java.lang.Object
- org.nexusformat.NexusFile

All Implemented Interfaces:: NeXusFileInterface

public class NexusFile
extends java.lang.Object
implements NeXusFileInterface

Field Summary

Fields
Modifier and Type	Field	Description
`protected int`	`handle`	This is the handle to the NeXus file handle.
`protected static int`	`MAXNAMELEN`	Maximum name length, must be VGNAMELENMAX in hlimits.h
`static int`	`NX_BINARY`
`static int`	`NX_BOOLEAN`
`static int`	`NX_CHAR`
`static int`	`NX_COMP_HUF`
`static int`	`NX_COMP_LZW`
`static int`	`NX_COMP_LZW_LVL0`
`static int`	`NX_COMP_LZW_LVL1`
`static int`	`NX_COMP_LZW_LVL2`
`static int`	`NX_COMP_LZW_LVL3`
`static int`	`NX_COMP_LZW_LVL4`
`static int`	`NX_COMP_LZW_LVL5`
`static int`	`NX_COMP_LZW_LVL6`
`static int`	`NX_COMP_LZW_LVL7`
`static int`	`NX_COMP_LZW_LVL8`
`static int`	`NX_COMP_LZW_LVL9`
`static int`	`NX_COMP_NONE`	constants for compression schemes
`static int`	`NX_COMP_RLE`
`static int`	`NX_FLOAT32`	constants for number types.
`static int`	`NX_FLOAT64`
`static int`	`NX_INT16`
`static int`	`NX_INT32`
`static int`	`NX_INT64`
`static int`	`NX_INT8`
`static int`	`NX_UINT16`
`static int`	`NX_UINT32`
`static int`	`NX_UINT64`
`static int`	`NX_UINT8`
`static int`	`NX_UNLIMITED`	constant denoting an unlimited dimension.
`static int`	`NXACC_CREATE`
`static int`	`NXACC_CREATE4`
`static int`	`NXACC_CREATE5`
`static int`	`NXACC_CREATEXML`
`static int`	`NXACC_NOSTRIP`
`static int`	`NXACC_RDWR`
`static int`	`NXACC_READ`	possible access codes, @see #NexusFile.

Constructor Summary

Constructors
Constructor Description

NexusFile(java.lang.String filename, int access)
constructs a new NexusFile Object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.util.Hashtable`	`attrdir()`	attrdir returns the attributes of the currently open dataset or the file global attributes if no dataset is open.
`void`	`close()`	close the NeXus file.
`protected void`	`close(int handle)`
`void`	`closedata()`	closedata closes an opened dataset.
`void`	`closegroup()`	closegroup closes access to the current group and steps down one step in group hierarchy.
`void`	`compmakedata(java.lang.String name, int type, int rank, int[] dim, int compression_type, int[] iChunk)`	compmakedata creates a new dataset with the specified characteristics in the current group.
`void`	`compmakedata(java.lang.String name, int type, int rank, long[] dim, int compression_type, long[] iChunk)`	compmakedata creates a new dataset with the specified characteristics in the current group.
`void`	`compress(int compression_type)`	causes the currently open dataset to be compressed on file.
`void`	`debugstop()`	debugstop is a debugging helper function which goes into an endless loop in the dynamic link library.
`void`	`finalize()`	removes all NeXus file data structures and closes the file.
`void`	`flush()`	flushes all pending data to disk.
`java.lang.Object`	`getattr(java.lang.String name)`	getattr retrieves the data associated with the attribute * name.
`void`	`getattr(java.lang.String name, java.lang.Object array, int[] args)`	getattr retrieves the data associated with the attribute name.
`void`	`getdata(java.lang.Object array)`	getdata reads the data from an previously openend dataset into array.
`NXlink`	`getdataID()`	getdataID gets the data necessary for linking the current dataset somewhere else.
`NXlink`	`getgroupID()`	getgroupID gets the data necessary for linking the current vGroup somewhere else.
`void`	`getinfo(int[] iDim, int[] args)`	getinfo retrieves information about a previously opened dataset.
`void`	`getinfo(long[] iDim, int[] args)`	getinfo retrieves information about a previously opened dataset.
`java.lang.String`	`getpath()`	return the current path into the NeXus file in the form of a Unix path string.
`void`	`getslab(int[] start, int[] size, java.lang.Object array)`	getslab reads a subset of a large dataset into array.
`void`	`getslab(long[] start, long[] size, java.lang.Object array)`	getslab reads a subset of a large dataset into array.
`java.util.Hashtable`	`groupdir()`	groupdir will retrieve the content of the currently open vGroup.
`protected int`	`init(java.lang.String filename, int access)`
`protected void`	`initattrdir(int handle)`
`protected void`	`initgroupdir(int handle)`
`java.lang.String`	`inquirefile()`	inquirefile inquires which file we are currently in.
`java.lang.String`	`isexternaldataset(java.lang.String name)`	nxisexternaldataset if the named dataset is is linked externally
`java.lang.String`	`isexternalgroup(java.lang.String name, java.lang.String nxclass)`	nxisexternalgroup test the group name, nxclass if it is linked externally
`void`	`linkexternal(java.lang.String name, java.lang.String nxclass, java.lang.String nxurl)`	linkexternal links group name, nxclass to the URL nxurl
`void`	`linkexternaldataset(java.lang.String name, java.lang.String nxurl)`	linkexternaldataset links dataset name to the URL nxurl
`void`	`makedata(java.lang.String name, int type, int rank, int[] dim)`	makedata creates a new dataset with the specified characteristics in the current group.
`void`	`makedata(java.lang.String name, int type, int rank, long[] dim)`	makedata creates a new dataset with the specified characteristics in the current group.
`void`	`makegroup(java.lang.String name, java.lang.String nxclass)`	makegroup creates a new group below the current group within the NeXus file hierarchy.
`void`	`makelink(NXlink target)`	makelink links the object described by target into the current vGroup.
`void`	`makenamedlink(java.lang.String name, NXlink target)`	makenamedlink links the object described by target into the current vGroup.
`protected int`	`nextattr(int handle, java.lang.String[] names, int[] args)`
`protected int`	`nextentry(int handle, java.lang.String[] names)`
`protected void`	`nxclosedata(int handle)`
`protected void`	`nxclosegroup(int handle)`
`protected void`	`nxcompress(int handle, int compression_type)`
`protected int`	`nxflush(int handle)`
`protected void`	`nxgetattr(int handle, java.lang.String name, byte[] bdata, int[] args)`
`protected void`	`nxgetattra(int handle, java.lang.String name, byte[] bdata)`
`protected void`	`nxgetattrainfo(int handle, java.lang.String name, int[] dim, int[] args)`
`protected void`	`nxgetdata(int handle, byte[] bdata)`
`protected void`	`nxgetdataid(int handle, NXlink link)`
`protected void`	`nxgetgroupid(int handle, NXlink link)`
`protected void`	`nxgetinfo(int handle, int[] iDim, int[] args)`
`protected void`	`nxgetinfo64(int handle, long[] iDim, int[] args)`
`protected int`	`nxgetnextattra(int handle, java.lang.String[] name, int[] dim, int[] args)`
`protected java.lang.String`	`nxgetpath(int handle)`
`protected void`	`nxgetslab(int handle, int[] Start, int[] size, byte[] bdata)`
`protected void`	`nxgetslab64(int handle, long[] Start, long[] size, byte[] bdata)`
`protected void`	`nxinquirefile(int handle, java.lang.String[] names)`
`protected int`	`nxisexternaldataset(int handle, java.lang.String name, java.lang.String[] nxurl)`
`protected int`	`nxisexternalgroup(int handle, java.lang.String name, java.lang.String nxclass, java.lang.String[] nxurl)`
`protected void`	`nxlinkexternal(int handle, java.lang.String name, java.lang.String nxclass, java.lang.String nxurl)`
`protected void`	`nxlinkexternaldataset(int handle, java.lang.String name, java.lang.String nxurl)`
`protected void`	`nxmakecompdata(int handle, java.lang.String name, int type, int rank, int[] dim, int iCompress, int[] iChunk)`
`protected void`	`nxmakecompdata64(int handle, java.lang.String name, int type, int rank, long[] dim, int iCompress, long[] iChunk)`
`protected void`	`nxmakedata(int handle, java.lang.String name, int type, int rank, int[] dim)`
`protected void`	`nxmakedata64(int handle, java.lang.String name, int type, int rank, long[] dim)`
`protected void`	`nxmakegroup(int handle, java.lang.String name, java.lang.String nxclass)`
`protected void`	`nxmakelink(int handle, NXlink target)`
`protected void`	`nxmakenamedlink(int handle, java.lang.String name, NXlink target)`
`protected void`	`nxopendata(int handle, java.lang.String name)`
`protected void`	`nxopengroup(int handle, java.lang.String name, java.lang.String nxclass)`
`protected void`	`nxopengrouppath(int handle, java.lang.String path)`
`protected void`	`nxopenpath(int handle, java.lang.String path)`
`protected void`	`nxopensourcepath(int handle)`
`protected void`	`nxputattr(int handle, java.lang.String name, byte[] array, int type)`
`protected void`	`nxputattra(int handle, java.lang.String name, byte[] bdata, int rank, int[] dim, int iType)`
`protected void`	`nxputdata(int handle, byte[] array)`
`protected void`	`nxputslab(int handle, byte[] array, int[] start, int[] size)`
`protected void`	`nxputslab64(int handle, byte[] array, long[] start, long[] size)`
`protected void`	`nxsetnumberformat(int handle, int type, java.lang.String format)`
`void`	`opendata(java.lang.String name)`	opendata opens an existing dataset for access.
`void`	`opengroup(java.lang.String name, java.lang.String nxclass)`	opengroup opens the group name with class nxclass.
`void`	`opengrouppath(java.lang.String path)`	opengrouppath opens groups and datsets accroding to the path string given.
`void`	`openpath(java.lang.String path)`	openpath opens groups and datsets accroding to the path string given.
`void`	`opensourcepath()`	opensourcepath opens the group from which the current item was linked Returns an error if the current item is not linked.
`void`	`putattr(java.lang.String name, java.lang.Object array, int iType)`	putattr adds a named attribute to a previously opened dataset or group or a global attribute if nothing is open.
`void`	`putattr(java.lang.String name, java.lang.Object array, int[] size, int iType)`	putattr adds a named attribute to a previously opened dataset or group or a global attribute if nothing is open.
`void`	`putdata(java.lang.Object array)`	putdata writes the data from array into a previously opened dataset.
`void`	`putslab(java.lang.Object array, int[] start, int[] size)`	putslab writes a subset of a larger dataset to a previously opened dataset.
`void`	`putslab(java.lang.Object array, long[] start, long[] size)`	putslab writes a subset of a larger dataset to a previously opened dataset.
`void`	`setnumberformat(int type, java.lang.String format)`	setnumberformat sets the number format for printing number when using the XML-NeXus format.

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

- Field Detail
  - NXACC_READ
```
public static final int NXACC_READ
```
    possible access codes, @see #NexusFile.
    
    See Also:
    
    Constant Field Values
  - NXACC_RDWR
```
public static final int NXACC_RDWR
```
    See Also:
    
    Constant Field Values
  - NXACC_CREATE
```
public static final int NXACC_CREATE
```
    See Also:
    
    Constant Field Values
  - NXACC_CREATE4
```
public static final int NXACC_CREATE4
```
    See Also:
    
    Constant Field Values
  - NXACC_CREATE5
```
public static final int NXACC_CREATE5
```
    See Also:
    
    Constant Field Values
  - NXACC_CREATEXML
```
public static final int NXACC_CREATEXML
```
    See Also:
    
    Constant Field Values
  - NXACC_NOSTRIP
```
public static final int NXACC_NOSTRIP
```
    See Also:
    
    Constant Field Values
  - NX_UNLIMITED
```
public static final int NX_UNLIMITED
```
    constant denoting an unlimited dimension.
    
    See Also:
    
    Constant Field Values
  - NX_FLOAT32
```
public static final int NX_FLOAT32
```
    constants for number types. @see #makedata, @see #putattr and others.
    
    See Also:
    
    Constant Field Values
  - NX_FLOAT64
```
public static final int NX_FLOAT64
```
    See Also:
    
    Constant Field Values
  - NX_INT8
```
public static final int NX_INT8
```
    See Also:
    
    Constant Field Values
  - NX_BINARY
```
public static final int NX_BINARY
```
    See Also:
    
    Constant Field Values
  - NX_UINT8
```
public static final int NX_UINT8
```
    See Also:
    
    Constant Field Values
  - NX_BOOLEAN
```
public static final int NX_BOOLEAN
```
    See Also:
    
    Constant Field Values
  - NX_INT16
```
public static final int NX_INT16
```
    See Also:
    
    Constant Field Values
  - NX_UINT16
```
public static final int NX_UINT16
```
    See Also:
    
    Constant Field Values
  - NX_INT32
```
public static final int NX_INT32
```
    See Also:
    
    Constant Field Values
  - NX_UINT32
```
public static final int NX_UINT32
```
    See Also:
    
    Constant Field Values
  - NX_INT64
```
public static final int NX_INT64
```
    See Also:
    
    Constant Field Values
  - NX_UINT64
```
public static final int NX_UINT64
```
    See Also:
    
    Constant Field Values
  - NX_CHAR
```
public static final int NX_CHAR
```
    See Also:
    
    Constant Field Values
  - NX_COMP_NONE
```
public static final int NX_COMP_NONE
```
    constants for compression schemes
    
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW
```
public static final int NX_COMP_LZW
```
    See Also:
    
    Constant Field Values
  - NX_COMP_RLE
```
public static final int NX_COMP_RLE
```
    See Also:
    
    Constant Field Values
  - NX_COMP_HUF
```
public static final int NX_COMP_HUF
```
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW_LVL0
```
public static final int NX_COMP_LZW_LVL0
```
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW_LVL1
```
public static final int NX_COMP_LZW_LVL1
```
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW_LVL2
```
public static final int NX_COMP_LZW_LVL2
```
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW_LVL3
```
public static final int NX_COMP_LZW_LVL3
```
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW_LVL4
```
public static final int NX_COMP_LZW_LVL4
```
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW_LVL5
```
public static final int NX_COMP_LZW_LVL5
```
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW_LVL6
```
public static final int NX_COMP_LZW_LVL6
```
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW_LVL7
```
public static final int NX_COMP_LZW_LVL7
```
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW_LVL8
```
public static final int NX_COMP_LZW_LVL8
```
    See Also:
    
    Constant Field Values
  - NX_COMP_LZW_LVL9
```
public static final int NX_COMP_LZW_LVL9
```
    See Also:
    
    Constant Field Values
  - MAXNAMELEN
```
protected static final int MAXNAMELEN
```
    Maximum name length, must be VGNAMELENMAX in hlimits.h
    
    See Also:
    
    Constant Field Values
  - handle
```
protected int handle
```
    This is the handle to the NeXus file handle.
- Constructor Detail
  - NexusFile
```
public NexusFile(java.lang.String filename,
                 int access)
          throws NexusException
```
    constructs a new NexusFile Object.
    
    Parameters:
    
    filename - The name of the NeXus file to access.
    
    access - The access mode for the file. Can only be one of the predefined NeXus access code NXACC.... These are:
    
    NXACC_CREATE
    or creating a new file.
    NXACC_RDWR
    For opening an existing file for modification or appending data.
    NXACC_READ
    For opening a file for reading.
    NXACC_NOSTRIP
    To keep leading and trailing whitespace on strings
    
    Throws:
    
    NexusException - when the file could not be found or an HDF error occurred.
- Method Detail
  - init
```
protected int init(java.lang.String filename,
                   int access)
```
  - close
```
protected void close(int handle)
```
  - nxflush
```
protected int nxflush(int handle)
```
  - flush
```
public void flush()
           throws NexusException
```
    flushes all pending data to disk. Closes any open SDS's.
    
    Specified by:
    
    flush in interface NeXusFileInterface
    
    Throws:
    
    NexusException - if an error occurs.
  - close
```
public void close()
           throws NexusException
```
    close the NeXus file. To make javalint and diamond happy
    
    Specified by:
    
    close in interface NeXusFileInterface
    
    Throws:
    
    NexusException
  - finalize
```
public void finalize()
              throws java.lang.Throwable
```
    removes all NeXus file data structures and closes the file. This function should automatically be called by the Java garbage collector whenever the NexusFile object falls into disuse. However the time when this is done is left to the garbage collector. My personal experience is that finalize might never be called. I suggest, to call finalize yourself when you are done with the NeXus file. finalize makes sure that multiple invocations will not do any harm.
    
    Specified by:
    
    finalize in interface NeXusFileInterface
    
    Overrides:
    
    finalize in class java.lang.Object
    
    Throws:
    
    java.lang.Throwable - because it is required by the definition of finalize.
  - nxmakegroup
```
protected void nxmakegroup(int handle,
                           java.lang.String name,
                           java.lang.String nxclass)
```
  - nxopengroup
```
protected void nxopengroup(int handle,
                           java.lang.String name,
                           java.lang.String nxclass)
```
  - nxopenpath
```
protected void nxopenpath(int handle,
                          java.lang.String path)
```
  - nxopengrouppath
```
protected void nxopengrouppath(int handle,
                               java.lang.String path)
```
  - nxclosegroup
```
protected void nxclosegroup(int handle)
```
  - nxgetpath
```
protected java.lang.String nxgetpath(int handle)
```
  - makegroup
```
public void makegroup(java.lang.String name,
                      java.lang.String nxclass)
               throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    makegroup creates a new group below the current group within the NeXus file hierarchy.
    
    Specified by:
    
    makegroup in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the group to create.
    
    nxclass - The classname of the group.
    
    Throws:
    
    NexusException - if an error occurs during this operation.
  - opengroup
```
public void opengroup(java.lang.String name,
                      java.lang.String nxclass)
               throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    opengroup opens the group name with class nxclass. The group must exist, otherwise an exception is thrown. opengroup is similar to a cd name in a filesystem.
    
    Specified by:
    
    opengroup in interface NeXusFileInterface
    
    Parameters:
    
    name - the name of the group to open.
    
    nxclass - the classname of the group to open.
    
    Throws:
    
    NexusException - when something goes wrong.
  - openpath
```
public void openpath(java.lang.String path)
              throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    openpath opens groups and datsets accroding to the path string given. The path syntax follows unix conventions. Both absolute and relative paths are possible. All objects of the path must exist.
    
    Specified by:
    
    openpath in interface NeXusFileInterface
    
    Parameters:
    
    path - The path string
    
    Throws:
    
    NexusException - when something goes wrong.
  - opengrouppath
```
public void opengrouppath(java.lang.String path)
                   throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    opengrouppath opens groups and datsets accroding to the path string given. The path syntax follows unix conventions. Both absolute and relative paths are possible. All objects of the path must exist. This function stops int the last group.
    
    Specified by:
    
    opengrouppath in interface NeXusFileInterface
    
    Parameters:
    
    path - The path string
    
    Throws:
    
    NexusException - when something goes wrong.
  - getpath
```
public java.lang.String getpath()
                         throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    return the current path into the NeXus file in the form of a Unix path string.
    
    Specified by:
    
    getpath in interface NeXusFileInterface
    
    Returns:
    
    A unix path string
    
    Throws:
    
    NexusException
  - closegroup
```
public void closegroup()
                throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    closegroup closes access to the current group and steps down one step in group hierarchy.
    
    Specified by:
    
    closegroup in interface NeXusFileInterface
    
    Throws:
    
    NexusException - when an error occurs during this operation.
  - nxmakedata
```
protected void nxmakedata(int handle,
                          java.lang.String name,
                          int type,
                          int rank,
                          int[] dim)
```
  - nxmakedata64
```
protected void nxmakedata64(int handle,
                            java.lang.String name,
                            int type,
                            int rank,
                            long[] dim)
```
  - nxmakecompdata
```
protected void nxmakecompdata(int handle,
                              java.lang.String name,
                              int type,
                              int rank,
                              int[] dim,
                              int iCompress,
                              int[] iChunk)
```
  - nxmakecompdata64
```
protected void nxmakecompdata64(int handle,
                                java.lang.String name,
                                int type,
                                int rank,
                                long[] dim,
                                int iCompress,
                                long[] iChunk)
```
  - nxopendata
```
protected void nxopendata(int handle,
                          java.lang.String name)
```
  - nxclosedata
```
protected void nxclosedata(int handle)
```
  - nxcompress
```
protected void nxcompress(int handle,
                          int compression_type)
```
  - compmakedata
```
public void compmakedata(java.lang.String name,
                         int type,
                         int rank,
                         int[] dim,
                         int compression_type,
                         int[] iChunk)
                  throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    compmakedata creates a new dataset with the specified characteristics in the current group. This data set will be compressed.
    
    Specified by:
    
    compmakedata in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the dataset.
    
    type - The number type of the dataset. Usually a constant from a selection of values.
    
    rank - The rank or number of dimensions of the dataset.
    
    dim - An array containing the length of each dimension. dim must have at least rank entries. Dimension passed as -1 denote an unlimited dimension.
    
    compression_type - determines the compression type.
    
    iChunk - With HDF-5, slabs can be written to compressed data sets. The size of these slabs is specified through the chunk array. This must have the rank values for the size of the chunk to be written in each dimension.
    
    Throws:
    
    NexusException - when the dataset could not be created.
  - compmakedata
```
public void compmakedata(java.lang.String name,
                         int type,
                         int rank,
                         long[] dim,
                         int compression_type,
                         long[] iChunk)
                  throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    compmakedata creates a new dataset with the specified characteristics in the current group. This data set will be compressed.
    
    Specified by:
    
    compmakedata in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the dataset.
    
    type - The number type of the dataset. Usually a constant from a selection of values.
    
    rank - The rank or number of dimensions of the dataset.
    
    dim - An array containing the length of each dimension. dim must have at least rank entries. Dimension passed as -1 denote an unlimited dimension.
    
    compression_type - determines the compression type.
    
    iChunk - With HDF-5, slabs can be written to compressed data sets. The size of these slabs is specified through the chunk array. This must have the rank values for the size of the chunk to be written in each dimension.
    
    Throws:
    
    NexusException - when the dataset could not be created.
  - makedata
```
public void makedata(java.lang.String name,
                     int type,
                     int rank,
                     int[] dim)
              throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    makedata creates a new dataset with the specified characteristics in the current group.
    
    Specified by:
    
    makedata in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the dataset.
    
    type - The number type of the dataset. Usually a constant from a selection of values.
    
    rank - The rank or number of dimensions of the dataset.
    
    dim - An array containing the length of each dimension. dim must have at least rank entries. Dimension passed as -1 denote an unlimited dimension.
    
    Throws:
    
    NexusException - when the dataset could not be created.
  - makedata
```
public void makedata(java.lang.String name,
                     int type,
                     int rank,
                     long[] dim)
              throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    makedata creates a new dataset with the specified characteristics in the current group.
    
    Specified by:
    
    makedata in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the dataset.
    
    type - The number type of the dataset. Usually a constant from a selection of values.
    
    rank - The rank or number of dimensions of the dataset.
    
    dim - An array containing the length of each dimension. dim must have at least rank entries. Dimension passed as -1 denote an unlimited dimension.
    
    Throws:
    
    NexusException - when the dataset could not be created.
  - opendata
```
public void opendata(java.lang.String name)
              throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    opendata opens an existing dataset for access. For instance for reading or writing.
    
    Specified by:
    
    opendata in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the dataset to open.
    
    Throws:
    
    NexusException - when the dataset does not exist or something else is wrong.
  - closedata
```
public void closedata()
               throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    closedata closes an opened dataset. Then no further access is possible without a call to opendata.
    
    Specified by:
    
    closedata in interface NeXusFileInterface
    
    Throws:
    
    NexusException - when an error occurrs.
  - compress
```
public void compress(int compression_type)
              throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    causes the currently open dataset to be compressed on file. This must be called after makedata and before writing to the dataset.
    
    Specified by:
    
    compress in interface NeXusFileInterface
    
    Parameters:
    
    compression_type - determines the type of compression to use.
    
    Throws:
    
    NexusException - when no dataset is open or an error occurs.
  - nxgetdata
```
protected void nxgetdata(int handle,
                         byte[] bdata)
```
  - nxgetslab
```
protected void nxgetslab(int handle,
                         int[] Start,
                         int[] size,
                         byte[] bdata)
```
  - nxgetslab64
```
protected void nxgetslab64(int handle,
                           long[] Start,
                           long[] size,
                           byte[] bdata)
```
  - getdata
```
public void getdata(java.lang.Object array)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    getdata reads the data from an previously openend dataset into array.
    
    Specified by:
    
    getdata in interface NeXusFileInterface
    
    Parameters:
    
    array - An n-dimensional array of the appropriate number type for the dataset. Make sure to have the right type and size here.
    
    Throws:
    
    NexusException - when either an error occurs or no dataset is open or array is not of the right type to hold the data.
  - getslab
```
public void getslab(int[] start,
                    int[] size,
                    java.lang.Object array)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    getslab reads a subset of a large dataset into array.
    
    Specified by:
    
    getslab in interface NeXusFileInterface
    
    Parameters:
    
    start - An array of dimension rank which contains the start position in the dataset from where to start reading.
    
    size - An array of dimension rank which contains the size in each dimension of the data subset to read.
    
    array - An array for holding the returned data values.
    
    Throws:
    
    NexusException - when either an error occurs or no dataset is open or array is not of the right type to hold the data.
  - getslab
```
public void getslab(long[] start,
                    long[] size,
                    java.lang.Object array)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    getslab reads a subset of a large dataset into array.
    
    Specified by:
    
    getslab in interface NeXusFileInterface
    
    Parameters:
    
    start - An array of dimension rank which contains the start position in the dataset from where to start reading.
    
    size - An array of dimension rank which contains the size in each dimension of the data subset to read.
    
    array - An array for holding the returned data values.
    
    Throws:
    
    NexusException - when either an error occurs or no dataset is open or array is not of the right type to hold the data.
  - nxputdata
```
protected void nxputdata(int handle,
                         byte[] array)
```
  - nxputslab
```
protected void nxputslab(int handle,
                         byte[] array,
                         int[] start,
                         int[] size)
```
  - nxputslab64
```
protected void nxputslab64(int handle,
                           byte[] array,
                           long[] start,
                           long[] size)
```
  - putdata
```
public void putdata(java.lang.Object array)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    putdata writes the data from array into a previously opened dataset.
    
    Specified by:
    
    putdata in interface NeXusFileInterface
    
    Parameters:
    
    array - The data to write.
    
    Throws:
    
    NexusException - when an error occurs.
  - putslab
```
public void putslab(java.lang.Object array,
                    int[] start,
                    int[] size)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    putslab writes a subset of a larger dataset to a previously opened dataset.
    
    Specified by:
    
    putslab in interface NeXusFileInterface
    
    Parameters:
    
    array - The data to write.
    
    start - An integer array of dimension rank which holds the startcoordinates of the data subset in the larger dataset.
    
    size - An integer array of dimension rank whidh holds the size in each dimension of the data subset to write.
    
    Throws:
    
    NexusException - when an error occurs.
  - putslab
```
public void putslab(java.lang.Object array,
                    long[] start,
                    long[] size)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    putslab writes a subset of a larger dataset to a previously opened dataset.
    
    Specified by:
    
    putslab in interface NeXusFileInterface
    
    Parameters:
    
    array - The data to write.
    
    start - An integer array of dimension rank which holds the startcoordinates of the data subset in the larger dataset.
    
    size - An integer array of dimension rank whidh holds the size in each dimension of the data subset to write.
    
    Throws:
    
    NexusException - when an error occurs.
  - nxgetattr
```
protected void nxgetattr(int handle,
                         java.lang.String name,
                         byte[] bdata,
                         int[] args)
```
  - nxputattr
```
protected void nxputattr(int handle,
                         java.lang.String name,
                         byte[] array,
                         int type)
```
  - nxputattra
```
protected void nxputattra(int handle,
                          java.lang.String name,
                          byte[] bdata,
                          int rank,
                          int[] dim,
                          int iType)
```
  - nxgetnextattra
```
protected int nxgetnextattra(int handle,
                             java.lang.String[] name,
                             int[] dim,
                             int[] args)
```
  - nxgetattra
```
protected void nxgetattra(int handle,
                          java.lang.String name,
                          byte[] bdata)
```
  - nxgetattrainfo
```
protected void nxgetattrainfo(int handle,
                              java.lang.String name,
                              int[] dim,
                              int[] args)
```
  - nextattr
```
protected int nextattr(int handle,
                       java.lang.String[] names,
                       int[] args)
```
  - initattrdir
```
protected void initattrdir(int handle)
```
  - initgroupdir
```
protected void initgroupdir(int handle)
```
  - getattr
```
public java.lang.Object getattr(java.lang.String name)
                         throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    getattr retrieves the data associated with the attribute * name.
    
    Specified by:
    
    getattr in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the attribute.
    
    Returns:
    
    The attribute data as an array.
    
    Throws:
    
    NexusException - when either an error occurs or the attribute could not be found.
  - getattr
```
public void getattr(java.lang.String name,
                    java.lang.Object array,
                    int[] args)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    getattr retrieves the data associated with the attribute name.
    
    Specified by:
    
    getattr in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the attribute.
    
    array - an array with sufficient space for holding the attribute data.
    
    args - An integer array holding the number of data elements in data as args[0], and the type as args[1]. Both values will be updated while reading.
    
    Throws:
    
    NexusException - when either an error occurs or the attribute could not be found.
  - putattr
```
public void putattr(java.lang.String name,
                    java.lang.Object array,
                    int iType)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    putattr adds a named attribute to a previously opened dataset or group or a global attribute if nothing is open.
    
    Specified by:
    
    putattr in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the attribute.
    
    array - The data of the attribute.
    
    iType - The number type of the attribute.
    
    Throws:
    
    NexusException - if an error occurs.
  - putattr
```
public void putattr(java.lang.String name,
                    java.lang.Object array,
                    int[] size,
                    int iType)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    putattr adds a named attribute to a previously opened dataset or group or a global attribute if nothing is open.
    
    Specified by:
    
    putattr in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the attribute.
    
    array - The data of the attribute.
    
    iType - The number type of the attribute.
    
    Throws:
    
    NexusException - if an error occurs.
  - attrdir
```
public java.util.Hashtable attrdir()
                            throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    attrdir returns the attributes of the currently open dataset or the file global attributes if no dataset is open.
    
    Specified by:
    
    attrdir in interface NeXusFileInterface
    
    Returns:
    
    A Hashtable which will hold the names of the attributes as keys. For each key there is an AttributeEntry class as value.
    
    Throws:
    
    NexusException - when an error occurs.
  - nxgetinfo
```
protected void nxgetinfo(int handle,
                         int[] iDim,
                         int[] args)
```
  - nxgetinfo64
```
protected void nxgetinfo64(int handle,
                           long[] iDim,
                           int[] args)
```
  - nxsetnumberformat
```
protected void nxsetnumberformat(int handle,
                                 int type,
                                 java.lang.String format)
```
  - nextentry
```
protected int nextentry(int handle,
                        java.lang.String[] names)
```
  - setnumberformat
```
public void setnumberformat(int type,
                            java.lang.String format)
                     throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    setnumberformat sets the number format for printing number when using the XML-NeXus format. For HDF4 and HDF5 this is ignored. If a dataset is open, the format for the dataset is set, if none is open the default setting for the number type is changed. The format must be a ANSII-C language format string.
    
    Specified by:
    
    setnumberformat in interface NeXusFileInterface
    
    Parameters:
    
    type - The NeXus type to set the format for.
    
    format - The new format to use.
    
    Throws:
    
    NexusException
  - getinfo
```
public void getinfo(int[] iDim,
                    int[] args)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    getinfo retrieves information about a previously opened dataset.
    
    Specified by:
    
    getinfo in interface NeXusFileInterface
    
    Parameters:
    
    iDim - An array which will be filled with the size of the dataset in each dimension.
    
    args - An integer array which will hold more information about the dataset after return. The fields: args[0] is the rank, args[1] is the number type.
    
    Throws:
    
    NexusException - when an error occurs.
  - getinfo
```
public void getinfo(long[] iDim,
                    int[] args)
             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    getinfo retrieves information about a previously opened dataset.
    
    Specified by:
    
    getinfo in interface NeXusFileInterface
    
    Parameters:
    
    iDim - An array which will be filled with the size of the dataset in each dimension.
    
    args - An integer array which will hold more information about the dataset after return. The fields: args[0] is the rank, args[1] is the number type.
    
    Throws:
    
    NexusException - when an error occurs.
  - groupdir
```
public java.util.Hashtable groupdir()
                             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    groupdir will retrieve the content of the currently open vGroup. groupdir is similar to an ls in unix.
    
    Specified by:
    
    groupdir in interface NeXusFileInterface
    
    Returns:
    
    A Hashtable which will hold the names of the items in the group as keys and the NeXus classname for vGroups or the string 'SDS' for datasets as values.
    
    Throws:
    
    NexusException - if an error occurs
  - nxgetgroupid
```
protected void nxgetgroupid(int handle,
                            NXlink link)
```
  - nxgetdataid
```
protected void nxgetdataid(int handle,
                           NXlink link)
```
  - nxmakelink
```
protected void nxmakelink(int handle,
                          NXlink target)
```
  - nxmakenamedlink
```
protected void nxmakenamedlink(int handle,
                               java.lang.String name,
                               NXlink target)
```
  - nxopensourcepath
```
protected void nxopensourcepath(int handle)
```
  - getgroupID
```
public NXlink getgroupID()
                  throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    getgroupID gets the data necessary for linking the current vGroup somewhere else.
    
    Specified by:
    
    getgroupID in interface NeXusFileInterface
    
    Returns:
    
    A NXlink object holding the link data.
    
    Throws:
    
    NexusException - if an error occurs.
  - getdataID
```
public NXlink getdataID()
                 throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    getdataID gets the data necessary for linking the current dataset somewhere else.
    
    Specified by:
    
    getdataID in interface NeXusFileInterface
    
    Returns:
    
    A NXlink object holding the link data.
    
    Throws:
    
    NexusException - if an error occurs.
  - makelink
```
public void makelink(NXlink target)
              throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    makelink links the object described by target into the current vGroup.
    
    Specified by:
    
    makelink in interface NeXusFileInterface
    
    Parameters:
    
    target - The Object to link into the current group.
    
    Throws:
    
    NexusException - if an error occurs.
  - makenamedlink
```
public void makenamedlink(java.lang.String name,
                          NXlink target)
                   throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    makenamedlink links the object described by target into the current vGroup. The object will have a new name in the group into which it is linked
    
    Specified by:
    
    makenamedlink in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of this object in the current group
    
    target - The Object to link into the current group.
    
    Throws:
    
    NexusException - if an error occurs.
  - opensourcepath
```
public void opensourcepath()
                    throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    opensourcepath opens the group from which the current item was linked Returns an error if the current item is not linked.
    
    Specified by:
    
    opensourcepath in interface NeXusFileInterface
    
    Throws:
    
    NexusException - if an error occurs.
  - nxinquirefile
```
protected void nxinquirefile(int handle,
                             java.lang.String[] names)
```
  - nxlinkexternal
```
protected void nxlinkexternal(int handle,
                              java.lang.String name,
                              java.lang.String nxclass,
                              java.lang.String nxurl)
```
  - nxlinkexternaldataset
```
protected void nxlinkexternaldataset(int handle,
                                     java.lang.String name,
                                     java.lang.String nxurl)
```
  - nxisexternalgroup
```
protected int nxisexternalgroup(int handle,
                                java.lang.String name,
                                java.lang.String nxclass,
                                java.lang.String[] nxurl)
```
  - nxisexternaldataset
```
protected int nxisexternaldataset(int handle,
                                  java.lang.String name,
                                  java.lang.String[] nxurl)
```
  - inquirefile
```
public java.lang.String inquirefile()
                             throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    inquirefile inquires which file we are currently in. This is a support function for external linking
    
    Specified by:
    
    inquirefile in interface NeXusFileInterface
    
    Returns:
    
    The current file
    
    Throws:
    
    NexusException - when things are wrong
  - linkexternal
```
public void linkexternal(java.lang.String name,
                         java.lang.String nxclass,
                         java.lang.String nxurl)
                  throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    linkexternal links group name, nxclass to the URL nxurl
    
    Specified by:
    
    linkexternal in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the vgroup to link to
    
    nxclass - The class name of the linked vgroup
    
    nxurl - The URL to the linked external file
    
    Throws:
    
    NexusException - if things are wrong
  - linkexternaldataset
```
public void linkexternaldataset(java.lang.String name,
                                java.lang.String nxurl)
                         throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    linkexternaldataset links dataset name to the URL nxurl
    
    Specified by:
    
    linkexternaldataset in interface NeXusFileInterface
    
    Parameters:
    
    name - The name of the dataset to link to
    
    nxurl - The URL to the linked external file
    
    Throws:
    
    NexusException - if things are wrong
  - isexternalgroup
```
public java.lang.String isexternalgroup(java.lang.String name,
                                        java.lang.String nxclass)
                                 throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    nxisexternalgroup test the group name, nxclass if it is linked externally
    
    Specified by:
    
    isexternalgroup in interface NeXusFileInterface
    
    Parameters:
    
    name - of the group to test
    
    nxclass - class of the group to test
    
    Returns:
    
    null when the group is not linked, else a string giving the URL of the linked resource
    
    Throws:
    
    NexusException - if things are wrong
  - isexternaldataset
```
public java.lang.String isexternaldataset(java.lang.String name)
                                   throws NexusException
```
    Description copied from interface: NeXusFileInterface
    
    nxisexternaldataset if the named dataset is is linked externally
    
    Specified by:
    
    isexternaldataset in interface NeXusFileInterface
    
    Parameters:
    
    name - of the dataset to test
    
    Returns:
    
    null when the it is not linked, else a string giving the URL of the linked resource
    
    Throws:
    
    NexusException - if things are wrong
  - debugstop
```
public void debugstop()
```
    debugstop is a debugging helper function which goes into an endless loop in the dynamic link library. Then a unix debugger may attach to the running java process using the pid, interrupt, set the loop variable to leave the loop, set a new breakpoint and continue debugging. This works with ladebug on DU40D. This is an developer support routine and should NEVER be called in normal code.

Class NexusFile

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

NXACC_READ

NXACC_RDWR

NXACC_CREATE

NXACC_CREATE4

NXACC_CREATE5

NXACC_CREATEXML

NXACC_NOSTRIP

NX_UNLIMITED

NX_FLOAT32

NX_FLOAT64

NX_INT8

NX_BINARY

NX_UINT8

NX_BOOLEAN

NX_INT16

NX_UINT16

NX_INT32

NX_UINT32

NX_INT64

NX_UINT64

NX_CHAR

NX_COMP_NONE

NX_COMP_LZW

NX_COMP_RLE

NX_COMP_HUF

NX_COMP_LZW_LVL0

NX_COMP_LZW_LVL1

NX_COMP_LZW_LVL2

NX_COMP_LZW_LVL3

NX_COMP_LZW_LVL4

NX_COMP_LZW_LVL5

NX_COMP_LZW_LVL6

NX_COMP_LZW_LVL7

NX_COMP_LZW_LVL8

NX_COMP_LZW_LVL9

MAXNAMELEN

handle

Constructor Detail

NexusFile

Method Detail

init

close

nxflush

flush

close

finalize

nxmakegroup

nxopengroup

nxopenpath

nxopengrouppath

nxclosegroup

nxgetpath

makegroup

opengroup

openpath

opengrouppath

getpath

closegroup

nxmakedata

nxmakedata64

nxmakecompdata

nxmakecompdata64

nxopendata

nxclosedata

nxcompress

compmakedata

compmakedata

makedata

makedata

opendata

closedata

compress

nxgetdata

nxgetslab