Public Member Functions | |
void | flush () throws NexusException |
flush writes all previously unsaved data to disk. | |
void | finalize () throws Throwable |
finalize closes the file. | |
void | close () throws NexusException |
close the NeXus file. | |
void | makegroup (String name, String nxclass) throws NexusException |
makegroup creates a new group below the current group within the NeXus file hierarchy. | |
void | opengroup (String name, String nxclass) throws NexusException |
opengroup opens the group name with class nxclass. | |
void | openpath (String path) throws NexusException |
openpath opens groups and datsets accroding to the path string given. | |
void | opengrouppath (String path) throws NexusException |
opengrouppath opens groups and datsets accroding to the path string given. | |
String | getpath () throws NexusException |
return the current path into the NeXus file in the form of a Unix path string. | |
void | closegroup () throws NexusException |
closegroup closes access to the current group and steps down one step in group hierarchy. | |
void | makedata (String name, int type, int rank, int dim[]) throws NexusException |
makedata creates a new dataset with the specified characteristics in the current group. | |
void | makedata (String name, int type, int rank, long dim[]) throws NexusException |
makedata creates a new dataset with the specified characteristics in the current group. | |
void | compmakedata (String name, int type, int rank, int dim[], int compression_type, int iChunk[]) throws NexusException |
compmakedata creates a new dataset with the specified characteristics in the current group. | |
void | compmakedata (String name, int type, int rank, long dim[], int compression_type, long iChunk[]) throws NexusException |
compmakedata creates a new dataset with the specified characteristics in the current group. | |
void | opendata (String name) throws NexusException |
opendata opens an existing dataset for access. | |
void | closedata () throws NexusException |
closedata closes an opened dataset. | |
void | compress (int compression_type) throws NexusException |
causes the currently open dataset to be compressed on file. | |
void | getdata (Object array) throws NexusException |
getdata reads the data from an previously openend dataset into array. | |
void | getslab (int start[], int size[], Object array) throws NexusException |
getslab reads a subset of a large dataset into array. | |
void | getslab (long start[], long size[], Object array) throws NexusException |
getslab reads a subset of a large dataset into array. | |
void | getattr (String name, Object data, int args[]) throws NexusException |
getattr retrieves the data associated with the attribute name. | |
void | putdata (Object array) throws NexusException |
putdata writes the data from array into a previously opened dataset. | |
void | putslab (Object array, int start[], int size[]) throws NexusException |
putslab writes a subset of a larger dataset to a previously opened dataset. | |
void | putslab (Object array, long start[], long size[]) throws NexusException |
putslab writes a subset of a larger dataset to a previously opened dataset. | |
void | putattr (String name, Object array, int iType) throws NexusException |
putattr adds a named attribute to a previously opened dataset or a global attribute if no dataset is open. | |
void | getinfo (int iDim[], int args[]) throws NexusException |
getinfo retrieves information about a previously opened dataset. | |
void | getinfo (long iDim[], int args[]) throws NexusException |
getinfo retrieves information about a previously opened dataset. | |
void | setnumberformat (int type, String format) throws NexusException |
setnumberformat sets the number format for printing number when using the XML-NeXus format. | |
Hashtable | groupdir () throws NexusException |
groupdir will retrieve the content of the currently open vGroup. | |
Hashtable | attrdir () throws NexusException |
attrdir returns the attributes of the currently open dataset or the file global attributes if no dataset is open. | |
NXlink | getgroupID () throws NexusException |
getgroupID gets the data necessary for linking the current vGroup somewhere else. | |
NXlink | getdataID () throws NexusException |
getdataID gets the data necessary for linking the current dataset somewhere else. | |
void | makelink (NXlink target) throws NexusException |
makelink links the object described by target into the current vGroup. | |
void | makenamedlink (String name, NXlink target) throws NexusException |
makenamedlink links the object described by target into the current vGroup. | |
void | opensourcepath () throws NexusException |
opensourcepath opens the group from which the current item was linked Returns an error if the current item is not linked. | |
String | inquirefile () throws NexusException |
inquirefile inquires which file we are currently in. | |
void | linkexternal (String name, String nxclass, String nxurl) throws NexusException |
linkexternal links group name, nxclass to the URL nxurl | |
void | linkexternaldataset (String name, String nxurl) throws NexusException |
linkexternaldataset links dataset name to the URL nxurl | |
String | isexternalgroup (String name, String nxclass) throws NexusException |
nxisexternalgroup test the group name, nxclass if it is linked externally | |
String | isexternaldataset (String name) throws NexusException |
nxisexternaldataset if the named dataset is is linked externally |
Definition at line 21 of file NeXusFileInterface.java.
Hashtable org.nexusformat.NeXusFileInterface.attrdir | ( | ) | throws NexusException |
attrdir returns the attributes of the currently open dataset or the file global attributes if no dataset is open.
NexusException | when an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.close | ( | ) | throws NexusException |
close the NeXus file.
To make javalint and diamond happy
NexusException |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.closedata | ( | ) | throws NexusException |
closedata closes an opened dataset.
Then no further access is possible without a call to opendata.
NexusException | when an HDF error occurrs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.closegroup | ( | ) | throws NexusException |
closegroup closes access to the current group and steps down one step in group hierarchy.
NexusException | when an HDF error occurs during this operation. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.compmakedata | ( | String | name, |
int | type, | ||
int | rank, | ||
int | dim[], | ||
int | compression_type, | ||
int | iChunk[] | ||
) | throws NexusException |
compmakedata creates a new dataset with the specified characteristics in the current group.
This data set will be compressed.
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. |
NexusException | when the dataset could not be created. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.compmakedata | ( | String | name, |
int | type, | ||
int | rank, | ||
long | dim[], | ||
int | compression_type, | ||
long | iChunk[] | ||
) | throws NexusException |
compmakedata creates a new dataset with the specified characteristics in the current group.
This data set will be compressed.
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. |
NexusException | when the dataset could not be created. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.compress | ( | int | compression_type | ) | throws NexusException |
causes the currently open dataset to be compressed on file.
This must be called after makedata and before writing to the dataset.
compression_type | determines the type of compression to use. |
NexusException | when no dataset is open or an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.finalize | ( | ) | throws Throwable |
finalize closes the file.
It is supposed to be called by the garbage collector when the object is collected. As this happens at discretion of the garbage collector it is safer to call finalize yourself, when a NeXus file needs to be closed. Multiple calls to finalize do no harm.
Throwable | because it is required by the definition of finalize. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.flush | ( | ) | throws NexusException |
flush writes all previously unsaved data to disk.
All directory searches are invalidated. Any open SDS is closed.
NexusException | if an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.getattr | ( | String | name, |
Object | data, | ||
int | args[] | ||
) | throws NexusException |
getattr retrieves the data associated with the attribute name.
name | The name of the attribute. |
data | 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. |
NexusException | when either an HDF error occurs or the attribute could not be found. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.getdata | ( | Object | array | ) | throws NexusException |
getdata reads the data from an previously openend dataset into array.
array | An n-dimensional array of the appropriate number type for the dataset. Make sure to have the right type and size here. |
NexusException | when either an HDF error occurs or no dataset is open or array is not of the right type to hold the data. |
Implemented in org.nexusformat.NexusFile.
NXlink org.nexusformat.NeXusFileInterface.getdataID | ( | ) | throws NexusException |
getdataID gets the data necessary for linking the current dataset somewhere else.
NexusException | if an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
NXlink org.nexusformat.NeXusFileInterface.getgroupID | ( | ) | throws NexusException |
getgroupID gets the data necessary for linking the current vGroup somewhere else.
NexusException | if an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.getinfo | ( | int | iDim[], |
int | args[] | ||
) | throws NexusException |
getinfo retrieves information about a previously opened dataset.
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. |
NexusException | when an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.getinfo | ( | long | iDim[], |
int | args[] | ||
) | throws NexusException |
getinfo retrieves information about a previously opened dataset.
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. |
NexusException | when an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
String org.nexusformat.NeXusFileInterface.getpath | ( | ) | throws NexusException |
return the current path into the NeXus file in the form of a Unix path string.
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.getslab | ( | int | start[], |
int | size[], | ||
Object | array | ||
) | throws NexusException |
getslab reads a subset of a large dataset into array.
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. |
NexusException | when either an HDF error occurs or no dataset is open or array is not of the right type to hold the data. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.getslab | ( | long | start[], |
long | size[], | ||
Object | array | ||
) | throws NexusException |
getslab reads a subset of a large dataset into array.
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. |
NexusException | when either an HDF error occurs or no dataset is open or array is not of the right type to hold the data. |
Implemented in org.nexusformat.NexusFile.
Hashtable org.nexusformat.NeXusFileInterface.groupdir | ( | ) | throws NexusException |
groupdir will retrieve the content of the currently open vGroup.
groupdir is similar to an ls in unix.
NexusException | if an HDF error occurs |
Implemented in org.nexusformat.NexusFile.
String org.nexusformat.NeXusFileInterface.inquirefile | ( | ) | throws NexusException |
inquirefile inquires which file we are currently in.
This is a support function for external linking
NexusException | when things are wrong |
Implemented in org.nexusformat.NexusFile.
String org.nexusformat.NeXusFileInterface.isexternaldataset | ( | String | name | ) | throws NexusException |
nxisexternaldataset if the named dataset is is linked externally
name | of the dataset to test |
NexusException | if things are wrong |
Implemented in org.nexusformat.NexusFile.
String org.nexusformat.NeXusFileInterface.isexternalgroup | ( | String | name, |
String | nxclass | ||
) | throws NexusException |
nxisexternalgroup test the group name, nxclass if it is linked externally
name | of the group to test |
nxclass | class of the group to test |
NexusException | if things are wrong |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.linkexternal | ( | String | name, |
String | nxclass, | ||
String | nxurl | ||
) | throws NexusException |
linkexternal links group name, nxclass to the URL nxurl
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 |
NexusException | if things are wrong |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.linkexternaldataset | ( | String | name, |
String | nxurl | ||
) | throws NexusException |
linkexternaldataset links dataset name to the URL nxurl
name | The name of the dataset to link to |
nxurl | The URL to the linked external file |
NexusException | if things are wrong |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.makedata | ( | String | name, |
int | type, | ||
int | rank, | ||
int | dim[] | ||
) | throws NexusException |
makedata creates a new dataset with the specified characteristics in the current group.
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. |
NexusException | when the dataset could not be created. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.makedata | ( | String | name, |
int | type, | ||
int | rank, | ||
long | dim[] | ||
) | throws NexusException |
makedata creates a new dataset with the specified characteristics in the current group.
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. |
NexusException | when the dataset could not be created. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.makegroup | ( | String | name, |
String | nxclass | ||
) | throws NexusException |
makegroup creates a new group below the current group within the NeXus file hierarchy.
name | The name of the group to create. |
nxclass | The classname of the group. |
NexusException | if an error occurs during this operation. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.makelink | ( | NXlink | target | ) | throws NexusException |
makelink links the object described by target into the current vGroup.
target | The Object to link into the current group. |
NexusException | if an error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.makenamedlink | ( | String | name, |
NXlink | target | ||
) | throws NexusException |
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
target | The Object to link into the current group. |
name | The name of this object in the current group |
NexusException | if an error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.opendata | ( | String | name | ) | throws NexusException |
opendata opens an existing dataset for access.
For instance for reading or writing.
name | The name of the dataset to open. |
NexusException | when the dataset does not exist or something else is wrong. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.opengroup | ( | String | name, |
String | nxclass | ||
) | throws NexusException |
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.
name | the name of the group to open. |
nxclass | the classname of the group to open. |
NexusException | when something goes wrong. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.opengrouppath | ( | String | path | ) | throws NexusException |
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.
path | The path string |
NexusException | when something goes wrong. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.openpath | ( | String | path | ) | throws NexusException |
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.
path | The path string |
NexusException | when something goes wrong. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.opensourcepath | ( | ) | throws NexusException |
opensourcepath opens the group from which the current item was linked Returns an error if the current item is not linked.
NexusException | if an error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.putattr | ( | String | name, |
Object | array, | ||
int | iType | ||
) | throws NexusException |
putattr adds a named attribute to a previously opened dataset or a global attribute if no dataset is open.
name | The name of the attribute. |
array | The data of the attribute. |
iType | The number type of the attribute. |
NexusException | if an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.putdata | ( | Object | array | ) | throws NexusException |
putdata writes the data from array into a previously opened dataset.
array | The data to write. |
NexusException | when an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.putslab | ( | Object | array, |
int | start[], | ||
int | size[] | ||
) | throws NexusException |
putslab writes a subset of a larger dataset to a previously opened dataset.
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. |
NexusException | when an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.putslab | ( | Object | array, |
long | start[], | ||
long | size[] | ||
) | throws NexusException |
putslab writes a subset of a larger dataset to a previously opened dataset.
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. |
NexusException | when an HDF error occurs. |
Implemented in org.nexusformat.NexusFile.
void org.nexusformat.NeXusFileInterface.setnumberformat | ( | int | type, |
String | format | ||
) | throws NexusException |
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.
type | The NeXus type to set the format for. |
format | The new format to use. |
Implemented in org.nexusformat.NexusFile.