protected static com.google.gson.GsonBuilder	addTypeAdapters(com.google.gson.GsonBuilder gsonBuilder)
ZarrV3DatasetAttributes	createDatasetAttributes(com.google.gson.JsonElement attributes)
boolean	exists(String pathName)
<T> T	getAttribute(String pathName, String key, Class<T> clazz)
<T> T	getAttribute(String pathName, String key, Type type)
com.google.gson.JsonElement	getAttributes(String pathName)
String	getAttributesKey()
ZarrV3DatasetAttributes	getConvertedDatasetAttributes(org.janelia.saalfeldlab.n5.DatasetAttributes attributes)
String	getDimensionSeparator()
<T> T	getRawAttribute(String pathName, String key, Class<T> clazz)
com.google.gson.JsonElement	getRawAttributes(String pathName)
org.janelia.saalfeldlab.n5.N5Reader.Version	getVersion()
protected static org.janelia.saalfeldlab.n5.N5Reader.Version	getVersion(com.google.gson.JsonElement json)
org.janelia.saalfeldlab.n5.N5Reader.Version	getVersion(String path)
protected boolean	isAttributes(String attributePath)
boolean	isDatasetFromAttributes(String normalCacheKey, com.google.gson.JsonElement attributes)
boolean	isGroupFromAttributes(String normalCacheKey, com.google.gson.JsonElement attributes)
boolean	isGroupFromContainer(String normalPath)
protected String	mapAttributeKey(String attributePath) Converts an attribute path
void	setDimensionSeparator(String dimensionSeparator)
String	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.CachedGsonKeyValueN5Reader

datasetExists, existsFromContainer, getAttributesFromContainer, getDatasetAttributes, groupExists, hasDatasetAttributes, isDatasetFromContainer, list, listFromContainer, newCache, normalGetDatasetAttributes

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

absoluteAttributesPath, absoluteGroupPath, blockExists, readBlock, readChunk, readChunks

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

listAttributes

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

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

Field Detail

datasetAttributesMap

protected HashMap<org.janelia.saalfeldlab.n5.DatasetAttributes,ZarrV3DatasetAttributes> datasetAttributesMap

VERSION

public static final org.janelia.saalfeldlab.n5.N5Reader.Version VERSION

ZARR_KEY

public static final String ZARR_KEY

See Also:

Constant Field Values

DEFAULT_DIMENSION_SEPARATOR

public static final String DEFAULT_DIMENSION_SEPARATOR

See Also:

Constant Field Values

dimensionSeparator

protected String dimensionSeparator

Constructor Detail

ZarrV3KeyValueReader

public ZarrV3KeyValueReader(boolean checkVersion,
                            org.janelia.saalfeldlab.n5.KeyValueAccess keyValueAccess,
                            String basePath,
                            com.google.gson.GsonBuilder gsonBuilder,
                            boolean cacheMeta)
                     throws org.janelia.saalfeldlab.n5.N5Exception

Opens an ZarrV3KeyValueReader at a given base path with a custom GsonBuilder to support custom attributes.

Parameters:

checkVersion - perform version check

keyValueAccess -

basePath - N5 base path

gsonBuilder - the gson builder

cacheMeta - 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.

ZarrV3KeyValueReader

public ZarrV3KeyValueReader(org.janelia.saalfeldlab.n5.KeyValueAccess keyValueAccess,
                            String basePath,
                            com.google.gson.GsonBuilder gsonBuilder,
                            boolean cacheMeta)
                     throws org.janelia.saalfeldlab.n5.N5Exception

Opens an ZarrV3KeyValueReader at a given base path with a custom GsonBuilder to support custom attributes.

Parameters:

keyValueAccess -

basePath - N5 base path

gsonBuilder - GSON builder

cacheMeta - 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.

ZarrV3KeyValueReader

protected ZarrV3KeyValueReader(boolean checkVersion,
                               org.janelia.saalfeldlab.n5.KeyValueAccess keyValueAccess,
                               String basePath,
                               com.google.gson.GsonBuilder gsonBuilder,
                               boolean cacheMeta,
                               boolean checkRootExists)

Method Detail

getDimensionSeparator

public String getDimensionSeparator()

setDimensionSeparator

public void setDimensionSeparator(String dimensionSeparator)

getAttributesKey

public String getAttributesKey()

Specified by:

getAttributesKey in interface org.janelia.saalfeldlab.n5.GsonN5Reader

Overrides:

getAttributesKey in class org.janelia.saalfeldlab.n5.N5KeyValueReader

getVersion

public org.janelia.saalfeldlab.n5.N5Reader.Version getVersion()
                                                       throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

getVersion

public org.janelia.saalfeldlab.n5.N5Reader.Version getVersion(String path)
                                                       throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

getVersion

protected static org.janelia.saalfeldlab.n5.N5Reader.Version getVersion(com.google.gson.JsonElement json)

exists

public boolean exists(String pathName)

isGroupFromContainer

public boolean isGroupFromContainer(String normalPath)

isGroupFromAttributes

public boolean isGroupFromAttributes(String normalCacheKey,
                                     com.google.gson.JsonElement attributes)

isDatasetFromAttributes

public boolean isDatasetFromAttributes(String normalCacheKey,
                                       com.google.gson.JsonElement attributes)

createDatasetAttributes

public ZarrV3DatasetAttributes createDatasetAttributes(com.google.gson.JsonElement attributes)

getConvertedDatasetAttributes

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

getRawAttributes

public com.google.gson.JsonElement getRawAttributes(String pathName)
                                             throws org.janelia.saalfeldlab.n5.N5Exception.N5IOException

Throws:

org.janelia.saalfeldlab.n5.N5Exception.N5IOException

getAttributes

public com.google.gson.JsonElement getAttributes(String pathName)
                                          throws org.janelia.saalfeldlab.n5.N5Exception.N5IOException

Throws:

org.janelia.saalfeldlab.n5.N5Exception.N5IOException

getAttribute

public <T> T getAttribute(String pathName,
                          String key,
                          Type type)
                   throws org.janelia.saalfeldlab.n5.N5Exception

Throws:

org.janelia.saalfeldlab.n5.N5Exception

getRawAttribute

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

getAttribute

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

toString

public String toString()

Overrides:

toString in class Object

addTypeAdapters

protected static com.google.gson.GsonBuilder addTypeAdapters(com.google.gson.GsonBuilder gsonBuilder)

mapAttributeKey

protected String mapAttributeKey(String attributePath)

Converts an attribute path

Parameters:

attributePath -

Returns:

isAttributes

protected boolean isAttributes(String attributePath)