Class 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
    • 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)
      • 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.
      • 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.
      • 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)
      • 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)
      • 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.
      • 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)
      • 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.