Interface NeXusFileInterface

  • All Known Implementing Classes:
    NexusFile

    public interface NeXusFileInterface
    • Method Summary

      All Methods Instance Methods Abstract 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.
      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 finalize()
      finalize closes the file.
      void flush()
      flush writes all previously unsaved 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 data, 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.
      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.
      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.
    • Method Detail

      • flush

        void flush()
            throws NexusException
        flush writes all previously unsaved data to disk. All directory searches are invalidated. Any open SDS is closed.
        Throws:
        NexusException - if an error occurs.
      • finalize

        void finalize()
               throws java.lang.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.
        Throws:
        java.lang.Throwable - because it is required by the definition of finalize.
      • makegroup

        void makegroup​(java.lang.String name,
                       java.lang.String nxclass)
                throws NexusException
        makegroup creates a new group below the current group within the NeXus file hierarchy.
        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

        void opengroup​(java.lang.String name,
                       java.lang.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.
        Parameters:
        name - the name of the group to open.
        nxclass - the classname of the group to open.
        Throws:
        NexusException - when something goes wrong.
      • openpath

        void openpath​(java.lang.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.
        Parameters:
        path - The path string
        Throws:
        NexusException - when something goes wrong.
      • opengrouppath

        void opengrouppath​(java.lang.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.
        Parameters:
        path - The path string
        Throws:
        NexusException - when something goes wrong.
      • getpath

        java.lang.String getpath()
                          throws NexusException
        return the current path into the NeXus file in the form of a Unix path string.
        Returns:
        A unix path string
        Throws:
        NexusException
      • closegroup

        void closegroup()
                 throws NexusException
        closegroup closes access to the current group and steps down one step in group hierarchy.
        Throws:
        NexusException - when an error occurs during this operation.
      • makedata

        void makedata​(java.lang.String name,
                      int type,
                      int rank,
                      int[] dim)
               throws NexusException
        makedata creates a new dataset with the specified characteristics in the current group.
        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

        void makedata​(java.lang.String name,
                      int type,
                      int rank,
                      long[] dim)
               throws NexusException
        makedata creates a new dataset with the specified characteristics in the current group.
        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.
      • compmakedata

        void compmakedata​(java.lang.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.
        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

        void compmakedata​(java.lang.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.
        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.
      • opendata

        void opendata​(java.lang.String name)
               throws NexusException
        opendata opens an existing dataset for access. For instance for reading or writing.
        Parameters:
        name - The name of the dataset to open.
        Throws:
        NexusException - when the dataset does not exist or something else is wrong.
      • closedata

        void closedata()
                throws NexusException
        closedata closes an opened dataset. Then no further access is possible without a call to opendata.
        Throws:
        NexusException - when an error occurrs.
      • compress

        void 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.
        Parameters:
        compression_type - determines the type of compression to use.
        Throws:
        NexusException - when no dataset is open or an error occurs.
      • getdata

        void getdata​(java.lang.Object array)
              throws NexusException
        getdata reads the data from an previously openend dataset into array.
        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

        void getslab​(int[] start,
                     int[] size,
                     java.lang.Object array)
              throws NexusException
        getslab reads a subset of a large dataset into array.
        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

        void getslab​(long[] start,
                     long[] size,
                     java.lang.Object array)
              throws NexusException
        getslab reads a subset of a large dataset into array.
        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.
      • getattr

        void getattr​(java.lang.String name,
                     java.lang.Object data,
                     int[] args)
              throws NexusException
        getattr retrieves the data associated with the attribute name.
        Parameters:
        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.
        Throws:
        NexusException - when either an error occurs or the attribute could not be found.
      • getattr

        java.lang.Object getattr​(java.lang.String name)
                          throws NexusException
        getattr retrieves the data associated with the attribute * name.
        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.
      • putdata

        void putdata​(java.lang.Object array)
              throws NexusException
        putdata writes the data from array into a previously opened dataset.
        Parameters:
        array - The data to write.
        Throws:
        NexusException - when an error occurs.
      • putslab

        void putslab​(java.lang.Object array,
                     int[] start,
                     int[] size)
              throws NexusException
        putslab writes a subset of a larger dataset to a previously opened dataset.
        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

        void putslab​(java.lang.Object array,
                     long[] start,
                     long[] size)
              throws NexusException
        putslab writes a subset of a larger dataset to a previously opened dataset.
        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.
      • putattr

        void putattr​(java.lang.String name,
                     java.lang.Object array,
                     int iType)
              throws NexusException
        putattr adds a named attribute to a previously opened dataset or group or a global attribute if nothing is open.
        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

        void putattr​(java.lang.String name,
                     java.lang.Object array,
                     int[] size,
                     int iType)
              throws NexusException
        putattr adds a named attribute to a previously opened dataset or group or a global attribute if nothing is open.
        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.
      • getinfo

        void getinfo​(int[] iDim,
                     int[] args)
              throws NexusException
        getinfo retrieves information about a previously opened dataset.
        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

        void getinfo​(long[] iDim,
                     int[] args)
              throws NexusException
        getinfo retrieves information about a previously opened dataset.
        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.
      • setnumberformat

        void setnumberformat​(int type,
                             java.lang.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.
        Parameters:
        type - The NeXus type to set the format for.
        format - The new format to use.
        Throws:
        NexusException
      • groupdir

        java.util.Hashtable groupdir()
                              throws NexusException
        groupdir will retrieve the content of the currently open vGroup. groupdir is similar to an ls in unix.
        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
      • attrdir

        java.util.Hashtable attrdir()
                             throws NexusException
        attrdir returns the attributes of the currently open dataset or the file global attributes if no dataset is open.
        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.
      • getgroupID

        NXlink getgroupID()
                   throws NexusException
        getgroupID gets the data necessary for linking the current vGroup somewhere else.
        Returns:
        A NXlink object holding the link data.
        Throws:
        NexusException - if an error occurs.
      • getdataID

        NXlink getdataID()
                  throws NexusException
        getdataID gets the data necessary for linking the current dataset somewhere else.
        Returns:
        A NXlink object holding the link data.
        Throws:
        NexusException - if an error occurs.
      • makelink

        void makelink​(NXlink target)
               throws NexusException
        makelink links the object described by target into the current vGroup.
        Parameters:
        target - The Object to link into the current group.
        Throws:
        NexusException - if an error occurs.
      • makenamedlink

        void makenamedlink​(java.lang.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
        Parameters:
        target - The Object to link into the current group.
        name - The name of this object in the current group
        Throws:
        NexusException - if an error occurs.
      • opensourcepath

        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.
        Throws:
        NexusException - if an error occurs.
      • inquirefile

        java.lang.String inquirefile()
                              throws NexusException
        inquirefile inquires which file we are currently in. This is a support function for external linking
        Returns:
        The current file
        Throws:
        NexusException - when things are wrong
      • linkexternal

        void linkexternal​(java.lang.String name,
                          java.lang.String nxclass,
                          java.lang.String nxurl)
                   throws NexusException
        linkexternal links group name, nxclass to the URL nxurl
        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

        void linkexternaldataset​(java.lang.String name,
                                 java.lang.String nxurl)
                          throws NexusException
        linkexternaldataset links dataset name to the URL nxurl
        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

        java.lang.String isexternalgroup​(java.lang.String name,
                                         java.lang.String nxclass)
                                  throws NexusException
        nxisexternalgroup test the group name, nxclass if it is linked externally
        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

        java.lang.String isexternaldataset​(java.lang.String name)
                                    throws NexusException
        nxisexternaldataset if the named dataset is is linked externally
        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