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org.eclipse.dawnsci.hdf5.nexus
Class NexusFileHDF5



java.lang.Object


org.eclipse.dawnsci.hdf5.nexus.NexusFileHDF5







All Implemented Interfaces:
java.lang.AutoCloseable, NexusFile




public class NexusFileHDF5
extends java.lang.Object
implements NexusFile











Nested Class Summary

Nested Classes 

Modifier and Type
Class and Description


static class 
NexusFileHDF5.NodeType 









Field Summary

Fields 

Modifier and Type
Field and Description


static java.nio.charset.Charset
UTF8 






Fields inherited from interface org.eclipse.dawnsci.nexus.NexusFile
COMPRESSION_LZW_L1, COMPRESSION_NONE, NX_URL_SCHEME, NXCLASS, NXCLASS_SEPARATOR








Constructor Summary

Constructors 

Constructor and Description


NexusFileHDF5(java.lang.String path) 


NexusFileHDF5(java.lang.String path,
             boolean enableSWMR) 









Method Summary

All Methods Static Methods Instance Methods Concrete Methods 

Modifier and Type
Method and Description


void
activateSwmrMode()
Activates SWMR mode.



void
addAttribute(Node node,
            Attribute... attribute)
Add (and write) attribute(s) to given node



void
addAttribute(java.lang.String path,
            Attribute... attribute)
Add (and write) attribute(s) to given path



void
addNode(GroupNode group,
       java.lang.String name,
       Node node)
Add node to group.



void
addNode(java.lang.String path,
       Node node)
Add node to given path.



void
close()
Close file



void
createAndOpenToWrite()
Create file and open to write



Attribute
createAttribute(IDataset attr)
Create attribute



DataNode
createData(GroupNode group,
          IDataset data)
Create data node in given group



DataNode
createData(GroupNode group,
          ILazyWriteableDataset data)
Create data node in given group



DataNode
createData(GroupNode group,
          ILazyWriteableDataset data,
          int compression)
Create data node with given name in given group



DataNode
createData(GroupNode group,
          java.lang.String name,
          IDataset data)
Create data node with given name in given group



DataNode
createData(GroupNode group,
          java.lang.String name,
          ILazyWriteableDataset data)
Create data node with given name in given group



DataNode
createData(GroupNode group,
          java.lang.String name,
          ILazyWriteableDataset data,
          int compression)
Create data node with given name in given group



DataNode
createData(java.lang.String path,
          IDataset data,
          boolean createPathIfNecessary)
Create data node with given path to its group and create path if necessary
 The name of the dataset is used as the name of the data node within the parent group.



DataNode
createData(java.lang.String path,
          ILazyWriteableDataset data,
          boolean createPathIfNecessary)
Create data node with given path to its group and create path if necessary
 The name of the dataset is used as the name of the data node within the parent group.



DataNode
createData(java.lang.String path,
          ILazyWriteableDataset data,
          int compression,
          boolean createPathIfNecessary)
Create data node with given name and path to its group and create path if necessary.



DataNode
createData(java.lang.String path,
          java.lang.String name,
          IDataset data,
          boolean createPathIfNecessary)
Create data node with given name and path to its group and create path if necessary.



DataNode
createData(java.lang.String path,
          java.lang.String name,
          ILazyWriteableDataset data,
          boolean createPathIfNecessary)
Create data node with given name and path to its group and create path if necessary.



DataNode
createData(java.lang.String path,
          java.lang.String name,
          ILazyWriteableDataset data,
          int compression,
          boolean createPathIfNecessary)
Create data node with given name and path to its group and create path if necessary



static NexusFile
createNexusFile(java.lang.String path)
Create a new Nexus file (overwriting any existing one)



static NexusFile
createNexusFile(java.lang.String path,
               boolean enableSWMR)
Create a new Nexus file (overwriting any existing one)



int
flush()
Flush data to filesystem



void
flushAllCachedDatasets()
Flush datasets cached when NexusFile.setCacheDataset(boolean) is set true



java.lang.String
getAttributeValue(java.lang.String fullAttributeKey)
The full attribute key is: @
 e.g.



DataNode
getData(GroupNode group,
       java.lang.String name)
Get data node in group with given name



DataNode
getData(java.lang.String path)
Get data node with given path



java.lang.String
getFilePath()
Returns the file path of this NexusFile



GroupNode
getGroup(GroupNode group,
        java.lang.String name,
        java.lang.String nxClass,
        boolean createPathIfNecessary)
Get group in group with given name and create path if necessary



GroupNode
getGroup(java.lang.String augmentedPath,
        boolean createPathIfNecessary)
Get group with given path and create path if necessary



Node
getNode(java.lang.String augmentedPath)
Get Node with given path.



java.lang.String
getPath(Node node)
Get path of node from internal tree



java.lang.String
getRoot()
Get the path of root node from internal tree



Tree
getTree()
Get the complete tree of data.



boolean
isPathValid(java.lang.String path)
Checks if a path within the file exists



void
link(java.lang.String source,
    java.lang.String destination)
Link source to a destination.



void
linkExternal(java.net.URI source,
            java.lang.String destination,
            boolean isGroup)
Link source in another file to a destination.



static NexusFile
openNexusFile(java.lang.String path)
Open an existing Nexus file to modify



static NexusFile
openNexusFileReadOnly(java.lang.String path)
Open an existing Nexus file to read only



void
openToRead()
Open file to only read



void
openToWrite(boolean createIfNecessary)
Open file to write



void
removeNode(GroupNode group,
          java.lang.String name)
Remove node from given group.



void
removeNode(java.lang.String path,
          java.lang.String name)
Remove node from given path.



void
setCacheDataset(boolean cacheDataset)
Sets the datasets written to to be held open until the file is closed
 
 With this value set to true, datasets will not be flushed until the file is closed,
 call NexusFile.flushAllCachedDatasets() to flush



void
setDebug(boolean debug)
Set to instrument some method calls via logging at the DEBUG level



void
setWritesAsync(boolean async)
Set to writes to be performed asynchronously for data nodes created after calling this







Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait














Field Detail





UTF8
public static final java.nio.charset.Charset UTF8









Constructor Detail





NexusFileHDF5
public NexusFileHDF5(java.lang.String path)







NexusFileHDF5
public NexusFileHDF5(java.lang.String path,
                     boolean enableSWMR)









Method Detail





createNexusFile
public static NexusFile createNexusFile(java.lang.String path)
                                 throws NexusException
Create a new Nexus file (overwriting any existing one)

Parameters:
path - 
Returns:
Nexus file
Throws:
NexusException








createNexusFile
public static NexusFile createNexusFile(java.lang.String path,
                                        boolean enableSWMR)
                                 throws NexusException
Create a new Nexus file (overwriting any existing one)

Parameters:
path - 
enableSWMR - 
Returns:
Nexus file
Throws:
NexusException








openNexusFile
public static NexusFile openNexusFile(java.lang.String path)
                               throws NexusException
Open an existing Nexus file to modify

Parameters:
path - 
Returns:
Nexus file
Throws:
NexusException








openNexusFileReadOnly
public static NexusFile openNexusFileReadOnly(java.lang.String path)
                                       throws NexusException
Open an existing Nexus file to read only

Parameters:
path - 
Returns:
Nexus file
Throws:
NexusException








getFilePath
public java.lang.String getFilePath()
Description copied from interface: NexusFile
Returns the file path of this NexusFile

Specified by:
getFilePath in interface NexusFile
Returns:
file path








openToRead
public void openToRead()
                throws NexusException
Description copied from interface: NexusFile
Open file to only read

Specified by:
openToRead in interface NexusFile
Throws:
NexusException








openToWrite
public void openToWrite(boolean createIfNecessary)
                 throws NexusException
Description copied from interface: NexusFile
Open file to write

Specified by:
openToWrite in interface NexusFile
Parameters:
createIfNecessary - if true, then create file if it does not exist
Throws:
NexusException








createAndOpenToWrite
public void createAndOpenToWrite()
                          throws NexusException
Description copied from interface: NexusFile
Create file and open to write

Specified by:
createAndOpenToWrite in interface NexusFile
Throws:
NexusException








setWritesAsync
public void setWritesAsync(boolean async)
Description copied from interface: NexusFile
Set to writes to be performed asynchronously for data nodes created after calling this

Specified by:
setWritesAsync in interface NexusFile








setDebug
public void setDebug(boolean debug)
Description copied from interface: NexusFile
Set to instrument some method calls via logging at the DEBUG level

Specified by:
setDebug in interface NexusFile








getPath
public java.lang.String getPath(Node node)
Description copied from interface: NexusFile
Get path of node from internal tree

Specified by:
getPath in interface NexusFile
Returns:
(depth-first) path of node








getRoot
public java.lang.String getRoot()
Description copied from interface: NexusFile
Get the path of root node from internal tree

Specified by:
getRoot in interface NexusFile
Returns:
root node path








getGroup
public GroupNode getGroup(java.lang.String augmentedPath,
                          boolean createPathIfNecessary)
                   throws NexusException
Description copied from interface: NexusFile
Get group with given path and create path if necessary

Specified by:
getGroup in interface NexusFile
Returns:
node or null if group does not exist at specified path
Throws:
NexusException








getNode
public Node getNode(java.lang.String augmentedPath)
             throws NexusException
Description copied from interface: NexusFile
Get Node with given path. Can be a GroupNode or a DataNode

Specified by:
getNode in interface NexusFile
Returns:
node or null if group does not exist at specified path
Throws:
NexusException








getGroup
public GroupNode getGroup(GroupNode group,
                          java.lang.String name,
                          java.lang.String nxClass,
                          boolean createPathIfNecessary)
                   throws NexusException
Description copied from interface: NexusFile
Get group in group with given name and create path if necessary

Specified by:
getGroup in interface NexusFile
Returns:
node or null
Throws:
NexusException - if node is not a group at specified path or group does not exist and not creating path








getData
public DataNode getData(java.lang.String path)
                 throws NexusException
Description copied from interface: NexusFile
Get data node with given path

Specified by:
getData in interface NexusFile
Returns:
node or null if data does not exist at specified path
Throws:
NexusException








getData
public DataNode getData(GroupNode group,
                        java.lang.String name)
                 throws NexusException
Description copied from interface: NexusFile
Get data node in group with given name

Specified by:
getData in interface NexusFile
Returns:
node or null if data does not exist in group
Throws:
NexusException








createData
public DataNode createData(java.lang.String path,
                           ILazyWriteableDataset data,
                           int compression,
                           boolean createPathIfNecessary)
                    throws NexusException
Description copied from interface: NexusFile
Create data node with given name and path to its group and create path if necessary.

Specified by:
createData in interface NexusFile
Parameters:
path - to parent group
data - name within parent group
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
public DataNode createData(java.lang.String path,
                           java.lang.String name,
                           ILazyWriteableDataset data,
                           int compression,
                           boolean createPathIfNecessary)
                    throws NexusException
Description copied from interface: NexusFile
Create data node with given name and path to its group and create path if necessary

Specified by:
createData in interface NexusFile
Parameters:
path - to parent group
name - name within parent group
data - dataset
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
public DataNode createData(java.lang.String path,
                           ILazyWriteableDataset data,
                           boolean createPathIfNecessary)
                    throws NexusException
Description copied from interface: NexusFile
Create data node with given path to its group and create path if necessary
 The name of the dataset is used as the name of the data node within the parent group.

Specified by:
createData in interface NexusFile
Parameters:
path - to group
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
public DataNode createData(java.lang.String path,
                           java.lang.String name,
                           ILazyWriteableDataset data,
                           boolean createPathIfNecessary)
                    throws NexusException
Description copied from interface: NexusFile
Create data node with given name and path to its group and create path if necessary.

Specified by:
createData in interface NexusFile
Parameters:
path - to parent group
name - name within parent group
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
public DataNode createData(GroupNode group,
                           ILazyWriteableDataset data,
                           int compression)
                    throws NexusException
Description copied from interface: NexusFile
Create data node with given name in given group

Specified by:
createData in interface NexusFile
Parameters:
group - parent group
data - name within group
compression - dataset
Returns:
node
Throws:
NexusException - when node already exists








createData
public DataNode createData(GroupNode group,
                           java.lang.String name,
                           ILazyWriteableDataset data,
                           int compression)
                    throws NexusException
Description copied from interface: NexusFile
Create data node with given name in given group

Specified by:
createData in interface NexusFile
Parameters:
group - parent group
data - dataset
Returns:
node
Throws:
NexusException - when node already exists








createData
public DataNode createData(GroupNode group,
                           ILazyWriteableDataset data)
                    throws NexusException
Description copied from interface: NexusFile
Create data node in given group

Specified by:
createData in interface NexusFile
Parameters:
group - parent group
data - dataset
Returns:
node
Throws:
NexusException - when node already exists








createData
public DataNode createData(GroupNode group,
                           java.lang.String name,
                           ILazyWriteableDataset data)
                    throws NexusException
Description copied from interface: NexusFile
Create data node with given name in given group

Specified by:
createData in interface NexusFile
Parameters:
group - parent group
name - name within group
data - dataset
Returns:
node
Throws:
NexusException - when node already exists








createData
public DataNode createData(java.lang.String path,
                           IDataset data,
                           boolean createPathIfNecessary)
                    throws NexusException
Description copied from interface: NexusFile
Create data node with given path to its group and create path if necessary
 The name of the dataset is used as the name of the data node within the parent group.

Specified by:
createData in interface NexusFile
Parameters:
path - to group
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
public DataNode createData(java.lang.String path,
                           java.lang.String name,
                           IDataset data,
                           boolean createPathIfNecessary)
                    throws NexusException
Description copied from interface: NexusFile
Create data node with given name and path to its group and create path if necessary.

Specified by:
createData in interface NexusFile
Parameters:
path - to parent group
name - name within parent group
Returns:
node or null if data does not exist at specified path
Throws:
NexusException - when node already exists








createData
public DataNode createData(GroupNode group,
                           IDataset data)
                    throws NexusException
Description copied from interface: NexusFile
Create data node in given group

Specified by:
createData in interface NexusFile
Parameters:
group - parent group
data - dataset
Returns:
node
Throws:
NexusException - when node already exists








createData
public DataNode createData(GroupNode group,
                           java.lang.String name,
                           IDataset data)
                    throws NexusException
Description copied from interface: NexusFile
Create data node with given name in given group

Specified by:
createData in interface NexusFile
Parameters:
group - parent group
name - name within group
data - dataset
Returns:
node
Throws:
NexusException - when node already exists








addNode
public void addNode(GroupNode group,
                    java.lang.String name,
                    Node node)
             throws NexusException
Description copied from interface: NexusFile
Add node to group. This will recursively add other nodes if the given node is a group node.

Specified by:
addNode in interface NexusFile
Throws:
NexusException - if node already exists in group with name








addNode
public void addNode(java.lang.String path,
                    Node node)
             throws NexusException
Description copied from interface: NexusFile
Add node to given path. This will recursively add other nodes if the given node is a group node.

Specified by:
addNode in interface NexusFile
Throws:
NexusException - if node already exists at given path or parts of path does not exist








removeNode
public void removeNode(GroupNode group,
                       java.lang.String name)
                throws NexusException
Description copied from interface: NexusFile
Remove node from given group.
 

 Note, this will fail if the file is in SWMR node

Specified by:
removeNode in interface NexusFile
Parameters:
group - parent group of node
name - name of node in parent group
Throws:
NexusException








removeNode
public void removeNode(java.lang.String path,
                       java.lang.String name)
                throws NexusException
Description copied from interface: NexusFile
Remove node from given path.
 

 Note, this will fail if the file is in SWMR node

Specified by:
removeNode in interface NexusFile
Parameters:
path - path to parent group of node
name - name of node in parent group
Throws:
NexusException








createAttribute
public Attribute createAttribute(IDataset attr)
Description copied from interface: NexusFile
Create attribute

Specified by:
createAttribute in interface NexusFile
Returns:
attribute








addAttribute
public void addAttribute(java.lang.String path,
                         Attribute... attribute)
                  throws NexusException
Description copied from interface: NexusFile
Add (and write) attribute(s) to given path

Specified by:
addAttribute in interface NexusFile
Throws:
NexusException








addAttribute
public void addAttribute(Node node,
                         Attribute... attribute)
                  throws NexusException
Description copied from interface: NexusFile
Add (and write) attribute(s) to given node

Specified by:
addAttribute in interface NexusFile
Throws:
NexusException








getAttributeValue
public java.lang.String getAttributeValue(java.lang.String fullAttributeKey)
                                   throws NexusException
Description copied from interface: NexusFile
The full attribute key is: @
 e.g. /entry1/data@napimount

Specified by:
getAttributeValue in interface NexusFile
Returns:
Throws:
NexusException








link
public void link(java.lang.String source,
                 java.lang.String destination)
          throws NexusException
Description copied from interface: NexusFile
Link source to a destination. If the destination ends in 
 then the source name is added to the destination.

Specified by:
link in interface NexusFile
Throws:
NexusException








linkExternal
public void linkExternal(java.net.URI source,
                         java.lang.String destination,
                         boolean isGroup)
                  throws NexusException
Description copied from interface: NexusFile
Link source in another file to a destination. If the destination ends in 
 then the source name is added to the destination.

Specified by:
linkExternal in interface NexusFile
Throws:
NexusException








activateSwmrMode
public void activateSwmrMode()
                      throws NexusException
Description copied from interface: NexusFile
Activates SWMR mode. The file must have been created as
 with SWMR enabled.

Specified by:
activateSwmrMode in interface NexusFile
Throws:
NexusException - if SWMR mode could not be activated








flush
public int flush()
          throws NexusException
Description copied from interface: NexusFile
Flush data to filesystem

Specified by:
flush in interface NexusFile
Returns:
the nexus int code for the flush or -1 if unsucessfull.
Throws:
NexusException








flushAllCachedDatasets
public void flushAllCachedDatasets()
Description copied from interface: NexusFile
Flush datasets cached when NexusFile.setCacheDataset(boolean) is set true

Specified by:
flushAllCachedDatasets in interface NexusFile








close
public void close()
           throws NexusException
Description copied from interface: NexusFile
Close file

Specified by:
close in interface java.lang.AutoCloseable
Specified by:
close in interface NexusFile
Throws:
NexusException








isPathValid
public boolean isPathValid(java.lang.String path)
Description copied from interface: NexusFile
Checks if a path within the file exists

Specified by:
isPathValid in interface NexusFile
Returns:
true if path exists








setCacheDataset
public void setCacheDataset(boolean cacheDataset)
Description copied from interface: NexusFile
Sets the datasets written to to be held open until the file is closed
 
 With this value set to true, datasets will not be flushed until the file is closed,
 call NexusFile.flushAllCachedDatasets() to flush

Specified by:
setCacheDataset in interface NexusFile








getTree
public Tree getTree()
Description copied from interface: NexusFile
Get the complete tree of data.

Specified by:
getTree in interface NexusFile
Returns:
tree or null if none exists.














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