Interface NeXusFileInterface

All Known Implementing Classes:
NexusFile

public interface NeXusFileInterface
  • Method Summary

    Modifier and Type
    Method
    Description
    attrdir returns the attributes of the currently open dataset or the file global attributes if no dataset is open.
    void
    close the NeXus file.
    void
    closedata closes an opened dataset.
    void
    closegroup closes access to the current group and steps down one step in group hierarchy.
    void
    compmakedata(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(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 closes the file.
    void
    flush writes all previously unsaved data to disk.
    getattr retrieves the data associated with the attribute * name.
    void
    getattr(String name, Object data, int[] args)
    getattr retrieves the data associated with the attribute name.
    void
    getdata(Object array)
    getdata reads the data from an previously openend dataset into array.
    getdataID gets the data necessary for linking the current dataset somewhere else.
    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.
    return the current path into the NeXus file in the form of a Unix path string.
    void
    getslab(int[] start, int[] size, Object array)
    getslab reads a subset of a large dataset into array.
    void
    getslab(long[] start, long[] size, Object array)
    getslab reads a subset of a large dataset into array.
    groupdir will retrieve the content of the currently open vGroup.
    inquirefile inquires which file we are currently in.
    nxisexternaldataset if the named dataset is is linked externally
    isexternalgroup(String name, String nxclass)
    nxisexternalgroup test the group name, nxclass if it is linked externally
    void
    linkexternal(String name, String nxclass, String nxurl)
    linkexternal links group name, nxclass to the URL nxurl
    void
    linkexternaldataset links dataset name to the URL nxurl
    void
    makedata(String name, int type, int rank, int[] dim)
    makedata creates a new dataset with the specified characteristics in the current group.
    void
    makedata(String name, int type, int rank, long[] dim)
    makedata creates a new dataset with the specified characteristics in the current group.
    void
    makegroup(String name, 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(String name, NXlink target)
    makenamedlink links the object described by target into the current vGroup.
    void
    opendata opens an existing dataset for access.
    void
    opengroup(String name, String nxclass)
    opengroup opens the group name with class nxclass.
    void
    opengrouppath opens groups and datsets accroding to the path string given.
    void
    openpath opens groups and datsets accroding to the path string given.
    void
    opensourcepath opens the group from which the current item was linked Returns an error if the current item is not linked.
    void
    putattr(String name, 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(String name, 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(Object array)
    putdata writes the data from array into a previously opened dataset.
    void
    putslab(Object array, int[] start, int[] size)
    putslab writes a subset of a larger dataset to a previously opened dataset.
    void
    putslab(Object array, long[] start, long[] size)
    putslab writes a subset of a larger dataset to a previously opened dataset.
    void
    setnumberformat(int type, String format)
    setnumberformat sets the number format for printing number when using the XML-NeXus format.
  • Method Details

    • 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 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:
      Throwable - because it is required by the definition of finalize.
    • close

      void close() throws NexusException
      close the NeXus file. To make javalint and diamond happy
      Throws:
      NexusException
    • makegroup

      void makegroup(String name, 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(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.
      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(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(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

      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(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(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(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(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(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(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, 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, 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(String name, 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

      Object getattr(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(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(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(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(String name, 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(String name, 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, 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

      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

      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(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:
      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

      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

      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(String name, String nxclass, 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(String name, 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

      String isexternalgroup(String name, 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

      String isexternaldataset(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