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Java HDF5 Interface (JHI5)

JHI5 Design Notes

Important Changes

Very Important Change: Version 3.0 (and above) of the JHI5 packages all HDF library
calls as "hdf.hd5flib", note that the "ncsa" has been removed.
Source code which used earlier versions of the JHI5 should be changed to
reflect this new implementation.

What it is

The Java HD5 Interface (JHI5) is a Java package (hdf.hdf5lib) that ``wraps around'' the HDF5 library.

There are over 460 functions in the HDF5 library (version 1.8). Ninety three of the functions are not supported in JHI5. Most of the unsupported functions have C function pointers, which is not currently implemented in JHI5. For a complete list of unsupported functions, please see unsupported functions.

Note: The JHI5 does not support HDF4 or earlier.  See the JHI.

The JHI5 may be used by any Java application that needs to access HDF5 files. It is extremely important to emphasize that this package is not a pure Java implementation of the HDF-5 library. The JHI5 calls the same HDF5 library that is used by C or FORTRAN programs. (Note that this product cannot be used in most network browsers because it accesses the local disk using native code.)

The Java HDF5 Interface consists of Java classes and a dynamically linked native library. The Java classes declare native methods, and the library contains C functions which implement the native methods. The C functions call the standard HDF5 library, which is linked as part of the same library on most platforms.

The central part of the JHI5 is the Java class hdf.hdf5lib.H5. The H5 class calls the standard (i.e., `native' code) HDF5 library, with native methods for most of the HDF5 functions.

How to use it

The JHI5 is used by Java classes to call the HDF5 library, in order to create HDF5 files, and read and write data in existing HDF5 files.

For example, the HDF5 library has the function H5Fopen to open an HDF5 file. The Java interface is the class hdf.hdf5lib.H5, which has a method:

static native int H5Fopen(String filename, int flags, int access );
The native method is implemented in C using the Java Native Method Interface (JNI). This is written something like the following:
JNIEXPORT jint
JNICALL Java_hdf_hdf5lib_H5_H5Fopen
( JNIEnv *env, jclass class, jstring hdfFile, jint flags, jint access)
 {

 /* ...convert Java String to (char *) */

 /* call the HDF library */
 retVal = H5Fopen((char *)file, (unsigned)flags, (hid_t)access );

 /* ... */
}
This C function calls the HDF5 library and returns the result appropriately.

There is one native method for each HDF entry point (several hundred in all), which are compiled with the HDF library into a dynamically loaded library (libjhdf5). Note that this library must be built for each platform.

To call the HDF `H5Fopen' function, a Java program would import the package 'hdf.hdf5lib.*', and invoke the method on the class 'H5'. The Java program would look something like this:

import hdf.hdf5lib.*;

{
 /* ... */

 try {
 file = H5.Hopen("myFile.hdf", flags, access );
 } catch (HDF5Exception ex) {
 //...
 }

 /* ... */
}
The H5 class automatically loads the native method implementations and the HDF-5 library.

To Obtain

The JHI5 is included with the HDF-Java Products.
- - Last modified: 25 July 2017