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HDF5
1.15.0.fc88fcd
API Reference
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This class is the Java interface for the HDF5 library.
This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps a single HDF5 entry point, generally with the arguments and return codes analogous to the C interface.
For details of the HDF5 library,
Mapping of arguments for Java
In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF5 Reference Manual.
HDF5 | Java |
H5T_NATIVE_INT | int, Integer |
H5T_NATIVE_SHORT | short, Short |
H5T_NATIVE_FLOAT | float, Float |
H5T_NATIVE_DOUBLE | double, Double |
H5T_NATIVE_CHAR | byte, Byte |
H5T_C_S1 | java.lang.String |
void * (i.e., pointer to ‘Any’) | Special – see Java Array Conversion |
General Rules for Passing Arguments and Results
In general, arguments passed IN to Java are the analogous basic types, as above. The exception is for arrays, which are discussed below.
The return value of Java methods is also the analogous type, as above. A major exception to that rule is that all HDF Java functions will raise an exception upon failure in the Java version, rather than just return int as in the C. Functions that return a value are declared equivalent to the C function. However, in most cases the Java method will raise an exception instead of returning an error code.
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. Where possible the Java function may return the OUT parameter as an object or basic type.
For instance, a function that returns two integers declared as:
h_err_t HDF5dummy( int *a1, int *a2)
For the Java interface, this would be declared:
public synchronized static native int HDF5dummy(int args[]);
OR
public synchronized static native int[] HDF5dummy();
where a1 is args[0] and a2 is args[1], and would be invoked:
H5.HDF5dummy(a);
OR
a = H5.HDF5dummy();
All the routines where this convention is used will have specific documentation of the details, given below.
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,
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 ondisk (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 Java Array Conversion 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:
and the parameter data can be any multi-dimensional array of numbers, such as float[][], or int[][][], or Double[][].
Constants and Enumerated Types
The HDF5 API defines a set of constants and enumerated values. Most of these values are available to Java programs via the class Constants and Enumerated Types 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 HDFConstants class looks up the values when initiated. The values can be accessed as public variables of the Java class, such as:
The Java application uses both types of constants the same way, the only difference is that the HDFConstants may have different values on different platforms.
The HDF5 error API (Error Handling (H5E)) manages the behavior of the error stack in the HDF5 library. This API is omitted 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 Errors and Exceptions HDF5Exception. There are two subclasses of HDF5Exception, HDF5 Library Errors and Exceptions HDF5LibraryException and Java Wrapper Errors and Exceptions 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 H5Eprint(). This may be used by Java exception handlers to print out the HDF5 error stack.
For details of the HDF5 library,