hdf.hdf5lib (JavaCPP Presets for HDF5 1.14.3-1.5.10 API)

Class Summary
Class Description

H5
This class is the Java interface for the HDF5 library.

HDF5Constants

HDFArray

HDFNativeData
Class Summary
Class	Description
H5	This class is the Java interface for the HDF5 library.
HDF5Constants
HDFArray
HDFNativeData
See Also:
ERRORS.
 
 Java does not support pass by reference of arguments, so arguments that are returned through OUT
 parameters
 must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in arrays.
 

 For instance, a function that returns two integers is declared:

 
       h_err_t HDF5dummy( int *a1, int *a2)
 

 For the Java interface, this would be declared:

  public synchronized static native void HDF5dummy(int args[]);
 

 where a1 is args[0] and a2 is args[1], and would be invoked:

  H5.HDF5dummy(a);
 

 
 All the routines where this convention is used will have specific documentation of the details, given
 below.
 

 Arrays
 

 HDF5 needs to read and write multi-dimensional arrays of any number type (and records). The HDF5 API
 describes the
 layout of the source and destination, and the data for the array passed as a block of bytes, for instance,

 
      herr_t H5Dread(long fid, long filetype, long memtype, long memspace, void *data);
 

 
 where ``void *'' means that the data may be any valid numeric type, and is a contiguous block of bytes that
 is the
 data for a multi-dimensional array. The other parameters describe the dimensions, rank, and datatype of the
 array on
 disk (source) and in memory (destination).
 

 For Java, this ``ANY'' is a problem, as the type of data must always be declared. Furthermore,
 multidimensional
 arrays are definitely not laid out contiguously in memory. It would be infeasible to declare a
 separate
 routine for every combination of number type and dimensionality. For that reason, the
  HDFArray class is used to discover the type, shape, and
 size of the
 data array at run time, and to convert to and from a contiguous array of bytes in synchronized static
 native C order.
 

 The upshot is that any Java array of numbers (either primitive or sub-classes of type Number) can be
 passed as
 an ``Object'', and the Java API will translate to and from the appropriate packed array of bytes needed by
 the C
 library. So the function above would be declared:

 
 public synchronized static native int H5Dread(long fid, long filetype, long memtype, long memspace, Object
 data);
 
            OPEN_IDS.addElement(id);

 and the parameter data can be any multi-dimensional array of numbers, such as float[][], or
 int[][][], or
 Double[][].
 
 HDF5 Constants
 

 The HDF5 API defines a set of constants and enumerated values. Most of these values are available to Java
 programs
 via the class  HDF5Constants. For example, the
 parameters for
 the h5open() call include two numeric values, HDFConstants.H5F_ACC_RDWR and
 HDF5Constants.H5P_DEFAULT. As would be expected, these numbers correspond to the C constants
 H5F_ACC_RDWR and H5P_DEFAULT.
 

 The HDF5 API defines a set of values that describe number types and sizes, such as "H5T_NATIVE_INT" and
 "hsize_t".
 These values are determined at run time by the HDF5 C library. To support these parameters, the Java class
  HDF5CDataTypes looks up the values when initiated.
 The values
 can be accessed as public variables of the Java class, such as:

 
 long data_type = HDF5CDataTypes.JH5T_NATIVE_INT;
 

 The Java application uses both types of constants the same way, the only difference is that the
 HDF5CDataTypes may have different values on different platforms.
 
 Error handling and Exceptions
 

 The HDF5 error API (H5E) manages the behavior of the error stack in the HDF5 library. This API is
 available from the
 JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is
 very natural
 for Java programming.
 

 The exceptions of the JHI5 are organized as sub-classes of the class
  HDF5Exception. There are two subclasses
 of
 HDF5Exception, @ref ERRORSLIB HDF5LibraryException
 and @ref ERRORSJAVA HDF5JavaException.
 The sub-classes of the former represent errors from the HDF5 C library,
 while sub-classes of the latter represent errors in the JHI5 wrapper and support code.
 

 The super-class HDF5LibraryException implements the method
 'printStackTrace()', which prints out the HDF5 error stack, as described
  in the HDF5 C API @ref H5Eprint(). This may be
 used by Java
 exception handlers to print out the HDF5 error stack.
Package hdf.hdf5lib
