Module org.hdfgroup.object
Package hdf.object.h5

Class H5File

Object
File
hdf.object.FileFormat
hdf.object.h5.H5File
All Implemented Interfaces:
Serializable, Comparable<File>
public class H5File
extends FileFormat
H5File is an implementation of the FileFormat class for HDF5 files.

The HDF5 file structure is made up of HObjects stored in a tree-like fashion. Each tree node represents an HDF5 object: a Group, Dataset, or Named Datatype. Starting from the root of the tree, rootObject, the tree can be traversed to find a specific object.

The following example shows the implementation of finding an object for a given path in FileFormat. User applications can directly call the static method FileFormat.findObject(file, objPath) to get the object. 

 HObject findObject(FileFormat file, String path) {
     if (file == null || path == null)
         return null;
     if (!path.endsWith("/"))
         path = path + "/";
     HObject theRoot = file.getRootObject();
     if (theRoot == null)
         return null;
     else if (path.equals("/"))
         return theRoot;

     Iterator local_it = ((Group) theRoot)
             .breadthFirstMemberList().iterator();
     HObject theObj = null;
     while (local_it.hasNext()) {
         theObj = local_it.next();
         String fullPath = theObj.getFullName() + "/";
         if (path.equals(fullPath) &&  theObj.getPath() != null ) {
             break;
     }
     return theObj;
 }
Version:
2.4 9/4/2007
Author:
Peter X. Cao
See Also:
Serialized Form

  • Field Details

  • Constructor Details

    • H5File

      public H5File()
      Constructs an H5File instance with an empty file name and read-only access.

    • H5File

      public H5File​(String fileName)
      Constructs an H5File instance with specified file name and read/write access.

      This constructor does not open the file for access, nor does it confirm that the file can be opened read/write.

      Parameters:
      fileName - A valid file name, with a relative or absolute path.
      Throws:
      NullPointerException - If the fileName argument is null.

    • H5File

      public H5File​(String fileName, int access)
      Constructs an H5File instance with specified file name and access.

      The access parameter values and corresponding behaviors:

      • READ: Read-only access; open() will fail file doesn't exist.
      • WRITE: Read/Write access; open() will fail if file doesn't exist or if file can't be opened with read/write access.
      • CREATE: Read/Write access; create a new file or truncate an existing one; open() will fail if file can't be created or if file exists but can't be opened read/write.

      This constructor does not open the file for access, nor does it confirm that the file can later be opened read/write or created.

      The flag returned by FileFormat.isReadOnly() is set to true if the access parameter value is READ, even though the file isn't yet open.

      Parameters:
      fileName - A valid file name, with a relative or absolute path.
      access - The file access flag, which determines behavior when file is opened. Acceptable values are READ, WRITE, and CREATE.
      Throws:
      NullPointerException - If the fileName argument is null.

  • Method Details

    • copyAttributes

      public static final void copyAttributes​(HObject src, HObject dst)
      Copies the attributes of one object to another object.

      This method copies all the attributes from one object (source object) to another (destination object). If an attribute already exists in the destination object, the attribute will not be copied. Attribute names exceeding 256 characters will be truncated in the destination object.

      The object can be an H5Group, an H5Dataset, or a named H5Datatype. This method is in the H5File class because there is no H5Object class and it is specific to HDF5 objects.

      The copy can fail for a number of reasons, including an invalid source or destination object, but no exceptions are thrown. The actual copy is carried out by the method: copyAttributes(long, long)

      Parameters:
      src - The source object.
      dst - The destination object.
      See Also:
      copyAttributes(long, long)

    • copyAttributes

      public static final void copyAttributes​(long src_id, long dst_id)
      Copies the attributes of one object to another object.

      This method copies all the attributes from one object (source object) to another (destination object). If an attribute already exists in the destination object, the attribute will not be copied. Attribute names exceeding 256 characters will be truncated in the destination object.

      The object can be an H5Group, an H5Dataset, or a named H5Datatype. This method is in the H5File class because there is no H5Object class and it is specific to HDF5 objects.

      The copy can fail for a number of reasons, including an invalid source or destination object identifier, but no exceptions are thrown.

      Parameters:
      src_id - The identifier of the source object.
      dst_id - The identifier of the destination object.

    • getAttribute

      public static final List<Attribute> getAttribute​(HObject obj) throws hdf.hdf5lib.exceptions.HDF5Exception
      Returns a list of attributes for the specified object.

      This method returns a list containing the attributes associated with the identified object. If there are no associated attributes, an empty list will be returned.

      Attribute names exceeding 256 characters will be truncated in the returned list.

      Parameters:
      obj - The HObject whose attributes are to be returned.
      Returns:
      The list of the object's attributes.
      Throws:
      hdf.hdf5lib.exceptions.HDF5Exception - If an underlying HDF library routine is unable to perform a step necessary to retrieve the attributes. A variety of failures throw this exception.
      See Also:
      getAttribute(HObject,int,int)

    • getAttribute

      public static final List<Attribute> getAttribute​(HObject obj, int idx_type, int order) throws hdf.hdf5lib.exceptions.HDF5Exception
      Returns a list of attributes for the specified object, in creation or alphabetical order.

      This method returns a list containing the attributes associated with the identified object. If there are no associated attributes, an empty list will be returned. The list of attributes returned can be in increasing or decreasing, creation or alphabetical order.

      Attribute names exceeding 256 characters will be truncated in the returned list.

      Parameters:
      obj - The HObject whose attributes are to be returned.
      idx_type - The type of index. Valid values are:
      • H5_INDEX_NAME: An alpha-numeric index by attribute name
      • H5_INDEX_CRT_ORDER: An index by creation order
      order - The index traversal order. Valid values are:
      • H5_ITER_INC: A top-down iteration incrementing the index position at each step.
      • H5_ITER_DEC: A bottom-up iteration decrementing the index position at each step.
      Returns:
      The list of the object's attributes.
      Throws:
      hdf.hdf5lib.exceptions.HDF5Exception - If an underlying HDF library routine is unable to perform a step necessary to retrieve the attributes. A variety of failures throw this exception.

    • updateReferenceDataset

      public static final void updateReferenceDataset​(H5File srcFile, H5File dstFile) throws Exception
      Updates values of scalar dataset object references in copied file.

      This method has very specific functionality as documented below, and the user is advised to pay close attention when dealing with files that contain references.

      When a copy is made from one HDF file to another, object references and dataset region references are copied, but the references in the destination file are not updated by the copy and are therefore invalid.

      When an entire file is copied, this method updates the values of the object references and dataset region references that are in scalar datasets in the destination file so that they point to the correct object(s) in the destination file. The method does not update references that occur in objects other than scalar datasets.

      In the current release, the updating of object references is not handled completely as it was not required by the projects that funded development. There is no support for updates when the copy does not include the entire file. Nor is there support for updating objects other than scalar datasets in full-file copies. This functionality will be extended as funding becomes available or, possibly, when the underlying HDF library supports the reference updates itself.

      Parameters:
      srcFile - The file that was copied.
      dstFile - The destination file where the object references will be updated.
      Throws:
      Exception - If there is a problem in the update process.

    • getLibversion

      public String getLibversion()
      Returns the version of the HDF5 library.
      Specified by:
      getLibversion in class FileFormat
      Returns:
      The library version.
      See Also:
      FileFormat.getLibversion()

    • isThisType

      public boolean isThisType​(FileFormat theFile)
      Checks if the specified FileFormat instance has the HDF5 format.
      Specified by:
      isThisType in class FileFormat
      Parameters:
      theFile - The FileFormat to be checked.
      Returns:
      True if this instance implements the specified FileFormat; otherwise returns false.
      See Also:
      FileFormat.isThisType(hdf.object.FileFormat)

    • isThisType

      public boolean isThisType​(String filename)
      Checks if the specified file has the HDF5 format.
      Specified by:
      isThisType in class FileFormat
      Parameters:
      filename - The name of the file to be checked.
      Returns:
      True if the format of the file matches the format of this instance; otherwise returns false.
      See Also:
      FileFormat.isThisType(java.lang.String)

    • createFile

      public FileFormat createFile​(String filename, int createFlag) throws Exception
      Creates an HDF5 file with the specified name and returns a new H5File instance associated with the file.
      Overrides:
      createFile in class FileFormat
      Parameters:
      filename - The filename; a pathname string.
      createFlag - The creation flag, which determines behavior when the file already exists. Acceptable values are FILE_CREATE_DELETE and FILE_CREATE_OPEN.
      Returns:
      the FileFormat instance.
      Throws:
      Exception - If the file cannot be created or if createFlag has unexpected value.
      See Also:
      FileFormat.createFile(java.lang.String, int), H5File(String, int)

    • createInstance

      public FileFormat createInstance​(String filename, int access) throws Exception
      Creates an H5File instance with specified file name and access.
      Specified by:
      createInstance in class FileFormat
      Parameters:
      filename - The filename; a pathname string.
      access - The file access flag, which determines behavior when file is opened. Acceptable values are READ, WRITE, and CREATE.
      Returns:
      the FileFormat instance.
      Throws:
      Exception - If there is a failure.
      See Also:
      FileFormat.createInstance(java.lang.String, int), H5File(String, int)

    • open

      public long open() throws Exception
      Opens file and returns a file identifier.
      Specified by:
      open in class FileFormat
      Returns:
      File identifier if successful; otherwise -1.
      Throws:
      Exception - If the file cannot be opened. The exceptions thrown vary depending on the implementing class.
      See Also:
      FileFormat.open()

    • open

      public long open​(int... indexList) throws Exception
      Opens file and returns a file identifier.
      Overrides:
      open in class FileFormat
      Parameters:
      indexList - The property list is the list of parameters, like index type and the index order. The index type can be alphabetical or creation. The index order can be increasing order or decreasing order.
      Returns:
      File identifier if successful; otherwise -1.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.
      See Also:
      FileFormat.open(int...)

    • setNewLibBounds

      public void setNewLibBounds​(String lowStr, String highStr) throws Exception
      Sets the bounds of new library versions.
      Overrides:
      setNewLibBounds in class FileFormat
      Parameters:
      lowStr - The earliest version of the library.
      highStr - The latest version of the library.
      Throws:
      Exception - If there is an error at the HDF5 library level.

    • setLibBounds

      public void setLibBounds​(String lowStr, String highStr) throws Exception
      Sets the bounds of library versions.
      Overrides:
      setLibBounds in class FileFormat
      Parameters:
      lowStr - The earliest version of the library.
      highStr - The latest version of the library.
      Throws:
      Exception - If there is an error at the HDF5 library level.

    • getLibBounds

      public int[] getLibBounds() throws Exception
      Gets the bounds of library versions.
      Overrides:
      getLibBounds in class FileFormat
      Returns:
      libver The earliest and latest version of the library.
      Throws:
      Exception - If there is an error at the HDF5 library level.

    • getLibBoundsDescription

      public String getLibBoundsDescription()
      Gets the bounds of library versions as text.
      Overrides:
      getLibBoundsDescription in class FileFormat
      Returns:
      libversion The earliest and latest version of the library.

    • close

      public void close() throws hdf.hdf5lib.exceptions.HDF5Exception
      Closes file associated with this H5File instance.
      Specified by:
      close in class FileFormat
      Throws:
      hdf.hdf5lib.exceptions.HDF5Exception - If there is an error at the HDF5 library level.
      See Also:
      FileFormat.close()

    • getRootObject

      public HObject getRootObject()
      Returns the root object of the open HDF5 File.
      Specified by:
      getRootObject in class FileFormat
      Returns:
      The root object of the file, or null if there is no associated file or if the associated file has not yet been opened.
      See Also:
      FileFormat.getRootObject()

    • get

      public HObject get​(String path) throws Exception
      Description copied from class: FileFormat
      Gets the HObject with the specified path from the file.

      This method returns the specified object from the file associated with this FileFormat instance.

      If the specified object is a group, groups and datasets that are members of the group will be accessible via the returned HObject instance. The exact contents of the returned HObject instance depends on whether or not FileFormat.open() was called previously for this file.

      • If the file was opened prior to this method call, the complete tree of objects under the group will be accessible via the returned HObject instance.
      • If the file was not opened prior to this method call, only the members immediately under the group will be accessible via the returned HOBject instance.

      The decision to have different behaviors was made to give users some control over the "cost" of the method. In many cases, a user wants only one level of a tree, and the performance penalty for loading the entire hierarchy of objects in a large and complex file can be significant. In the case where open() has already been called, the HObject instances have already been created in memory and can be returned quickly. If open() has not been called, this method creates the HObject instances before returning the requested HObject.

      For example, say we have the following structure in our file: 

              /g0                      Group
        /g0/dataset_comp         Dataset {50, 10}
        /g0/dataset_int          Dataset {50, 10}
        /g0/g00                  Group
        /g0/g00/dataset_float    Dataset {50, 10}
        /g0/g01                  Group
        /g0/g01/dataset_string   Dataset {50, 10}
      • If open() is called before get(), the full structure of file is loaded into memory. The call get("/g0") returns the instance for /g0 with the information necessary to access /g0/dataset_comp, /g0/dataset_int, /g0/g00, /g0/g00/dataset_float, /g0/g01, and /g0/g01/dataset_string.
      • If open() is not called before get(), only the objects immediately under the specified group are accessible via the returned HObject instance. In this example, the call get("/go") returns the instance for /g0 with the information necessary to access /g0/dataset_comp, /g0/dataset_int, /g0/g00, and /g0/g01.
      Specified by:
      get in class FileFormat
      Parameters:
      path - Full path of the data object to be returned.
      Returns:
      The object if it exists in the file; otherwise null.
      Throws:
      Exception - If there are unexpected problems in trying to retrieve the object. The exceptions thrown vary depending on the implementing class.

    • createNamedDatatype

      public Datatype createNamedDatatype​(Datatype tnative, String name) throws Exception
      Creates a named datatype in a file.

      The following code creates a named datatype in a file. 

       H5File file = (H5File) h5file.createInstance("test_hdf5.h5", FileFormat.WRITE);
 Datatype dtype = file.createDatatype(
                             Datatype.CLASS_INTEGER,
                             4,
                             Datatype.NATIVE,
                             Datatype.NATIVE,
                             basetype);
 H5Datatype h5dtype = file.createNamedDatatype(
                             dtype,
                             null,
                             "Native Integer");
      Overrides:
      createNamedDatatype in class FileFormat
      Parameters:
      tnative - native datatype previously created
      name - name of the datatype to create, e.g. "Native Integer".
      Returns:
      The new datatype if successful; otherwise returns null.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.

    • createDatatype

      public Datatype createDatatype​(int tclass, int tsize, int torder, int tsign) throws Exception
      Methods related to Datatypes and HObjects in HDF5 Files. Strictly speaking, these methods aren't related to H5File and the actions could be carried out through the H5Group, H5Datatype and H5*DS classes. But, in some cases they allow a null input and expect the generated object to be of HDF5 type. So, we put them in the H5File class so that we create the proper type of HObject... H5Group for example. Here again, if there could be Implementation Class methods we'd use those. But, since we can't override class methods (they can only be shadowed in Java), these are instance methods.
      Specified by:
      createDatatype in class FileFormat
      Parameters:
      tclass - class of datatype, e.g. Datatype.CLASS_INTEGER
      tsize - size of the datatype in bytes, e.g. 4 for 32-bit integer.
      torder - order of the byte endian, e.g. Datatype.ORDER_LE.
      tsign - signed or unsigned of an integer, e.g. Datatype.SIGN_NONE.
      Returns:
      The new datatype object if successful; otherwise returns null.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.

    • createDatatype

      public Datatype createDatatype​(int tclass, int tsize, int torder, int tsign, Datatype tbase) throws Exception
      Description copied from class: FileFormat
      Creates a new datatype in memory.

      The following code creates an instance of H5Datatype in memory. 

       H5File file = (H5File) h5file.createInstance("test_hdf5.h5", FileFormat.WRITE);
 H5Datatype dtype = file.createDatatype(
                             Datatype.CLASS_INTEGER,
                             4,
                             Datatype.NATIVE,
                             Datatype.NATIVE,
                             basetype);
      Overrides:
      createDatatype in class FileFormat
      Parameters:
      tclass - class of datatype, e.g. Datatype.CLASS_INTEGER
      tsize - size of the datatype in bytes, e.g. 4 for 32-bit integer.
      torder - order of the byte endian, e.g. Datatype.ORDER_LE.
      tsign - signed or unsigned of an integer, e.g. Datatype.SIGN_NONE.
      tbase - the base datatype of the new datatype
      Returns:
      The new datatype object if successful; otherwise returns null.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.

    • createScalarDS

      public Dataset createScalarDS​(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, Object fillValue, Object data) throws Exception
      Description copied from class: FileFormat
      Creates a new dataset in a file with/without chunking/compression.

      The following example creates a 2D integer dataset of size 100X50 at the root group in an HDF5 file. 

       String name = "2D integer";
 Group pgroup = (Group) getRootObject();
 Datatype dtype = new H5Datatype(Datatype.CLASS_INTEGER, // class
         4, // size in bytes
         Datatype.ORDER_LE, // byte order
         Datatype.SIGN_NONE); // unsigned
 long[] dims = { 100, 50 };
 long[] maxdims = dims;
 long[] chunks = null; // no
 // chunking
 int gzip = 0; // no compression
 Object data = null; // no initial data values
 Dataset d = (H5File) file.createScalarDS(name, pgroup, dtype, dims, maxdims, chunks, gzip, data);
      Specified by:
      createScalarDS in class FileFormat
      Parameters:
      name - name of the new dataset, e.g. "2D integer"
      pgroup - parent group where the new dataset is created.
      type - datatype of the new dataset.
      dims - dimension sizes of the new dataset, e.g. long[] dims = {100, 50}.
      maxdims - maximum dimension sizes of the new dataset, null if maxdims is the same as dims.
      chunks - chunk sizes of the new dataset, null if no chunking.
      gzip - GZIP compression level (1 to 9), 0 or negative values if no compression.
      fillValue - default value.
      data - data written to the new dataset, null if no data is written to the new dataset.
      Returns:
      The new dataset if successful; otherwise returns null
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.

    • createCompoundDS

      public Dataset createCompoundDS​(String name, Group pgroup, long[] dims, long[] maxdims, long[] chunks, int gzip, String[] memberNames, Datatype[] memberDatatypes, int[] memberSizes, Object data) throws Exception
      Description copied from class: FileFormat
      Creates a new compound dataset in a file with/without chunking and compression.

      The following example creates a compressed 2D compound dataset with size of 100X50 in a root group. The compound dataset has two members, x and y. Member x is an interger, member y is an 1-D float array of size 10. 

       String name = "2D compound";
 Group pgroup = (Group) getRootObject();
 long[] dims = {100, 50};
 long[] chunks = {1, 50};
 int gzip = 9;
 String[] memberNames = {"x", "y"};

 Datatype[] memberDatatypes = {
     new H5Datatype(Datatype.CLASS_INTEGER, Datatype.NATIVE,
                    Datatype.NATIVE, Datatype.NATIVE)
     new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE,
                    Datatype.NATIVE, Datatype.NATIVE));

 int[] memberSizes = {1, 10};
 Object data = null; // no initial data values
 Dataset d = (H5File)file.createCompoundDS(name, pgroup, dims, null,
           chunks, gzip, memberNames, memberDatatypes, memberSizes, null);
      Overrides:
      createCompoundDS in class FileFormat
      Parameters:
      name - name of the new dataset
      pgroup - parent group where the new dataset is created.
      dims - dimension sizes of the new dataset.
      maxdims - maximum dimension sizes of the new dataset, null if maxdims is the same as dims.
      chunks - chunk sizes of the new dataset, null if no chunking.
      gzip - GZIP compression level (1 to 9), 0 or negative values if no compression.
      memberNames - names of the members.
      memberDatatypes - datatypes of the members.
      memberSizes - array sizes of the members.
      data - data written to the new dataset, null if no data is written to the new dataset.
      Returns:
      new dataset object if successful; otherwise returns null
      Throws:
      UnsupportedOperationException - If the implementing class does not support compound datasets.
      Exception - The exceptions thrown vary depending on the implementing class.

    • createImage

      public Dataset createImage​(String name, Group pgroup, Datatype type, long[] dims, long[] maxdims, long[] chunks, int gzip, int ncomp, int interlace, Object data) throws Exception
      Description copied from class: FileFormat
      Creates a new image in a file.

      The following example creates a 2D image of size 100X50 in a root group. 

       String name = "2D image";
 Group pgroup = (Group) getRootObject();
 Datatype dtype = new H5Datatype(Datatype.CLASS_INTEGER, 1, Datatype.NATIVE, Datatype.SIGN_NONE);
 long[] dims = {100, 50};
 long[] maxdims = dims;
 long[] chunks = null; // no chunking
 int gzip = 0; // no compression
 int ncomp = 3; // RGB true color image
 int interlace = ScalarDS.INTERLACE_PIXEL;
 Object data = null; // no initial data values
 Dataset d = (H5File) file.createScalarDS(name, pgroup, dtype, dims, maxdims, chunks, gzip, ncomp, interlace, data);
      Specified by:
      createImage in class FileFormat
      Parameters:
      name - name of the new image, "2D image".
      pgroup - parent group where the new image is created.
      type - datatype of the new image.
      dims - dimension sizes of the new dataset, e.g. long[] dims = {100, 50}.
      maxdims - maximum dimension sizes of the new dataset, null if maxdims is the same as dims.
      chunks - chunk sizes of the new dataset, null if no chunking.
      gzip - GZIP compression level (1 to 9), 0 or negative values if no compression.
      ncomp - number of components of the new image, e.g. int ncomp = 3; // RGB true color image.
      interlace - interlace mode of the image. Valid values are ScalarDS.INTERLACE_PIXEL, ScalarDS.INTERLACE_PLANEL and ScalarDS.INTERLACE_LINE.
      data - data value of the image, null if no data.
      Returns:
      The new image object if successful; otherwise returns null
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.

    • createGroup

      public Group createGroup​(String name, Group pgroup) throws Exception
      Creates a new group with specified name in existing group.
      Specified by:
      createGroup in class FileFormat
      Parameters:
      name - The name of the new group.
      pgroup - The parent group, or null.
      Returns:
      The new group if successful; otherwise returns null.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.
      See Also:
      FileFormat.createGroup(java.lang.String, hdf.object.Group)

    • createGroup

      public Group createGroup​(String name, Group pgroup, long... gplist) throws Exception
      Creates a new group with specified name in existing group and with the group creation properties list, gplist.
      Overrides:
      createGroup in class FileFormat
      Parameters:
      name - The name of a new group.
      pgroup - The parent group object.
      gplist - The group creation properties, in which the order of the properties conforms the HDF5 library API, H5Gcreate(), i.e. lcpl, gcpl and gapl, where
      • lcpl : Property list for link creation
      • gcpl : Property list for group creation
      • gapl : Property list for group access
      Returns:
      The new group if successful; otherwise returns null.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.
      See Also:
      H5Group.create(java.lang.String, hdf.object.Group, long...)

    • createGcpl

      public long createGcpl​(int creationorder, int maxcompact, int mindense) throws Exception
      Creates the group creation property list identifier, gcpl. This identifier is used when creating Groups.
      Overrides:
      createGcpl in class FileFormat
      Parameters:
      creationorder - The order in which the objects in a group should be created. It can be Tracked or Indexed.
      maxcompact - The maximum number of links to store in the group in a compact format.
      mindense - The minimum number of links to store in the indexed format.Groups which are in indexed format and in which the number of links falls below this threshold are automatically converted to compact format.
      Returns:
      The gcpl identifier.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.
      See Also:
      FileFormat.createGcpl(int, int, int)

    • createLink

      public HObject createLink​(Group parentGroup, String name, Object currentObj) throws Exception
      Description copied from class: FileFormat
      Creates a link to an existing object in the open file.

      If linkGroup is null, the new link is created in the root group.

      Overrides:
      createLink in class FileFormat
      Parameters:
      parentGroup - The group where the link is created.
      name - The name of the link.
      currentObj - The existing object the new link will reference.
      Returns:
      The object pointed to by the new link if successful; otherwise returns null.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.

    • createLink

      public HObject createLink​(Group parentGroup, String name, HObject currentObj, int lType) throws Exception
      Creates a link to an object in the open file.

      If parentGroup is null, the new link is created in the root group.

      Overrides:
      createLink in class FileFormat
      Parameters:
      parentGroup - The group where the link is created.
      name - The name of the link.
      currentObj - The existing object the new link will reference.
      lType - The type of link to be created. It can be a hard link, a soft link or an external link.
      Returns:
      The object pointed to by the new link if successful; otherwise returns null.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.

    • createLink

      public HObject createLink​(Group parentGroup, String name, String currentObj, int lType) throws Exception
      Creates a soft or external link to object in a file that does not exist at the time the link is created.
      Overrides:
      createLink in class FileFormat
      Parameters:
      parentGroup - The group where the link is created.
      name - The name of the link.
      currentObj - The name of the object the new link will reference. The object doesn't have to exist.
      lType - The type of link to be created.
      Returns:
      The H5Link object pointed to by the new link if successful; otherwise returns null.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.

    • reloadTree

      public void reloadTree​(Group g)
      reload the sub-tree structure from file.

      reloadTree(Group g) is useful when the structure of the group in file is changed while the group structure in memory is not changed.

      Parameters:
      g - the group where the structure is to be reloaded in memory

    • copy

      public HObject copy​(HObject srcObj, Group dstGroup, String dstName) throws Exception
      Description copied from class: FileFormat
      Copies the source object to a new destination.

      This method copies the source object to a destination group, and assigns the specified name to the new object.

      The copy may take place within a single file or across files. If the source object and destination group are in different files, the files must have the same file format (both HDF5 for example).

      The source object can be a group, a dataset, or a named datatype. This method copies the object along with all of its attributes and other properties. If the source object is a group, this method also copies all objects and sub-groups below the group.

      The following example shows how to use the copy method to create two copies of an existing HDF5 file structure in a new HDF5 file. One copy will be under /copy1 and the other under /copy2 in the new file. 

       // Open the existing file with the source object.
 H5File existingFile = new H5File("existingFile.h5", FileFormat.READ);
 existingFile.open();
 // Our source object will be the root group.
 HObject srcObj = existingFile.get("/");
 // Create a new file.
 H5File newFile = new H5File("newFile.h5", FileFormat.CREATE);
 newFile.open();
 // Both copies in the new file will have the root group as their
 // destination group.
 Group dstGroup = (Group) newFile.get("/");
 // First copy goes to "/copy1" and second goes to "/copy2".
 // Notice that we can use either H5File instance to perform the copy.
 HObject copy1 = existingFile.copy(srcObj, dstGroup, "copy1");
 HObject copy2 = newFile.copy(srcObj, dstGroup, "copy2");
 // Close both the files.
 file.close();
 newFile.close();
      Specified by:
      copy in class FileFormat
      Parameters:
      srcObj - The object to copy.
      dstGroup - The destination group for the new object.
      dstName - The name of the new object. If dstName is null, the name of srcObj will be used.
      Returns:
      The new object, or null if the copy fails.
      Throws:
      Exception - are specific to the implementing class.

    • delete

      public void delete​(HObject obj) throws Exception
      Description copied from class: FileFormat
      Deletes an object from a file.
      Specified by:
      delete in class FileFormat
      Parameters:
      obj - The object to delete.
      Throws:
      Exception - The exceptions thrown vary depending on the implementing class.

    • writeAttribute

      public void writeAttribute​(HObject obj, Attribute attr, boolean attrExisted) throws hdf.hdf5lib.exceptions.HDF5Exception
      Description copied from class: FileFormat
      Attaches a given attribute to an object.

      If an HDF(4&5) attribute exists in file, the method updates its value. If the attribute does not exist in file, it creates the attribute in file and attaches it to the object. It will fail to write a new attribute to the object where an attribute with the same name already exists. To update the value of an existing attribute in file, one needs to get the instance of the attribute by getMetadata(), change its values, and use writeAttribute() to write the value.

      Specified by:
      writeAttribute in class FileFormat
      Parameters:
      obj - The object to which the attribute is attached to.
      attr - The atribute to attach.
      attrExisted - The indicator if the given attribute exists.
      Throws:
      hdf.hdf5lib.exceptions.HDF5Exception

    • open

      public long open​(long plist) throws Exception
      Opens a file with specific file access property list.

      This function does the same as "long open()" except the you can also pass an HDF5 file access property to file open. For example, 

       // All open objects remaining in the file are closed then file is closed
 long plist = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
 H5.H5Pset_fclose_degree(plist, HDF5Constants.H5F_CLOSE_STRONG);
 long fid = open(plist);
      Parameters:
      plist - a file access property list identifier.
      Returns:
      the file identifier if successful; otherwise returns negative value.
      Throws:
      Exception - If there is a failure.

    • getLinkTargetName

      public static String getLinkTargetName​(HObject obj) throws Exception
      Retrieves the name of the target object that is being linked to.
      Parameters:
      obj - The current link object.
      Returns:
      The name of the target object.
      Throws:
      Exception - If there is an error at the HDF5 library level.

    • exportDataset

      public void exportDataset​(String file_export_name, String file_name, String object_path, int binary_order) throws Exception
      Export dataset.
      Overrides:
      exportDataset in class FileFormat
      Parameters:
      file_export_name - The file name to export data into.
      file_name - The name of the HDF5 file containing the dataset.
      object_path - The full path of the dataset to be exported.
      binary_order - The data byte order
      Throws:
      Exception - If there is a failure.

    • renameAttribute

      public void renameAttribute​(HObject obj, String oldAttrName, String newAttrName) throws Exception
      Renames an attribute.
      Overrides:
      renameAttribute in class FileFormat
      Parameters:
      obj - The object whose attribute is to be renamed.
      oldAttrName - The current name of the attribute.
      newAttrName - The new name of the attribute.
      Throws:
      Exception - If there is an error at the HDF5 library level.

    • renameObject

      public static void renameObject​(HObject obj, String newName) throws Exception
      Rename the given object
      Parameters:
      obj - the object to be renamed.
      newName - the new name of the object.
      Throws:
      Exception - If there is a failure.

    • renameObject

      public static void renameObject​(HObject obj, String newPath, String newName) throws Exception
      Rename the given object
      Parameters:
      obj - the object to be renamed.
      newPath - the new path of the object.
      newName - the new name of the object.
      Throws:
      Exception - If there is a failure.

    • getIndexTypeValue

      public static int getIndexTypeValue​(String strtype)

    • getIndexOrderValue

      public static int getIndexOrderValue​(String strorder)

    • getIndexType

      public int getIndexType​(String strtype)
      Overrides:
      getIndexType in class FileFormat

    • getIndexType

      public int getIndexType()

    • setIndexType

      public void setIndexType​(int indexType)
      Overrides:
      setIndexType in class FileFormat

    • getIndexOrder

      public int getIndexOrder​(String strorder)
      Overrides:
      getIndexOrder in class FileFormat

    • getIndexOrder

      public int getIndexOrder()

    • setIndexOrder

      public void setIndexOrder​(int indexOrder)
      Overrides:
      setIndexOrder in class FileFormat