org.janelia.saalfeldlab.n5.universe.container

Class ContainerMetadataNode

java.lang.Object

org.janelia.saalfeldlab.n5.universe.container.ContainerMetadataNode

All Implemented Interfaces:

AutoCloseable, org.janelia.saalfeldlab.n5.GsonN5Reader, org.janelia.saalfeldlab.n5.GsonN5Writer, org.janelia.saalfeldlab.n5.N5Reader, org.janelia.saalfeldlab.n5.N5Writer

public class ContainerMetadataNode
extends Object
implements org.janelia.saalfeldlab.n5.GsonN5Writer

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

Modifier and Type	Field and Description
protected HashMap<String,com.google.gson.JsonElement>	attributes
protected Map<String,ContainerMetadataNode>	children
protected com.google.gson.Gson	gson
protected String	path

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

NO_VERSION, VERSION, VERSION_KEY

Constructor Summary

Constructors

Constructor and Description
ContainerMetadataNode()
ContainerMetadataNode(ContainerMetadataNode other)
ContainerMetadataNode(HashMap<String,com.google.gson.JsonElement> attributes, Map<String,ContainerMetadataNode> children, com.google.gson.Gson gson)
ContainerMetadataNode(com.google.gson.JsonObject attributes, Map<String,ContainerMetadataNode> children, com.google.gson.Gson gson)

Method Summary

Modifier and Type	Method and Description
void	addChild(String relativepath, ContainerMetadataNode child)
void	addPathsRecursive() Adds path attributes to this node and recursively to its children.
void	addPathsRecursive(String thisPath) Adds path attributes to this node and recursively to its children.
boolean	blockExists(String pathName, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long... gridPosition)
static ContainerMetadataNode	build(org.janelia.saalfeldlab.n5.N5Reader n5, com.google.gson.Gson gson)
static <N extends org.janelia.saalfeldlab.n5.GsonN5Reader & org.janelia.saalfeldlab.n5.N5Reader> ContainerMetadataNode	build(org.janelia.saalfeldlab.n5.N5Reader n5, String dataset, com.google.gson.Gson gson)
static <N extends org.janelia.saalfeldlab.n5.GsonN5Reader & org.janelia.saalfeldlab.n5.N5Reader> ContainerMetadataNode	buildGson(N n5, String dataset, com.google.gson.Gson gson)
static <N extends org.janelia.saalfeldlab.n5.GsonN5Reader> ContainerMetadataNode	buildHelper(N n5, N5TreeNode baseNode)
static ContainerMetadataNode	buildHelperN5(org.janelia.saalfeldlab.n5.N5Reader n5, N5TreeNode baseNode, com.google.gson.Gson gson)
static <T extends org.janelia.saalfeldlab.n5.N5Reader> ContainerMetadataNode	buildN5(T n5, String dataset, com.google.gson.Gson gson)
ContainerMetadataNode	childRelative(String normRelativePath)
void	createGroup(String pathName)
boolean	deleteBlock(String datasetPath, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long... gridPosition)
boolean	deleteBlock(String pathName, long... gridPosition)
boolean	deleteChunk(String datasetPath, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long... gridPosition)
boolean	deleteChunk(String pathName, long... gridPosition)
boolean	exists(String pathName)
Stream<ContainerMetadataNode>	flatten()
Stream<ContainerMetadataNode>	flattenLeaves()
com.google.gson.JsonElement	getAttributes(String pathName)
String	getAttributesKey()
Optional<ContainerMetadataNode>	getChild(String relativePath)
Optional<ContainerMetadataNode>	getChild(String relativePath, String groupSeparator)
Stream<String>	getChildPathsRecursive(String thisPath)
Map<String,ContainerMetadataNode>	getChildren()
Stream<ContainerMetadataNode>	getChildrenStream()
HashMap<String,com.google.gson.JsonElement>	getContainerAttributes()
com.google.gson.Gson	getGson()
static Optional<HashMap<String,com.google.gson.JsonElement>>	getMetadataMapN5(org.janelia.saalfeldlab.n5.N5Reader n5, String dataset, com.google.gson.Gson gson)
Optional<ContainerMetadataNode>	getNode(String path)
Optional<ContainerMetadataNode>	getParent(String path)
String	getPath()
URI	getURI()
String	groupPath(String... nodes)
String[]	list(String pathName)
Stream<ContainerMetadataNode>	pathToChild(String path) Returns a stream of nodes for the given path.
org.janelia.saalfeldlab.n5.DataBlock<?>	readBlock(String pathName, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long... gridPosition)
org.janelia.saalfeldlab.n5.DataBlock<?>	readChunk(String pathName, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long... gridPosition)
boolean	remove()
boolean	remove(String pathName)
boolean	removeAttribute(String pathName, String key)
<T> T	removeAttribute(String pathName, String key, Class<T> clazz)
boolean	removeAttributes(String pathName, List<String> attributes)
<T> void	setAttribute(String pathName, String key, T attribute)
void	setAttributes(String groupPath, com.google.gson.JsonElement attributes)
void	setAttributes(String pathName, Map<String,?> attributes)
static Optional<com.google.gson.JsonObject>	stringToJson(String s, com.google.gson.Gson gson)
<T> void	writeBlock(String pathName, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, org.janelia.saalfeldlab.n5.DataBlock<T> dataBlock)
<T> void	writeChunk(String pathName, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, org.janelia.saalfeldlab.n5.DataBlock<T> dataBlock)
<T> void	writeRegion(String datasetPath, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long[] min, long[] size, org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier<T> dataBlocks, boolean writeFully)
<T> void	writeRegion(String datasetPath, org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes, long[] min, long[] size, org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier<T> dataBlocks, boolean writeFully, ExecutorService exec)

Methods inherited from class java.lang.Object

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

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

createDatasetAttributes, getAttribute, getAttribute, getDatasetAttributes, listAttributes

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

createDataset, createDataset, deleteChunks, setDatasetAttributes, setVersion, writeChunks, writeSerializedBlock

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

close, datasetExists, deepList, deepList, deepList, deepList, deepList, deepListDatasets, deepListDatasets, deepListDatasets, deepListDatasets, deepListHelper, getConvertedDatasetAttributes, getGroupSeparator, getVersion, readChunks, readSerializedBlock

Field Detail

path

protected String path

attributes

protected HashMap<String,com.google.gson.JsonElement> attributes

children

protected Map<String,ContainerMetadataNode> children

gson

protected final transient com.google.gson.Gson gson

Constructor Detail

ContainerMetadataNode

public ContainerMetadataNode()

ContainerMetadataNode

public ContainerMetadataNode(HashMap<String,com.google.gson.JsonElement> attributes,
                             Map<String,ContainerMetadataNode> children,
                             com.google.gson.Gson gson)

ContainerMetadataNode

public ContainerMetadataNode(com.google.gson.JsonObject attributes,
                             Map<String,ContainerMetadataNode> children,
                             com.google.gson.Gson gson)

ContainerMetadataNode

public ContainerMetadataNode(ContainerMetadataNode other)

Method Detail

getContainerAttributes

public HashMap<String,com.google.gson.JsonElement> getContainerAttributes()

getAttributes

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

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception.N5IOException

getChildren

public Map<String,ContainerMetadataNode> getChildren()

getChildrenStream

public Stream<ContainerMetadataNode> getChildrenStream()

flatten

public Stream<ContainerMetadataNode> flatten()

flattenLeaves

public Stream<ContainerMetadataNode> flattenLeaves()

addChild

public void addChild(String relativepath,
                     ContainerMetadataNode child)

pathToChild

public Stream<ContainerMetadataNode> pathToChild(String path)

Returns a stream of nodes for the given path.

Parameters:

path - full or relative path

Returns:

stream of nodes

getPath

public String getPath()

Returns:

the path to this node from the root.

getChildPathsRecursive

public Stream<String> getChildPathsRecursive(String thisPath)

addPathsRecursive

public void addPathsRecursive()

Adds path attributes to this node and recursively to its children.

addPathsRecursive

public void addPathsRecursive(String thisPath)

Adds path attributes to this node and recursively to its children.

Parameters:

thisPath - path to a node

getParent

public Optional<ContainerMetadataNode> getParent(String path)

getNode

public Optional<ContainerMetadataNode> getNode(String path)

getChild

public Optional<ContainerMetadataNode> getChild(String relativePath)

childRelative

public ContainerMetadataNode childRelative(String normRelativePath)

getChild

public Optional<ContainerMetadataNode> getChild(String relativePath,
                                                String groupSeparator)

exists

public boolean exists(String pathName)

Specified by:

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

blockExists

public boolean blockExists(String pathName,
                           org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                           long... gridPosition)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

list

public String[] list(String pathName)
              throws org.janelia.saalfeldlab.n5.N5Exception.N5IOException

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception.N5IOException

setAttribute

public <T> void setAttribute(String pathName,
                             String key,
                             T attribute)

Specified by:

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

setAttributes

public void setAttributes(String pathName,
                          Map<String,?> attributes)

Specified by:

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

setAttributes

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

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

removeAttribute

public boolean removeAttribute(String pathName,
                               String key)

Specified by:

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

removeAttribute

public <T> T removeAttribute(String pathName,
                             String key,
                             Class<T> clazz)

Specified by:

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

removeAttributes

public boolean removeAttributes(String pathName,
                                List<String> attributes)

Specified by:

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

createGroup

public void createGroup(String pathName)

Specified by:

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

remove

public boolean remove(String pathName)

Specified by:

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

remove

public boolean remove()

Specified by:

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

writeChunk

public <T> void writeChunk(String pathName,
                           org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                           org.janelia.saalfeldlab.n5.DataBlock<T> dataBlock)

Specified by:

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

writeBlock

public <T> void writeBlock(String pathName,
                           org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                           org.janelia.saalfeldlab.n5.DataBlock<T> dataBlock)

Specified by:

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

writeRegion

public <T> void writeRegion(String datasetPath,
                            org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                            long[] min,
                            long[] size,
                            org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier<T> dataBlocks,
                            boolean writeFully)
                     throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

writeRegion

public <T> void writeRegion(String datasetPath,
                            org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                            long[] min,
                            long[] size,
                            org.janelia.saalfeldlab.n5.N5Writer.DataBlockSupplier<T> dataBlocks,
                            boolean writeFully,
                            ExecutorService exec)
                     throws org.janelia.saalfeldlab.n5.N5Exception,
                            InterruptedException,
                            ExecutionException

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

InterruptedException

ExecutionException

deleteChunk

public boolean deleteChunk(String pathName,
                           long... gridPosition)

Specified by:

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

deleteChunk

public boolean deleteChunk(String datasetPath,
                           org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                           long... gridPosition)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

deleteBlock

public boolean deleteBlock(String pathName,
                           long... gridPosition)

Specified by:

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

deleteBlock

public boolean deleteBlock(String datasetPath,
                           org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                           long... gridPosition)
                    throws org.janelia.saalfeldlab.n5.N5Exception

Specified by:

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

Throws:

org.janelia.saalfeldlab.n5.N5Exception

readChunk

public org.janelia.saalfeldlab.n5.DataBlock<?> readChunk(String pathName,
                                                         org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                                                         long... gridPosition)

Specified by:

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

readBlock

public org.janelia.saalfeldlab.n5.DataBlock<?> readBlock(String pathName,
                                                         org.janelia.saalfeldlab.n5.DatasetAttributes datasetAttributes,
                                                         long... gridPosition)

Specified by:

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

build

public static <N extends org.janelia.saalfeldlab.n5.GsonN5Reader & org.janelia.saalfeldlab.n5.N5Reader> ContainerMetadataNode build(org.janelia.saalfeldlab.n5.N5Reader n5,
                                                                                                                                    String dataset,
                                                                                                                                    com.google.gson.Gson gson)

build

public static ContainerMetadataNode build(org.janelia.saalfeldlab.n5.N5Reader n5,
                                          com.google.gson.Gson gson)

buildGson

public static <N extends org.janelia.saalfeldlab.n5.GsonN5Reader & org.janelia.saalfeldlab.n5.N5Reader> ContainerMetadataNode buildGson(N n5,
                                                                                                                                        String dataset,
                                                                                                                                        com.google.gson.Gson gson)
                                                                                                                                 throws InterruptedException,
                                                                                                                                        ExecutionException

Throws:

InterruptedException

ExecutionException

buildHelper

public static <N extends org.janelia.saalfeldlab.n5.GsonN5Reader> ContainerMetadataNode buildHelper(N n5,
                                                                                                    N5TreeNode baseNode)

buildN5

public static <T extends org.janelia.saalfeldlab.n5.N5Reader> ContainerMetadataNode buildN5(T n5,
                                                                                            String dataset,
                                                                                            com.google.gson.Gson gson)
                                                                                     throws InterruptedException,
                                                                                            ExecutionException

Throws:

InterruptedException

ExecutionException

buildHelperN5

public static ContainerMetadataNode buildHelperN5(org.janelia.saalfeldlab.n5.N5Reader n5,
                                                  N5TreeNode baseNode,
                                                  com.google.gson.Gson gson)

getMetadataMapN5

public static Optional<HashMap<String,com.google.gson.JsonElement>> getMetadataMapN5(org.janelia.saalfeldlab.n5.N5Reader n5,
                                                                                     String dataset,
                                                                                     com.google.gson.Gson gson)

stringToJson

public static Optional<com.google.gson.JsonObject> stringToJson(String s,
                                                                com.google.gson.Gson gson)

groupPath

public String groupPath(String... nodes)

Specified by:

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

getGson

public com.google.gson.Gson getGson()

Specified by:

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

getURI

public URI getURI()

Specified by:

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

getAttributesKey

public String getAttributesKey()

Specified by:

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