* 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, see the HDF5 Documentation at: http://hdfgroup.org/HDF5/ *
* Mapping of arguments for Java * *
* In general, arguments to the HDF Java API are straightforward translations * from the 'C' API described in the HDF Reference Manual. *
* *
| HDF-5 | *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 HDFArray | *
*
* 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 functions that return * SUCCEED/FAIL are declared boolean in the Java version, rather than * int as in the C. Functions that return a value or else FAIL are * declared the equivalent to the C function. However, in most cases the Java * method will raise an exception instead of returning an error code. See Errors and Exceptions below. *
* 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 int 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(int fid, int filetype, int memtype, int 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 * layed 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(int fid, int filetype, * int memtype, int memspace, Object data); ** * and the parameter data can be any multi-dimensional array of numbers, * such as float[][], or int[][][], or Double[][]. *
* HDF-5 Constants
*
* The HDF-5 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 HDF-5 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 HDF-5 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:
*
*
* Error handling and Exceptions
*
* The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5
* 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
* HDF5Exception. There are two subclasses of HDF5Exception,
*
* HDF5LibraryException and
* HDF5JavaException. The sub-classes of the former represent errors
* from the HDF-5 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 HDF-5 error stack, as
* described in the HDF-5 C API H5Eprint(). This may be used by
* Java exception handlers to print out the HDF-5 error stack.
*
* This is called by the static initializer, so this should never need to be
* explicitly called by a Java program.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
private synchronized static native int H5dont_atexit()
throws HDF5LibraryException;
/**
* Turn off error handling By default, the C library prints the error stack
* of the HDF-5 C library on stdout. This behavior may be disabled by
* calling H5error_off().
*/
public synchronized static native int H5error_off();
/**
* H5garbage_collect collects on all free-lists of all types.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5garbage_collect()
throws HDF5LibraryException;
/**
* H5get_libversion retrieves the major, minor, and release numbers of the
* version of the HDF library which is linked to the application.
*
* @param libversion
* The version information of the HDF library.
*
*
* This may be used by exception handlers to assure that the error condition
* in the HDF-5 library has been reset.
*
* @return Returns a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Eclear() throws HDF5LibraryException
{
H5Eclear2(HDF5Constants.H5E_DEFAULT);
return 0;
}
/**
* H5Eclear clears the error stack specified by estack_id, or, if estack_id
* is set to H5E_DEFAULT, the error stack for the current thread.
*
* @param stack_id
* IN: Error stack identifier.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static void H5Eclear(int err_stack) throws HDF5LibraryException
{
H5Eclear2(err_stack);
}
/**
* H5Eclear2 clears the error stack specified by estack_id, or, if estack_id
* is set to H5E_DEFAULT, the error stack for the current thread.
*
* @see public static void H5Eclear(int err_stack)
**/
public synchronized static native void H5Eclear2(int err_stack)
throws HDF5LibraryException;
/**
* H5Eclose_msg closes an error message identifier, which can be either a
* major or minor message.
*
* @param err_id
* IN: Error message identifier.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Eclose_msg(int err_id)
throws HDF5LibraryException;
/**
* H5Eclose_stack closes the object handle for an error stack and releases
* its resources.
*
* @param stack_id
* IN: Error stack identifier.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Eclose_stack(int stack_id)
throws HDF5LibraryException;
/**
* H5Ecreate_msg adds an error message to an error class defined by client
* library or application program.
*
* @param cls_id
* IN: Error class identifier.
* @param msg_type
* IN: The type of the error message.
* @param msg
* IN: The error message.
*
* @return a message identifier
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - msg is null.
**/
public synchronized static native int H5Ecreate_msg(int cls_id,
int msg_type, String msg)
throws HDF5LibraryException, NullPointerException;
/**
* H5Ecreate_stack creates a new empty error stack and returns the new
* stack's identifier.
*
* @param none
*
* @return an error stack identifier
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Ecreate_stack()
throws HDF5LibraryException;
//int H5Eget_auto(H5E_auto1_t func, PointerByReference client_data);
//{
//return H5Eget_auto1(func, client_data);
//}
//int H5Eget_auto1(H5E_auto1_t func, PointerByReference client_data);
//int H5Eset_auto(H5E_auto1_t func, Pointer client_data);
//{
//return H5Eset_auto1(func, client_data);
//}
//int H5Eset_auto1(H5E_auto1_t func, Pointer client_data);
/**
* H5Eget_class_name retrieves the name of the error class specified by the
* class identifier.
*
* @param class_id
* IN: Error class identifier.
*
* @return the name of the error class
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native String H5Eget_class_name(int class_id)
throws HDF5LibraryException, NullPointerException;
// long H5Eget_class_name(int class_id, String name, IntegerType size);
/**
* H5Eget_current_stack copies the current error stack and returns an error
* stack identifier for the new copy.
*
* @param none
*
* @return an error stack identifier
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Eget_current_stack()
throws HDF5LibraryException;
/**
* H5Eset_current_stack replaces the content of the current error stack with
* a copy of the content of the error stack specified by estack_id.
*
* @param stack_id
* IN: Error stack identifier.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Eset_current_stack(int stack_id)
throws HDF5LibraryException;
/**
* H5Eget_msg retrieves the error message including its length and type.
*
* @param msg_id
* IN: Name of the error class.
* @param type
* OUT: The type of the error message. Valid values are H5E_MAJOR
* and H5E_MINOR.
*
* @return the error message
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native String H5Eget_msg(int msg_id,
int[] type_list) throws HDF5LibraryException;
// long H5Eget_msg(int msg_id, H5E_TYPE type, String msg, IntegerType size);
//
///**
//* H5Eget_major returns a string that describes the error.
//*
//* @deprecated As of HDF5 1.8
//*
//* @param major IN: Major error number.
//*
//* @return string describing the error
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//**/
//public synchronized static native String H5Eget_major(int major)
//throws HDF5LibraryException;
//
///**
//* H5Eget_minor returns a string that describes the error.
//*
//* @deprecated As of HDF5 1.8
//*
//* @param minor IN: Error stack identifier.
//*
//* @return string describing the error
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//**/
//public synchronized static native String H5Eget_minor(int minor)
//throws HDF5LibraryException;
/**
* H5Eget_num retrieves the number of error records in the error stack
* specified by estack_id (including major, minor messages and description).
*
* @param stack_id
* IN: Error stack identifier.
*
* @return the number of error messages
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native long H5Eget_num(int stack_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Eprint1 prints the error stack specified by estack_id on the specified
* stream, stream.
*
* @param stream
* IN: File pointer, or stderr if null.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Eprint2(int, Object)}
**/
@Deprecated
public synchronized static native void H5Eprint1(Object stream)
throws HDF5LibraryException;
/**
* H5Eprint2 prints the error stack specified by estack_id on the specified
* stream, stream.
*
* @param stack_id
* IN: Error stack identifier.If the identifier is H5E_DEFAULT,
* the current error stack will be printed.
* @param stream
* IN: File pointer, or stderr if null.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Eprint2(int err_stack,
Object stream) throws HDF5LibraryException;
//public static int H5Epush(String file, String func, int line,
//int maj_id, int min_id, String msg)
//{
//H5Epush1(file, func, line, maj_id, min_id, msg);
//}
//private synchronized static native int H5Epush1(String file, String func,
//int line,
//int maj_id, int min_id, String msg);
//public static int H5Epush(int err_stack, String file, String func, int
//line,
//int cls_id, int maj_id, int min_id, String msg, ...)
//{
//H5Epush2(err_stack, file, func, line, cls_id, maj_id, min_id, msg, ...);
//}
//public synchronized static native int H5Epush2(int err_stack, String
//file, String func, int line,
//int cls_id, int maj_id, int min_id, String msg, ...);
/**
* H5Epop deletes the number of error records specified in count from the
* top of the error stack specified by estack_id (including major, minor
* messages and description).
*
* @param stack_id
* IN: Error stack identifier.
* @param count
* IN: Version of the client library or application to which the
* error class belongs.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Epop(int stack_id, long count)
throws HDF5LibraryException;
/**
* H5Eregister_class registers a client library or application program to
* the HDF5 error API so that the client library or application program can
* report errors together with HDF5 library.
*
* @param cls_name
* IN: Name of the error class.
* @param lib_name
* IN: Name of the client library or application to which the
* error class belongs.
* @param version
* IN: Version of the client library or application to which the
* error class belongs.
*
* @return a class identifier
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native int H5Eregister_class(String cls_name,
String lib_name, String version)
throws HDF5LibraryException, NullPointerException;
/**
* H5Eunregister_class removes the error class specified by class_id.
*
* @param class_id
* IN: Error class identifier.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Eunregister_class(int class_id)
throws HDF5LibraryException;
//
//int H5Ewalk(H5E_direction_t direction, H5E_walk1_t func,
//Pointer client_data)
//{
//return H5Ewalk1(direction, func, client_data);
//}
//int H5Ewalk1(H5E_direction_t direction, H5E_walk1_t func,
//Pointer client_data);
////Error stack traversal callback function pointers
//public interface H5E_walk2_t extends Callback
//{
//int callback(int n, H5E_error2_t err_desc, Pointer client_data);
//}
//public interface H5E_auto2_t extends Callback
//{
//int callback(int estack, Pointer client_data);
//}
//int H5Ewalk(int err_stack, H5E_direction_t direction, H5E_walk2_t func,
//Pointer client_data)
//{
//return H5Ewalk2(err_stack, direction, func, client_data);
//}
//int H5Ewalk2(int err_stack, H5E_direction_t direction, H5E_walk2_t func,
//Pointer client_data);
//int H5Eget_auto(int estack_id, H5E_auto2_t func, PointerByReference
//client_data);
//{
//return H5Eget_auto2(estack_id, func, client_data);
//}
//int H5Eget_auto2(int estack_id, H5E_auto2_t func, PointerByReference
//client_data);
//int H5Eset_auto(int estack_id, H5E_auto2_t func, Pointer client_data);
//{
//return H5Eset_auto2(estack_id, func, client_data);
//}
//int H5Eset_auto2(int estack_id, H5E_auto2_t func, Pointer client_data);
//////////////////////////////////////////////////////////////
////
//H5F: File Interface Functions //
////
//////////////////////////////////////////////////////////////
/**
* H5Fclose terminates access to an HDF5 file.
*
* @param file_id
* Identifier of a file to terminate access to.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Fclose(int file_id) throws HDF5LibraryException
{
if (file_id <0)
throw new HDF5LibraryException("Negative ID");;
OPEN_IDS.removeElement(file_id);
return _H5Fclose(file_id);
}
private synchronized static native int _H5Fclose(int file_id)
throws HDF5LibraryException;
/**
* H5Fopen opens an existing file and is the primary function for accessing
* existing HDF5 files.
*
* @param name
* Name of the file to access.
* @param flags
* File access flags.
* @param access_id
* Identifier for the file access properties list.
*
* @return a file identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public static int H5Fopen(String name, int flags, int access_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Fopen(name, flags, access_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Fopen(String name, int flags,
int access_id) throws HDF5LibraryException, NullPointerException;
/**
* H5Freopen reopens an HDF5 file.
*
* @param file_id
* Identifier of a file to terminate and reopen access to.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @return a new file identifier if successful
**/
public static int H5Freopen(int file_id) throws HDF5LibraryException
{
int id = _H5Freopen(file_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Freopen(int file_id)
throws HDF5LibraryException;
/**
* H5Fcreate is the primary function for creating HDF5 files.
*
* @param name
* Name of the file to access.
* @param flags
* File access flags. Possible values include:
*
* After this call completes, the file (or object) is in a consistent state
* and all data written to date is assured to be permanent.
*
* @param object_id
* Identifier of object used to identify the file.
* object_id can be any object associated with the file,
* including the file itself, a dataset, a group, an attribute,
* or a named data type.
* @param scope
* specifies the scope of the flushing action, in the case that
* the HDF-5 file is not a single physical file.
*
* Valid values are:
*
* Note: this routine changed name with HDF5.1.2.2. If using an earlier
* version, use 'configure --enable-hdf5_1_2_1' so this routine will link to
* the old name.
*
* @param fapl_id
* IN File access property list
* @param gc_ref
* OUT GC is on (true) or off (false)
*
* @return non-negative if succeed
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - array is null.
**/
public synchronized static native int H5Pget_gc_references(int fapl_id,
boolean[] gc_ref) throws HDF5LibraryException, NullPointerException;
public synchronized static native boolean H5Pget_gcreferences(int fapl_id)
throws HDF5LibraryException;
/*
* Earlier versions of the HDF5 library had a different name. This is
* included as an alias.
*/
public synchronized static int H5Pget_gc_reference(int fapl_id,
boolean[] gc_ref) throws HDF5LibraryException, NullPointerException
{
return H5Pget_gc_references(fapl_id, gc_ref);
}
/**
* H5Pset_gc_references Sets the flag for garbage collecting references for
* the file. Default value for garbage collecting references is off.
*
* @param fapl_id
* IN File access property list
* @param gc_ref
* IN set GC on (true) or off (false)
*
* @return non-negative if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_gc_references(int fapl_id,
boolean gc_ref) throws HDF5LibraryException;
public synchronized static native int H5Pget_hyper_vector_size(int dxpl_id,
long[] vector_size)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_hyper_vector_size(int dxpl_id,
long vector_size) throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_istore_k queries the 1/2 rank of an indexed storage B-tree.
*
* @param plist
* IN: Identifier of property list to query.
* @param ik
* OUT: Pointer to location to return the chunked storage B-tree
* 1/2 rank.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - ik array is null.
**/
public synchronized static native int H5Pget_istore_k(int plist, int[] ik)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_istore_k sets the size of the parameter used to control the
* B-trees for indexing chunked datasets.
*
* @param plist
* IN: Identifier of property list to query.
* @param ik
* IN: 1/2 rank of chunked storage B-tree.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_istore_k(int plist, int ik)
throws HDF5LibraryException;
/**
* H5Pget_layout returns the layout of the raw data for a dataset.
*
* @param plist
* IN: Identifier for property list to query.
*
* @return the layout type of a dataset creation property list if
* successful. Otherwise returns H5D_LAYOUT_ERROR (-1).
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pget_layout(int plist)
throws HDF5LibraryException;
/**
* H5Pset_layout sets the type of storage used store the raw data for a
* dataset.
*
* @param plist
* IN: Identifier of property list to query.
* @param layout
* IN: Type of storage layout for raw data.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_layout(int plist, int layout)
throws HDF5LibraryException;
/**
* H5Pget_libver_bounds retrieves the lower and upper bounds on the HDF5 Library versions that indirectly determine the object formats versions used when creating objects in the file.
* @param fapl_id IN: File access property list identifier
* @param libver
* The earliest/latest version of the library that will be used for writing objects.
*
*
* The start and end buffers must be large enough to hold the dataspace rank
* number of coordinates.
*
* @param spaceid
* Identifier of dataspace to release.
* @param start
* coordinates of lowest corner of bounding box.
* @param end
* coordinates of highest corner of bounding box.
*
* @return a non-negative value if successful,with start and end
* initialized.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - start or end is null.
**/
public synchronized static native int H5Sget_select_bounds(int spaceid,
long[] start, long[] end)
throws HDF5LibraryException, NullPointerException;
/**
* H5Sget_select_elem_npoints returns the number of element points in the
* current dataspace selection.
*
* @param spaceid
* Identifier of dataspace to release.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native long H5Sget_select_elem_npoints(
int spaceid) throws HDF5LibraryException;
/**
* H5Sget_select_elem_pointlist returns an array of of element points in the
* current dataspace selection. The point coordinates have the same
* dimensionality (rank) as the dataspace they are located within, one
* coordinate per point.
*
* @param spaceid
* Identifier of dataspace to release.
* @param startpoint
* first point to retrieve
* @param numpoints
* number of points to retrieve
* @param buf
* returns points startblock to startblock+num-1, each points is
* rank longs.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - buf is null.
**/
public synchronized static native int H5Sget_select_elem_pointlist(
int spaceid, long startpoint, long numpoints, long[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The
* block coordinates have the same dimensionality (rank) as the dataspace
* they are located within. The list of blocks is formatted as follows:
*
*
* WARNING: This call only affects the C-data, even if it succeeds,
* there may be no visible effect on Java objects.
*
* @param type_id IN: Identifier of datatype to modify.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tpack(int type_id)
throws HDF5LibraryException;
//public synchronized static native int H5Tregister(H5T_pers_t pers, String name, int src_id, int dst_id,
//H5T_conv_t func)
//throws HDF5LibraryException, NullPointerException;
//
//public synchronized static native int H5Tunregister(H5T_pers_t pers, String name, int src_id, int dst_id,
//H5T_conv_t func)
//throws HDF5LibraryException, NullPointerException;
/**
* H5Tvlen_create creates a new variable-length (VL) dataype.
*
* @param base_id IN: Identifier of parent datatype.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Tvlen_create(int base_id) throws HDF5LibraryException
{
int id = _H5Tvlen_create(base_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Tvlen_create(int base_id)
throws HDF5LibraryException;
//////////////////////////////////////////////////////////////
////
//H5Z: Filter Interface Functions //
////
//////////////////////////////////////////////////////////////
public synchronized static native int H5Zfilter_avail(int filter)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Zget_filter_info(int filter)
throws HDF5LibraryException;
public synchronized static native int H5Zunregister(int filter)
throws HDF5LibraryException, NullPointerException;
}
* int 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.
*
*
* @version HDF5 1.2
* See also:
* ncsa.hdf.hdf5lib.HDFArray
*
* ncsa.hdf.hdf5lib.HDF5Constants
*
* ncsa.hdf.hdf5lib.HDF5CDataTypes
*
* ncsa.hdf.hdf5lib.HDF5Exception
*
* http://hdfgroup.org/HDF5"
**/
public class H5 implements java.io.Serializable {
/**
*
*/
private static final long serialVersionUID = 6129888282117053288L;
/**
* The version number of the HDF5 library:
* LIB_VERSION[0]: The major version of the library.
* LIB_VERSION[1]: The minor version of the library.
* LIB_VERSION[2]: The release number of the library.
*
* Make sure to update the verions number when a different library is used.
*/
public final static int LIB_VERSION[] = { 1, 8, 10 };
public final static String H5PATH_PROPERTY_KEY = "ncsa.hdf.hdf5lib.H5.hdf5lib";
// add system property to load library by name from library path, via
// System.loadLibrary()
public final static String H5_LIBRARY_NAME_PROPERTY_KEY = "ncsa.hdf.hdf5lib.H5.loadLibraryName";
/** logging level: 0 -- information, 1 -- warning message, 2 -- failure */
public static int LOGGING_LEVEL = 2;
private static Logger s_logger;
private static String s_libraryName;
private static boolean isLibraryLoaded = false;
private final static boolean IS_CRITICAL_PINNING = true;
private final static Vector
* libversion[0] = The major version of the library.
* libversion[1] = The minor version of the library.
* libversion[2] = The release number of the library.
*
* @return a non-negative value if successful, along with the version
* information.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5get_libversion(int[] libversion)
throws HDF5LibraryException;
public synchronized static native int H5set_free_list_limits(
int reg_global_lim, int reg_list_lim, int arr_global_lim,
int arr_list_lim, int blk_global_lim, int blk_list_lim)
throws HDF5LibraryException;
//////////////////////////////////////////////////////////////
////
//H5A: HDF5 1.8 Attribute Interface API Functions //
////
//////////////////////////////////////////////////////////////
/**
* H5Aclose terminates access to the attribute specified by its identifier,
* attr_id.
*
* @param attr_id
* IN: Attribute to release access to.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Aclose(int attr_id) throws HDF5LibraryException
{
if (attr_id < 0)
throw new HDF5LibraryException("Negative ID");;
OPEN_IDS.removeElement(attr_id);
return _H5Aclose(attr_id);
}
private synchronized static native int _H5Aclose(int attr_id)
throws HDF5LibraryException;
/**
* H5Acopy copies the content of one attribute to another.
*
* @param src_aid
* the identifier of the source attribute
* @param dst_aid
* the identifier of the destinaiton attribute
*/
public synchronized static native int H5Acopy(int src_aid, int dst_aid)
throws HDF5LibraryException;
/**
* H5Acreate creates an attribute which is attached to the object specified
* with loc_id.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Acreate( int, String, int, int, int, int) }
*
* @param loc_id
* IN: Object (dataset, group, or named datatype) to be attached
* to.
* @param name
* IN: Name of attribute to create.
* @param type_id
* IN: Identifier of datatype for attribute.
* @param space_id
* IN: Identifier of dataspace for attribute.
* @param create_plist
* IN: Identifier of creation property list (currently not used).
*
* @return an attribute identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
@Deprecated
public static int H5Acreate(int loc_id, String name, int type_id,
int space_id, int create_plist)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Acreate(loc_id, name, type_id, space_id, create_plist);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Acreate(int loc_id, String name,
int type_id, int space_id, int create_plist)
throws HDF5LibraryException, NullPointerException;
/**
* H5Acreate creates an attribute, attr_name, which is attached to the object specified by the identifier loc_id.
*
* @param loc_id IN: Location or object identifier; may be dataset or group
* @param attr_name IN: Attribute name
* @param type_id IN: Attribute datatype identifier
* @param space_id IN: Attribute dataspace identifier
* @param acpl_id IN: Attribute creation property list identifier
* @param aapl_id IN: Attribute access property list identifier
*
* @return An attribute identifier if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - Name is null.
**/
public static int H5Acreate( int loc_id, String attr_name, int type_id, int space_id, int acpl_id, int aapl_id )
throws HDF5LibraryException, NullPointerException
{
int id = _H5Acreate2(loc_id, attr_name, type_id, space_id, acpl_id, aapl_id );
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
/**
* H5Acreate2 an attribute, attr_name, which is attached to the object
* specified by the identifier loc_id.
*
* @see public static int H5Acreate( int loc_id, String attr_name, int
* type_id, int space_id, int acpl_id, int aapl_id )
**/
private synchronized static native int _H5Acreate2( int loc_id, String attr_name, int type_id, int space_id, int acpl_id, int aapl_id )
throws HDF5LibraryException, NullPointerException;
/**
* H5Acreate_by_name creates an attribute, attr_name, which is attached to the object specified by loc_id and obj_name.
*
* @param loc_id IN: Location or object identifier; may be dataset or group
* @param obj_name IN: Name, relative to loc_id, of object that attribute is to be attached to
* @param attr_name IN: Attribute name
* @param type_id IN: Attribute datatype identifier
* @param space_id IN: Attribute dataspace identifier
* @param acpl_id IN: Attribute creation property list identifier (currently not used).
* @param aapl_id IN: Attribute access property list identifier (currently not used).
* @param lapl_id IN: Link access property list
*
* @return An attribute identifier if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public static int H5Acreate_by_name(int loc_id, String obj_name, String attr_name, int type_id, int space_id, int acpl_id, int aapl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Acreate_by_name(loc_id, obj_name, attr_name, type_id, space_id, acpl_id, aapl_id, lapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Acreate_by_name(int loc_id, String obj_name, String attr_name, int type_id, int space_id,
int acpl_id, int aapl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Adelete removes the attribute specified by its name, name, from a
* dataset, group, or named datatype.
*
* @param loc_id
* IN: Identifier of the dataset, group, or named datatype.
* @param name
* IN: Name of the attribute to delete.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native int H5Adelete(int loc_id, String name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Adelete_by_idx removes an attribute, specified by its location in an index, from an object.
*
* @param loc_id IN: Location or object identifier; may be dataset or group
* @param obj_name IN: Name of object, relative to location, from which attribute is to be removed
* @param idx_type IN: Type of index
* @param order IN: Order in which to iterate over index
* @param n IN: Offset within index
* @param lapl_id IN: Link access property list identifier
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - obj_name is null.
**/
public synchronized static native void H5Adelete_by_idx(int loc_id, String obj_name, int idx_type, int order, long n, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Adelete_by_name removes the attribute attr_name from an object specified by location and name, loc_id and obj_name, respectively.
*
* @param loc_id IN: Location or object identifier; may be dataset or group
* @param obj_name IN: Name of object, relative to location, from which attribute is to be removed
* @param attr_name IN: Name of attribute to delete
* @param lapl_id IN: Link access property list identifier.
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native int H5Adelete_by_name(int loc_id, String obj_name, String attr_name, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Aexists determines whether the attribute attr_name exists on the object specified by obj_id.
*
* @param obj_id IN: Object identifier.
* @param attr_name IN: Name of the attribute.
*
* @return boolean true if an attribute with a given name exists.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - attr_name is null.
**/
public synchronized static native boolean H5Aexists(int obj_id, String attr_name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Aexists_by_name determines whether the attribute attr_name exists on an object. That object is specified by its location and name,
* loc_id and obj_name, respectively.
*
* @param loc_id IN: Location of object to which attribute is attached .
* @param obj_name IN: Name, relative to loc_id, of object that attribute is attached to.
* @param attr_name IN: Name of attribute.
* @param lapl_id IN: Link access property list identifier.
*
* @return boolean true if an attribute with a given name exists, otherwise returns false.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native boolean H5Aexists_by_name(int obj_id, String obj_name, String attr_name, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Aget_info retrieves attribute information, by attribute identifier.
*
* @param attr_id IN: Attribute identifier
*
* @return A buffer(H5A_info_t) for Attribute information
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native H5A_info_t H5Aget_info(int attr_id)
throws HDF5LibraryException;
/**
* H5Aget_info_by_idx Retrieves attribute information, by attribute index position.
*
* @param loc_id IN: Location of object to which attribute is attached
* @param obj_name IN: Name of object to which attribute is attached, relative to location
* @param idx_type IN: Type of index
* @param order IN: Index traversal order
* @param n IN: Attribute's position in index
* @param lapl_id IN: Link access property list
*
* @return A buffer(H5A_info_t) for Attribute information
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - obj_name is null.
**/
public synchronized static native H5A_info_t H5Aget_info_by_idx(int loc_id, String obj_name, int idx_type, int order, long n, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Aget_info_by_name Retrieves attribute information, by attribute name.
*
* @param loc_id IN: Location of object to which attribute is attached
* @param obj_name IN: Name of object to which attribute is attached, relative to location
* @param attr_name IN: Attribute name
* @param lapl_id IN: Link access property list
*
* @return A buffer(H5A_info_t) for Attribute information
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - obj_name is null.
**/
public synchronized static native H5A_info_t H5Aget_info_by_name(int loc_id, String obj_name, String attr_name, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Aget_name retrieves the name of an attribute specified by the
* identifier, attr_id.
*
* @param attr_id
* IN: Identifier of the attribute.
* @param buf_size
* IN: The size of the buffer to store the name in.
* @param name
* OUT: Buffer to store name in.
*
* @exception ArrayIndexOutOfBoundsException
* JNI error writing back array
* @exception ArrayStoreException
* JNI error writing back array
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
* @exception IllegalArgumentException
* - bub_size <= 0.
*
* @return the length of the attribute's name if successful.
**/
public synchronized static native long H5Aget_name(int attr_id,
long buf_size, String[] name)
throws ArrayIndexOutOfBoundsException, ArrayStoreException,
HDF5LibraryException, NullPointerException,
IllegalArgumentException;
public static long H5Aget_name(int attr_id, String[] name)
throws ArrayIndexOutOfBoundsException, ArrayStoreException,
HDF5LibraryException, NullPointerException,
IllegalArgumentException
{
long len = H5Aget_name(attr_id, 0, null);
return H5Aget_name(attr_id, len+1, name);
}
/**
* H5Aget_name_by_idx retrieves the name of an attribute that is attached to an object, which is specified by its location and name,
* loc_id and obj_name, respectively.
*
* @param attr_id IN: Attribute identifier
* @param obj_name IN: Name of object to which attribute is attached, relative to location
* @param idx_type IN: Type of index
* @param order IN: Index traversal order
* @param n IN: Attribute's position in index
* @param lapl_id IN: Link access property list
*
* @return String for Attribute name.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - obj_name is null.
**/
public synchronized static native String H5Aget_name_by_idx(int loc_id, String obj_name, int idx_type, int order, long n, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Aget_num_attrs returns the number of attributes attached to the object
* specified by its identifier, loc_id.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Oget_info( int )}
*
* @param loc_id
* IN: Identifier of a group, dataset, or named datatype.
*
* @return the number of attributes if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
@Deprecated
public synchronized static native int H5Aget_num_attrs(int loc_id)
throws HDF5LibraryException;
/**
* H5Aget_space retrieves a copy of the dataspace for an attribute.
*
* @param attr_id
* IN: Identifier of an attribute.
*
* @return attribute dataspace identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Aget_space(int attr_id) throws HDF5LibraryException
{
int id = _H5Aget_space(attr_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Aget_space(int attr_id)
throws HDF5LibraryException;
/**
* H5Aget_storage_size returns the amount of storage that is required for the specified attribute, attr_id.
*
* @param attr_id IN: Identifier of the attribute to query.
*
* @return the amount of storage size allocated for the attribute; otherwise returns 0 (zero)
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native long H5Aget_storage_size(int attr_id)
throws HDF5LibraryException;
/**
* H5Aget_type retrieves a copy of the datatype for an attribute.
*
* @param attr_id
* IN: Identifier of an attribute.
*
* @return a datatype identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Aget_type(int attr_id) throws HDF5LibraryException
{
int id = _H5Aget_type(attr_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Aget_type(int attr_id)
throws HDF5LibraryException;
/**
* H5Aopen opens an existing attribute, attr_name, that is attached to an object specified an object identifier, object_id.
*
* @param obj_id IN: Identifer for object to which attribute is attached
* @param attr_name IN: Name of attribute to open
* @param aapl_id IN: Attribute access property list identifier
*
* @return An attribute identifier if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - Name is null.
**/
public static int H5Aopen(int obj_id, String attr_name, int aapl_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Aopen(obj_id, attr_name, aapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Aopen(int obj_id, String attr_name, int aapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Aopen_by_idx opens an existing attribute that is attached to an object specified by location and name, loc_id and obj_name, respectively
*
* @param loc_id IN: Location of object to which attribute is attached
* @param obj_name IN: Name of object to which attribute is attached, relative to location
* @param idx_type IN: Type of index
* @param order IN: Index traversal order
* @param n IN: Attribute's position in index
* @param aapl_id IN: Attribute access property list
* @param lapl_id IN: Link access property list
*
* @return An attribute identifier if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - Name is null.
**/
public static int H5Aopen_by_idx(int loc_id, String obj_name, int idx_type, int order ,long n, int aapl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Aopen_by_idx(loc_id, obj_name, idx_type, order , n, aapl_id, lapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Aopen_by_idx(int loc_id, String obj_name, int idx_type, int order ,long n, int aapl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Aopen_by_name Opens an attribute for an object by object name and attribute name
*
* @param loc_id IN: Location from which to find object to which attribute is attached
* @param obj_name IN: Name of object to which attribute is attached, relative to loc_id
* @param attr_name IN: Name of attribute to open
* @param aapl_id IN: Attribute access property list
* @param lapl_id IN: Link access property list identifier
*
* @return Returns an attribute identifier if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - obj_name is null.
**/
public static int H5Aopen_by_name(int loc_id, String obj_name, String attr_name, int aapl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Aopen_by_name(loc_id, obj_name, attr_name, aapl_id, lapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
/**
* H5Aopen_idx opens an attribute which is attached to the object specified
* with loc_id. The location object may be either a group, dataset, or named
* datatype, all of which may have any sort of attribute.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Aopen_by_idx(int, String, int, int, long, int, int) }
*
* @param loc_id
* IN: Identifier of the group, dataset, or named datatype
* attribute
* @param idx
* IN: Index of the attribute to open.
*
* @return attribute identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
@Deprecated
public static int H5Aopen_idx(int loc_id, int idx)
throws HDF5LibraryException
{
int id = _H5Aopen_idx(loc_id, idx);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Aopen_idx(int loc_id, int idx)
throws HDF5LibraryException;
/**
* H5Aopen_name opens an attribute specified by its name, name, which is
* attached to the object specified with loc_id.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Aopen_by_name(int, String, String, int, int)}
*
* @param loc_id
* IN: Identifier of a group, dataset, or named datatype
* atttribute
* @param name
* IN: Attribute name.
*
* @return attribute identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
@Deprecated
public static int H5Aopen_name(int loc_id, String name)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Aopen_name(loc_id, name);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Aopen_name(int loc_id, String name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Aread reads an attribute, specified with attr_id. The attribute's
* memory datatype is specified with mem_type_id. The entire attribute is
* read into buf from the file.
*
* @param attr_id
* IN: Identifier of an attribute to read.
* @param mem_type_id
* IN: Identifier of the attribute datatype (in memory).
* @param buf
* IN: Buffer for data to be read.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - data buffer is null.
**/
public synchronized static native int H5Aread(int attr_id, int mem_type_id,
byte[] buf) throws HDF5LibraryException, NullPointerException;
/**
* H5Aread reads an attribute, specified with attr_id. The attribute's
* memory datatype is specified with mem_type_id. The entire attribute is
* read into data object from the file.
*
* @param attr_id
* IN: Identifier of an attribute to read.
* @param mem_type_id
* IN: Identifier of the attribute datatype (in memory).
* @param obj
* IN: Object for data to be read.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - data buffer is null. See public synchronized static
* native int H5Aread( )
**/
public synchronized static int H5Aread(int attr_id, int mem_type_id,
Object obj) throws HDF5Exception, NullPointerException
{
HDFArray theArray = new HDFArray(obj);
byte[] buf = theArray.emptyBytes();
// This will raise an exception if there is an error
int status = H5Aread(attr_id, mem_type_id, buf);
// No exception: status really ought to be OK
if (status >= 0) {
obj = theArray.arrayify(buf);
}
return status;
}
public synchronized static native int H5AreadVL(int attr_id,
int mem_type_id, String[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Arename changes the name of attribute that is attached to the object specified by loc_id.
* The attribute named old_attr_name is renamed new_attr_name.
*
* @param loc_id IN: Location or object identifier; may be dataset or group
* @param old_attr_name IN: Prior attribute name
* @param new_attr_name IN: New attribute name
*
* @return A non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - Name is null.
**/
public synchronized static native int H5Arename(int loc_id, String old_attr_name, String new_attr_name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Arename_by_name changes the name of attribute that is attached to the object specified by loc_id and obj_name.
* The attribute named old_attr_name is renamed new_attr_name.
*
* @param loc_id IN: Location or object identifier; may be dataset or group
* @param obj_name IN: Name of object, relative to location, whose attribute is to be renamed
* @param old_attr_name IN: Prior attribute name
* @param new_attr_name IN: New attribute name
* @param lapl_id IN: Link access property list
*
* @return A non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - Name is null.
**/
public synchronized static native int H5Arename_by_name(int loc_id, String obj_name, String old_attr_name, String new_attr_name, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Awrite writes an attribute, specified with attr_id. The attribute's
* memory datatype is specified with mem_type_id. The entire attribute is
* written from buf to the file.
*
* @param attr_id
* IN: Identifier of an attribute to write.
* @param mem_type_id
* IN: Identifier of the attribute datatype (in memory).
* @param buf
* IN: Data to be written.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - data is null.
**/
public synchronized static native int H5Awrite(int attr_id,
int mem_type_id, byte[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Awrite writes an attribute, specified with attr_id. The attribute's
* memory datatype is specified with mem_type_id. The entire attribute is
* written from data object to the file.
*
* @param attr_id
* IN: Identifier of an attribute to write.
* @param mem_type_id
* IN: Identifier of the attribute datatype (in memory).
* @param obj
* IN: Data object to be written.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - data object is null. See public synchronized static
* native int H5Awrite(int attr_id, int mem_type_id, byte[]
* buf);
**/
public synchronized static int H5Awrite(int attr_id, int mem_type_id,
Object obj) throws HDF5Exception, NullPointerException
{
HDFArray theArray = new HDFArray(obj);
byte[] buf = theArray.byteify();
int retVal = H5Awrite(attr_id, mem_type_id, buf);
buf = null;
theArray = null;
return retVal;
}
//////////////////////////////////////////////////////////////
////
//H5D: Datasets Interface Functions //
////
//////////////////////////////////////////////////////////////
public synchronized static native int H5Dchdir_ext(String dir_name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dclose ends access to a dataset specified by dataset_id and releases
* resources used by it.
*
* @param dataset_id
* Identifier of the dataset to finish access to.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Dclose(int dataset_id) throws HDF5LibraryException
{
if (dataset_id < 0)
throw new HDF5LibraryException("Negative ID");
OPEN_IDS.removeElement(dataset_id);
return _H5Dclose(dataset_id);
}
private synchronized static native int _H5Dclose(int dataset_id)
throws HDF5LibraryException;
/**
* H5Dcopy copies the content of one dataset to another dataset.
*
* @param src_did
* the identifier of the source dataset
* @param dst_did
* the identifier of the destinaiton dataset
*/
public synchronized static native int H5Dcopy(int src_did, int dst_did)
throws HDF5LibraryException;
/**
* H5Dcreate creates a data set with a name, name, in the file or in the
* group specified by the identifier loc_id.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Dcreate(int, String, int, int, int, int, int) }
*
* @param loc_id
* Identifier of the file or group to create the dataset within.
* @param name
* The name of the dataset to create.
* @param type_id
* Identifier of the datatype to use when creating the dataset.
* @param space_id
* Identifier of the dataspace to use when creating the dataset.
* @param create_plist_id
* Identifier of the set creation property list.
*
* @return a dataset identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
@Deprecated
public static int H5Dcreate(int loc_id, String name, int type_id,
int space_id, int create_plist_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Dcreate(loc_id, name, type_id, space_id, create_plist_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Dcreate(int loc_id, String name,
int type_id, int space_id, int create_plist_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dcreate creates a new dataset named name at the
* location specified by loc_id.
*
* @param loc_id IN: Location identifier
* @param name IN: Dataset name
* @param type_id IN: Datatype identifier
* @param space_id IN: Dataspace identifier
* @param lcpl_id IN: Identifier of link creation property list.
* @param dcpl_id IN: Identifier of dataset creation property list.
* @param dapl_id IN: Identifier of dataset access property list.
*
* @return a dataset identifier
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public static int H5Dcreate(int loc_id, String name, int type_id,
int space_id, int lcpl_id, int dcpl_id, int dapl_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Dcreate2(loc_id, name, type_id, space_id, lcpl_id, dcpl_id, dapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
/**
* H5Dcreate2 creates a new dataset named name at the
* location specified by loc_id.
*
* @see public static int H5Dcreate(int loc_id, String name, int type_id,
* int space_id, int lcpl_id, int dcpl_id, int dapl_id)
**/
private synchronized static native int _H5Dcreate2(int loc_id, String name, int type_id,
int space_id, int lcpl_id, int dcpl_id, int dapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dcreate_anon creates a dataset in the file specified by loc_id.
*
* @param loc_id IN: Location identifier
* @param type_id IN: Datatype identifier
* @param space_id IN: Dataspace identifier
* @param lcpl_id IN: Identifier of link creation property list.
* @param dcpl_id IN: Identifier of dataset creation property list.
* @param dapl_id IN: Identifier of dataset access property list.
*
* @return a dataset identifier
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Dcreate_anon(int loc_id, int type_id, int space_id,
int dcpl_id, int dapl_id)
throws HDF5LibraryException
{
int id = _H5Dcreate_anon(loc_id, type_id, space_id, dcpl_id, dapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Dcreate_anon(int loc_id, int type_id, int space_id,
int dcpl_id, int dapl_id)
throws HDF5LibraryException;
/**
* H5Dextend verifies that the dataset is at least of size size.
*
* @param dataset_id IN: Identifier of the dataset.
* @param size IN: Array containing the new magnitude of each dimension.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - size array is null.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Dset_extent(int, long[]) }
**/
@Deprecated
public synchronized static native int H5Dextend(int dataset_id, byte[] size)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dextend verifies that the dataset is at least of size size.
*
* @param dataset_id IN: Identifier of the dataset.
* @param size IN: Array containing the new magnitude of each dimension.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - size array is null.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Dset_extent(int, long[]) }
**/
@Deprecated
public synchronized static int H5Dextend(int dataset_id, long[] size)
throws HDF5Exception, NullPointerException
{
int rval = -1;
HDFArray theArray = new HDFArray(size);
byte[] buf = theArray.byteify();
rval = H5Dextend(dataset_id, buf);
buf = null;
theArray = null;
return rval;
}
/**
* H5Dfill explicitly fills the dataspace selection in memory, space_id,
* with the fill value specified in fill.
*
* @param fill IN: Pointer to the fill value to be used.
* @param fill_type IN: Fill value datatype identifier.
* @param buf IN/OUT: Pointer to the memory buffer containing the selection to be filled.
* @param buf_type IN: Datatype of dataspace elements to be filled.
* @param space IN: Dataspace describing memory buffer and containing the selection to be filled.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - buf is null.
**/
public synchronized static native void H5Dfill(byte[] fill, int fill_type, byte[] buf, int buf_type, int space)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dget_access_plist returns an identifier for a copy of the
* dataset access property list for a dataset.
*
* @param dset_id IN: Identifier of the dataset to query.
*
* @return a dataset access property list identifier
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Dget_access_plist(int dset_id)
throws HDF5LibraryException;
/**
* H5Dget_create_plist returns an identifier for a copy of the dataset
* creation property list for a dataset.
*
* @param dataset_id
* Identifier of the dataset to query.
* @return a dataset creation property list identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Dget_create_plist(int dataset_id)
throws HDF5LibraryException
{
int id = _H5Dget_create_plist(dataset_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Dget_create_plist(int dataset_id)
throws HDF5LibraryException;
/** H5Dget_offset returns the address in the file of the dataset dset_id.
*
* @param dset_id IN: Identifier of the dataset in question
*
* @return the offset in bytes.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native long H5Dget_offset(int dset_id)
throws HDF5LibraryException;
/**
* H5Dget_space returns an identifier for a copy of the dataspace for a
* dataset.
*
* @param dataset_id
* Identifier of the dataset to query.
*
* @return a dataspace identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Dget_space(int dataset_id) throws HDF5LibraryException
{
int id = _H5Dget_space(dataset_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Dget_space(int dataset_id)
throws HDF5LibraryException;
/**
* H5Dget_space_status determines whether space has been
* allocated for the dataset dset_id.
*
* @param dset_id IN: Identifier of the dataset to query.
*
* @return the space allocation status
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Dget_space_status(int dset_id)
throws HDF5LibraryException;
/**
* H5Dget_space_status determines whether space has been
* allocated for the dataset dset_id.
*
* @param dset_id IN: Identifier of the dataset to query.
*
* @return the space allocation status
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Dget_space_status(int dset_id,
int[] status) throws HDF5LibraryException, NullPointerException
{
return _H5Dget_space_status(dset_id, status);
}
private synchronized static native int _H5Dget_space_status(int dset_id,
int[] status) throws HDF5LibraryException, NullPointerException;
/**
* H5Dget_storage_size returns the amount of storage that is required for
* the dataset.
*
* @param dataset_id
* Identifier of the dataset in question
*
* @return he amount of storage space allocated for the dataset.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native long H5Dget_storage_size(int dataset_id)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Dget_type returns an identifier for a copy of the datatype for a
* dataset.
*
* @param dataset_id
* Identifier of the dataset to query.
*
* @return a datatype identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Dget_type(int dataset_id) throws HDF5LibraryException
{
int id = _H5Dget_type(dataset_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Dget_type(int dataset_id)
throws HDF5LibraryException;
public synchronized static native int H5Dgetdir_ext(String[] dir_name,
int size) throws HDF5LibraryException, NullPointerException;
//// Define the operator function pointer for H5Diterate()
//public interface H5D_operator_t extends Callback {
//int callback(Pointer elem, int type_id, int ndim,
// LongByReference point, Pointer operator_data);
//}
/**
* H5Diterate iterates over all the data elements in the memory buffer buf,
* executing the callback function operator once for each such data element.
*
* @param buf IN/OUT: Pointer to the memory containing the elements to iterate over.
* @param buf_type IN: Buffer datatype identifier.
* @param space IN: Dataspace describing memory buffer.
* @param op IN: Callback function to operate on each value.
* @param op_data IN/OUT: Pointer to any user-efined data for use by operator function.
*
* @return returns the return value of the first operator that returns a positive value, or zero if all members were
* processed with no operator returning non-zero.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - buf is null.
**/
public synchronized static native int H5Diterate(byte[] buff, int buf_type, int space,
H5D_iterate_cb op, H5D_iterate_t op_data)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dopen opens the existing dataset specified by a location identifier
* and name, loc_id and name, respectively.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Dopen(int, String, int) }
*
* @param loc_id IN: Location identifier
* @param name IN: Dataset name
*
* @return a dataset identifier if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
@Deprecated
public static int H5Dopen(int loc_id, String name)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Dopen(loc_id, name);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Dopen(int loc_id, String name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dopen opens the existing dataset specified by a location identifier
* and name, loc_id and name, respectively.
*
* @param loc_id IN: Location identifier
* @param name IN: Dataset name
* @param dapl_id IN: Identifier of dataset access property list.
*
* @return a dataset identifier if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public static int H5Dopen(int loc_id, String name, int dapl_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Dopen2(loc_id, name, dapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
/**
* H5Dopen2 opens the existing dataset specified by a location identifier
* and name, loc_id and name, respectively.
*
* @see public static int H5Dopen(int loc_id, String name, int dapl_id)
**/
private synchronized static native int _H5Dopen2(int loc_id, String name, int dapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dread reads a (partial) dataset, specified by its identifier
* dataset_id, from the file into the application memory buffer buf.
*
* @param dataset_id
* Identifier of the dataset read from.
* @param mem_type_id
* Identifier of the memory datatype.
* @param mem_space_id
* Identifier of the memory dataspace.
* @param file_space_id
* Identifier of the dataset's dataspace in the file.
* @param xfer_plist_id
* Identifier of a transfer property list for this I/O operation.
* @param buf
* Buffer to store data read from the file.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - data buffer is null.
**/
public synchronized static native int H5Dread(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, byte[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread(int dataset_id, int mem_type_id,
int mem_space_id, int file_space_id, int xfer_plist_id, byte[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id,
xfer_plist_id, buf, true);
}
public synchronized static int H5Dread(int dataset_id, int mem_type_id,
int mem_space_id, int file_space_id, int xfer_plist_id, Object obj)
throws HDF5Exception, HDF5LibraryException, NullPointerException
{
return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id,
xfer_plist_id, obj, true);
}
/**
* H5Dread reads a (partial) dataset, specified by its identifier
* dataset_id, from the file into the application data object.
*
* @param dataset_id
* Identifier of the dataset read from.
* @param mem_type_id
* Identifier of the memory datatype.
* @param mem_space_id
* Identifier of the memory dataspace.
* @param file_space_id
* Identifier of the dataset's dataspace in the file.
* @param xfer_plist_id
* Identifier of a transfer property list for this I/O operation.
* @param obj
* Object to store data read from the file.
*
* @return a non-negative value if successful
*
* @exception HDF5Exception
* - Failure in the data conversion.
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - data object is null.
**/
public synchronized static int H5Dread(int dataset_id, int mem_type_id,
int mem_space_id, int file_space_id, int xfer_plist_id, Object obj,
boolean isCriticalPinning)
throws HDF5Exception, HDF5LibraryException, NullPointerException
{
int status = -1;
boolean is1D = false;
Class dataClass = obj.getClass();
if (!dataClass.isArray()) {
throw (new HDF5JavaException("H5Dread: data is not an array"));
}
String cname = dataClass.getName();
is1D = (cname.lastIndexOf('[') == cname.indexOf('['));
char dname = cname.charAt(cname.lastIndexOf("[") + 1);
if (is1D && (dname == 'B')) {
status = H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (byte[]) obj,
isCriticalPinning);
}
else if (is1D && (dname == 'S')) {
status = H5Dread_short(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (short[]) obj,
isCriticalPinning);
}
else if (is1D && (dname == 'I')) {
status = H5Dread_int(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (int[]) obj,
isCriticalPinning);
}
else if (is1D && (dname == 'J')) {
status = H5Dread_long(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (long[]) obj);
}
else if (is1D && (dname == 'F')) {
status = H5Dread_float(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (float[]) obj,
isCriticalPinning);
}
else if (is1D && (dname == 'D')) {
status = H5Dread_double(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (double[]) obj,
isCriticalPinning);
}
else if (H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
status = H5Dread_reg_ref(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (String[]) obj);
}
else if (is1D && (dataClass.getComponentType() == String.class)) {
// Rosetta Biosoftware - add support for
// Strings (variable length)
if (H5.H5Tis_variable_str(mem_type_id)) {
status = H5DreadVL(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (Object[]) obj);
}
else {
status = H5Dread_string(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (String[]) obj);
}
}
else {
// Create a data buffer to hold the data
// into a Java Array
HDFArray theArray = new HDFArray(obj);
byte[] buf = theArray.emptyBytes();
// will raise exception if read fails
status = H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, isCriticalPinning);
if (status >= 0) {
// convert the data into a Java
// Array */
obj = theArray.arrayify(buf);
}
// clean up these: assign 'null' as hint
// to gc() */
buf = null;
theArray = null;
}
return status;
}
public synchronized static native int H5Dread_double(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, double[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_double(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, double[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dread_double(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dread_float(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, float[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_float(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, float[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dread_float(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dread_int(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, int[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_int(int dataset_id, int mem_type_id,
int mem_space_id, int file_space_id, int xfer_plist_id, int[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dread_int(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dread_long(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, long[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_long(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, long[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dread_long(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dread_reg_ref(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, String[] buf)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Dread_short(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, short[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dread_short(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, short[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dread_short(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dread_string(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, String[] buf)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5DreadVL(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, Object[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dset_extent sets the current dimensions of the chunked dataset dset_id
* to the sizes specified in size.
*
* @param dset_id IN: Chunked dataset identifier.
* @param size IN: Array containing the new magnitude of each dimension of the dataset.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - size is null.
**/
public synchronized static native void H5Dset_extent(int dset_id, long size[])
throws HDF5LibraryException, NullPointerException;
private synchronized static native int _H5Aopen_by_name(int loc_id, String obj_name, String attr_name,int aapl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Dvlen_get_buf_size(int dataset_id,
int type_id, int space_id, int[] size) throws HDF5LibraryException;
/**
* H5Dvlen_get_buf_size determines the number of bytes required to store the VL data from
* the dataset, using the space_id for the selection in the dataset on disk and the
* type_id for the memory representation of the VL data in memory.
*
* @param dset_id IN: Identifier of the dataset read from.
* @param type_id IN: Identifier of the datatype.
* @param space_id IN: Identifier of the dataspace.
*
* @return the size in bytes of the memory buffer required to store the VL data.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - buf is null.
**/
public synchronized static native long H5Dvlen_get_buf_size_long(int dset_id, int type_id, int space_id)
throws HDF5LibraryException;
//int H5Dvlen_get_buf_size(int dset_id, int type_id, int space_id, LongByReference size);
/**
*
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - buf is null.
**/
public synchronized static native int H5Dvlen_reclaim(int type_id,
int space_id, int xfer_plist_id, byte[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier
* dataset_id, from the application memory buffer buf into the file.
*
* @param dataset_id
* Identifier of the dataset read from.
* @param mem_type_id
* Identifier of the memory datatype.
* @param mem_space_id
* Identifier of the memory dataspace.
* @param file_space_id
* Identifier of the dataset's dataspace in the file.
* @param xfer_plist_id
* Identifier of a transfer property list for this I/O operation.
* @param buf
* Buffer with data to be written to the file.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native int H5Dwrite(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, byte[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite(int dataset_id, int mem_type_id,
int mem_space_id, int file_space_id, int xfer_plist_id, byte[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id,
xfer_plist_id, buf, true);
}
public synchronized static int H5Dwrite(int dataset_id, int mem_type_id,
int mem_space_id, int file_space_id, int xfer_plist_id, Object obj)
throws HDF5Exception, HDF5LibraryException, NullPointerException
{
return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id,
xfer_plist_id, obj, true);
}
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier
* dataset_id, from the application memory data object into the file.
*
* @param dataset_id
* Identifier of the dataset read from.
* @param mem_type_id
* Identifier of the memory datatype.
* @param mem_space_id
* Identifier of the memory dataspace.
* @param file_space_id
* Identifier of the dataset's dataspace in the file.
* @param xfer_plist_id
* Identifier of a transfer property list for this I/O operation.
* @param obj
* Object with data to be written to the file.
*
* @return a non-negative value if successful
*
* @exception HDF5Exception
* - Failure in the data conversion.
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - data object is null.
**/
public synchronized static int H5Dwrite(int dataset_id, int mem_type_id,
int mem_space_id, int file_space_id, int xfer_plist_id, Object obj,
boolean isCriticalPinning)
throws HDF5Exception, HDF5LibraryException, NullPointerException
{
int status = -1;
boolean is1D = false;
Class dataClass = obj.getClass();
if (!dataClass.isArray()) {
throw (new HDF5JavaException("H5Dread: data is not an array"));
}
String cname = dataClass.getName();
is1D = (cname.lastIndexOf('[') == cname.indexOf('['));
char dname = cname.charAt(cname.lastIndexOf("[") + 1);
if (is1D && (dname == 'B')) {
status = H5Dwrite(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (byte[]) obj,
isCriticalPinning);
}
else if (is1D && (dname == 'S')) {
status = H5Dwrite_short(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (short[]) obj,
isCriticalPinning);
}
else if (is1D && (dname == 'I')) {
status = H5Dwrite_int(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (int[]) obj,
isCriticalPinning);
}
else if (is1D && (dname == 'J')) {
status = H5Dwrite_long(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (long[]) obj,
isCriticalPinning);
}
else if (is1D && (dname == 'F')) {
status = H5Dwrite_float(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (float[]) obj,
isCriticalPinning);
}
else if (is1D && (dname == 'D')) {
status = H5Dwrite_double(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (double[]) obj,
isCriticalPinning);
}
// Rosetta Biosoftware - call into H5DwriteString
// for variable length Strings
else if ((H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_STRING)
&& H5.H5Tis_variable_str(mem_type_id) && dataClass.isArray()
&& (dataClass.getComponentType() == String.class) && is1D) {
status = H5DwriteString(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, (String[]) obj);
}
else {
HDFArray theArray = new HDFArray(obj);
byte[] buf = theArray.byteify();
/* will raise exception on error */
status = H5Dwrite(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, isCriticalPinning);
// clean up these: assign 'null' as hint to
// gc() */
buf = null;
theArray = null;
}
return status;
}
public synchronized static native int H5Dwrite_double(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, double[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_double(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, double[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dwrite_double(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dwrite_float(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, float[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_float(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, float[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dwrite_float(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dwrite_int(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, int[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_int(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, int[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dwrite_int(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dwrite_long(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, long[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_long(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, long[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dwrite_long(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, true);
}
public synchronized static native int H5Dwrite_short(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, short[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Dwrite_short(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, short[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Dwrite_short(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf, true);
}
/**
* H5DwriteString writes a (partial) variable length String dataset,
* specified by its identifier dataset_id, from the application memory
* buffer buf into the file.
*
* @param dataset_id
* Identifier of the dataset read from.
* @param mem_type_id
* Identifier of the memory datatype.
* @param mem_space_id
* Identifier of the memory dataspace.
* @param file_space_id
* Identifier of the dataset's dataspace in the file.
* @param xfer_plist_id
* Identifier of a transfer property list for this I/O operation.
* @param buf
* Buffer with data to be written to the file.
*
* @return a non-negative value if successful
*
* @author contributed by Rosetta Biosoftware
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native int H5DwriteString(int dataset_id,
int mem_type_id, int mem_space_id, int file_space_id,
int xfer_plist_id, String[] buf)
throws HDF5LibraryException, NullPointerException;
//////////////////////////////////////////////////////////////
////
//H5E: Error Stack //
////
//////////////////////////////////////////////////////////////
/**
* H5Eauto_is_v2 determines whether the error auto reporting function for an
* error stack conforms to the H5E_auto2_t typedef or the H5E_auto1_t
* typedef.
*
* @param stack_id
* IN: Error stack identifier.
*
* @return boolean true if the error stack conforms to H5E_auto2_t and false
* if it conforms to H5E_auto1_t.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native boolean H5Eauto_is_v2(int err_stack)
throws HDF5LibraryException;
/**
* H5Eclear clears the error stack for the current thread. H5Eclear can fail
* if there are problems initializing the library.
*
*
*
* @param create_id
* File creation property list identifier, used when modifying
* default file meta-data. Use H5P_DEFAULT for default access
* properties.
* @param access_id
* File access property list identifier. If parallel file access
* is desired, this is a collective call according to the
* communicator stored in the access_id (not supported in Java).
* Use H5P_DEFAULT for default access properties.
*
* @return a file identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public static int H5Fcreate(String name, int flags, int create_id,
int access_id) throws HDF5LibraryException, NullPointerException
{
int id = _H5Fcreate(name, flags, create_id, access_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Fcreate(String name, int flags,
int create_id, int access_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Fflush causes all buffers associated with a file or object to be
* immediately flushed (written) to disk without removing the data from the
* (memory) cache.
*
*
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Fflush(int object_id, int scope)
throws HDF5LibraryException;
/**
* H5Fget_access_plist returns the file access property list identifier of
* the specified file.
*
* @param file_id
* Identifier of file to get access property list of
*
* @return a file access property list identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Fget_access_plist(int file_id)
throws HDF5LibraryException
{
int id = _H5Fget_access_plist(file_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Fget_access_plist(int file_id)
throws HDF5LibraryException;
/**
* H5Fget_create_plist returns a file creation property list identifier
* identifying the creation properties used to create this file.
*
* @param file_id
* Identifier of the file to get creation property list
*
* @return a file creation property list identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Fget_create_plist(int file_id)
throws HDF5LibraryException
{
int id = _H5Fget_create_plist(file_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Fget_create_plist(int file_id)
throws HDF5LibraryException;
public synchronized static native long H5Fget_filesize(int file_id)
throws HDF5LibraryException;
/**
* H5Fget_freespace returns the amount of space that is unused by any
* objects in the file.
*
* @param file_id
* IN: File identifier for a currently-open HDF5 file
*
* @return the amount of free space in the file
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native long H5Fget_freespace(int file_id)
throws HDF5LibraryException;
///**
//* H5Fget_info returns global information for the file associated with the
//* object identifier obj_id.
//*
//* @param obj_id IN: Object identifier for any object in the file.
//*
//* @return the structure containing global file information.
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//**/
//public synchronized static native H5F_info_t H5Fget_info(int obj_id)
//throws HDF5LibraryException, NullPointerException;
//int H5Fget_info(int obj_id, H5F_info_t file_info);
/**
* H5Fget_intent retrieves the intended access mode flag passed with H5Fopen
* when the file was opened.
*
* @param file_id
* IN: File identifier for a currently-open HDF5 file
*
* @return the intended access mode flag, as originally passed with H5Fopen.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Fget_intent(int file_id)
throws HDF5LibraryException;
// int H5Fget_intent(int file_id, IntByReference intent);
///**
//* H5Fget_mdc_config loads the current metadata cache configuration into
//* the instance of H5AC_cache_config_t pointed to by the config_ptr
//parameter.
//*
//* @param file_id IN: Identifier of the target file
//* @param config_ptr IN/OUT: Pointer to the instance of
//H5AC_cache_config_t in which the current metadata cache configuration is
//to be reported.
//*
//* @return none
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//* @exception NullPointerException - config_ptr is null.
//**/
//public synchronized static native void H5Fget_mdc_config(int file_id,
//H5AC_cache_config_t config_ptr)
//throws HDF5LibraryException, NullPointerException;
//
///**
//* H5Fset_mdc_config attempts to configure the file's metadata cache
//according to the configuration supplied.
//*
//* @param file_id IN: Identifier of the target file
//* @param config_ptr IN: Pointer to the instance of H5AC_cache_config_t
//containing the desired configuration.
//*
//* @return none
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//* @exception NullPointerException - config_ptr is null.
//**/
//public synchronized static native int H5Fset_mdc_config(int file_id,
//H5AC_cache_config_t config_ptr)
//throws HDF5LibraryException, NullPointerException;
/**
* H5Fget_mdc_hit_rate queries the metadata cache of the target file to
* obtain its hit rate (cache hits / (cache hits + cache misses)) since the
* last time hit rate statistics were reset.
*
* @param file_id
* IN: Identifier of the target file.
*
* @return the double in which the hit rate is returned.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native double H5Fget_mdc_hit_rate(int file_id)
throws HDF5LibraryException;
/**
* H5Fget_mdc_size queries the metadata cache of the target file for the
* desired size information.
*
* @param file_id
* IN: Identifier of the target file.
* @param metadata_cache
* OUT: Current metadata cache information
*
*
*
* @return current number of entries in the cache
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - metadata_cache is null.
**/
public synchronized static native int H5Fget_mdc_size(int file_id,
long[] metadata_cache)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Fget_name retrieves the name of the file to which the object obj_id
* belongs.
*
* @param obj_id
* IN: Identifier of the object for which the associated filename
* is sought.
*
* @return the filename.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native String H5Fget_name(int obj_id)
throws HDF5LibraryException;
// long H5Fget_name(int obj_id, Buffer name/*out*/, long size);
public synchronized static native String H5Fget_name(int obj_id, int size)
throws HDF5LibraryException;
/**
* H5Fget_obj_count returns the number of open object identifiers for the
* file.
*
* @param file_id
* IN: File identifier for a currently-open HDF5 file
* @param types
* IN: Type of object for which identifiers are to be returned.
*
*
*
* @return the number of open objects.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Fget_obj_count(int file_id,
int types) throws HDF5LibraryException;
/**
* H5Fget_obj_count returns the number of open object identifiers for the
* file.
*
* @param file_id
* IN: File identifier for a currently-open HDF5 file
* @param types
* IN: Type of object for which identifiers are to be returned.
*
*
*
* @return the number of open objects.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native long H5Fget_obj_count_long(int file_id,
int types) throws HDF5LibraryException;
/**
* H5Fget_obj_ids returns the list of identifiers for all open HDF5 objects
* fitting the specified criteria.
*
* @param file_id
* IN: File identifier for a currently-open HDF5 file
* @param types
* IN: Type of object for which identifiers are to be returned.
* @param max_objs
* IN: Maximum number of object identifiers to place into
* obj_id_list.
* @param obj_id_list
* OUT: Pointer to the returned list of open object identifiers.
*
* @return the number of objects placed into obj_id_list.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - obj_id_list is null.
**/
public synchronized static native int H5Fget_obj_ids(int file_id,
int types, int max, int[] obj_id_list)
throws HDF5LibraryException, NullPointerException;
/**
* H5Fget_obj_ids returns the list of identifiers for all open HDF5 objects
* fitting the specified criteria.
*
* @param file_id
* IN: File identifier for a currently-open HDF5 file
* @param types
* IN: Type of object for which identifiers are to be returned.
* @param max_objs
* IN: Maximum number of object identifiers to place into
* obj_id_list.
* @param obj_id_list
* OUT: Pointer to the returned list of open object identifiers.
*
* @return the number of objects placed into obj_id_list.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - obj_id_list is null.
**/
public synchronized static native long H5Fget_obj_ids_long(int file_id,
int types, long max_objs, int[] obj_id_list)
throws HDF5LibraryException, NullPointerException;
///**
//* H5Fget_vfd_handle returns a pointer to the file handle from the
//low-level file driver
//* currently being used by the HDF5 library for file I/O.
//*
//* @param file_id IN: Identifier of the file to be queried.
//* @param fapl IN: File access property list identifier.
//*
//* @return a pointer to the file handle being used by the low-level
//virtual file driver.
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//**/
//public synchronized static native Pointer file_handle
//H5Fget_vfd_handle(int file_id, int fapl)
//throws HDF5LibraryException;
/**
* H5Fis_hdf5 determines whether a file is in the HDF5 format.
*
* @param name
* File name to check format.
*
* @return true if is HDF-5, false if not.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native boolean H5Fis_hdf5(String name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Fmount mounts the file specified by child_id onto the group specified
* by loc_id and name using the mount properties plist_id.
*
* @param loc_id
* The identifier for the group onto which the file specified by
* child_id is to be mounted.
* @param name
* The name of the group onto which the file specified by
* child_id is to be mounted.
* @param child_id
* The identifier of the file to be mounted.
* @param plist_id
* The identifier of the property list to be used.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native int H5Fmount(int loc_id, String name,
int child_id, int plist_id)
throws HDF5LibraryException, NullPointerException;
/**
* Given a mount point, H5Funmount dissassociates the mount point's file
* from the file mounted there.
*
* @param loc_id
* The identifier for the location at which the specified file is
* to be unmounted.
* @param name
* The name of the file to be unmounted.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native int H5Funmount(int loc_id, String name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Freset_mdc_hit_rate_stats resets the hit rate statistics counters in
* the metadata cache associated with the specified file.
*
* @param file_id
* IN: Identifier of the target file.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Freset_mdc_hit_rate_stats(
int file_id) throws HDF5LibraryException;
// ////////////////////////////////////////////////////////////
// //
// H5G: Group Interface Functions //
// //
// ////////////////////////////////////////////////////////////
/**
* H5Gclose releases resources used by a group which was opened by a call to
* H5Gcreate() or H5Gopen().
*
* @param group_id
* Group identifier to release.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Gclose(int group_id) throws HDF5LibraryException
{
if (group_id < 0)
throw new HDF5LibraryException("Negative ID");;
OPEN_IDS.removeElement(group_id);
return _H5Gclose(group_id);
}
private synchronized static native int _H5Gclose(int group_id)
throws HDF5LibraryException;
/**
* H5Gcreate creates a new group with the specified name at the specified
* location, loc_id.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Gcreate(int, String, int, int, int) }
*
* @param loc_id
* The file or group identifier.
* @param name
* The absolute or relative name of the new group.
* @param size_hint
* An optional parameter indicating the number of bytes to
* reserve for the names that will appear in the group.
*
* @return a valid group identifier for the open group if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
@Deprecated
public static int H5Gcreate(int loc_id, String name, long size_hint)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Gcreate(loc_id, name, size_hint);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Gcreate(int loc_id, String name,
long size_hint) throws HDF5LibraryException, NullPointerException;
/**
* H5Gcreate creates a new group with the specified name at the specified
* location, loc_id.
*
* @param loc_id
* IN: The file or group identifier.
* @param name
* IN: The absolute or relative name of the new group.
* @param lcpl_id
* IN: Identifier of link creation property list.
* @param gcpl_id
* IN: Identifier of group creation property list.
* @param gapl_id
* IN: Identifier of group access property list. (No group access
* properties have been implemented at this time; use
* H5P_DEFAULT.)
*
* @return a valid group identifier
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public static int H5Gcreate(int loc_id, String name,
int lcpl_id, int gcpl_id, int gapl_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Gcreate2(loc_id, name, lcpl_id, gcpl_id, gapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Gcreate2(int loc_id, String name,
int lcpl_id, int gcpl_id, int gapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Gcreate_anon creates a new empty group in the file specified by loc_id.
*
* @param loc_id
* IN: File or group identifier specifying the file in which the
* new group is to be created.
* @param gcpl_id
* IN: Identifier of group creation property list.
* @param gapl_id
* IN: Identifier of group access property list. (No group access
* properties have been implemented at this time; use
* H5P_DEFAULT.)
*
* @return a valid group identifier
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Gcreate_anon(int loc_id,
int gcpl_id, int gapl_id) throws HDF5LibraryException
{
int id = _H5Gcreate_anon(loc_id, gcpl_id, gapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Gcreate_anon(int loc_id,
int gcpl_id, int gapl_id) throws HDF5LibraryException;
/**
* H5Gget_comment retrieves the comment for the the object name. The comment
* is returned in the buffer comment.
*
* @param loc_id
* IN: Identifier of the file, group, dataset, or datatype.
* @param name
* IN: Name of the object whose comment is to be set or reset.
* @param bufsize
* IN: Anticipated size of the buffer required to hold comment.
* @param comment
* OUT: The comment.
* @return the number of characters in the comment, counting the null
* terminator, if successful
*
* @exception ArrayIndexOutOfBoundsException
* - JNI error writing back data
* @exception ArrayStoreException
* - JNI error writing back data
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
* @exception IllegalArgumentException
* - size < 1, comment is invalid.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Oget_comment(int)}
**/
@Deprecated
public synchronized static native int H5Gget_comment(int loc_id,
String name, int bufsize, String[] comment)
throws ArrayIndexOutOfBoundsException, ArrayStoreException,
HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Gset_comment sets the comment for the the object name to comment. Any
* previously existing comment is overwritten.
*
* @param loc_id
* IN: Identifier of the file, group, dataset, or datatype.
* @param name
* IN: Name of the object whose comment is to be set or reset.
* @param comment
* IN: The new comment.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name or comment is null.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Oset_comment(int, String)}
**/
@Deprecated
public synchronized static native int H5Gset_comment(int loc_id,
String name, String comment)
throws HDF5LibraryException, NullPointerException;
/**
* H5Gget_create_plist returns an identifier for the group creation property
* list associated with the group specified by group_id.
*
* @param group_id
* IN: Identifier of the group.
*
* @return an identifier for the group's creation property list
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Gget_create_plist(int group_id)
throws HDF5LibraryException;
/**
* H5Gget_info retrieves information about the group specified by group_id.
* The information is returned in the group_info struct.
*
* @param group_id
* IN: Identifier of the group.
*
* @return a structure in which group information is returned
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native H5G_info_t H5Gget_info(int group_id)
throws HDF5LibraryException;
// int H5Gget_info(int loc_id, H5G_info_t ginfo);
/**
* H5Gget_info_by_idx retrieves information about a group, according to the
* group's position within an index.
*
* @param group_id
* IN: File or group identifier.
* @param group_name
* IN: Name of group for which information is to be retrieved.
* @param idx_type
* IN: Type of index by which objects are ordered
* @param order
* IN: Order of iteration within index
* @param n
* IN: Attribute's position in index
* @param lapl_id
* IN: Link access property list.
*
* @return a structure in which group information is returned
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native H5G_info_t H5Gget_info_by_idx(
int group_id, String group_name, int idx_type, int order, long n,
int lapl_id) throws HDF5LibraryException, NullPointerException;
// int H5Gget_info_by_idx(int group_id, String group_name,
// H5_index_t idx_type, H5_iter_order_t order, long n, H5G_info_t ginfo, int
// lapl_id);
/**
* H5Gget_info_by_name retrieves information about the group group_name
* located in the file or group specified by loc_id.
*
* @param group_id
* IN: File or group identifier.
* @param name
* IN: Name of group for which information is to be retrieved.
* @param lapl_id
* IN: Link access property list.
*
* @return a structure in which group information is returned
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native H5G_info_t H5Gget_info_by_name(
int group_id, String name, int lapl_id)
throws HDF5LibraryException, NullPointerException;
// int H5Gget_info_by_name(int group_id, String name, H5G_info_t ginfo, int
// lapl_id);
/**
* H5Gget_linkval returns size characters of the link value through the
* value argument if loc_id (a file or group identifier) and name specify a
* symbolic link.
*
* @param loc_id
* IN: Identifier of the file, group, dataset, or datatype.
* @param name
* IN: Name of the object whose link value is to be checked.
* @param size
* IN: Maximum number of characters of value to be returned.
* @param value
* OUT: Link value.
*
* @return a non-negative value, with the link value in value, if
* successful.
*
* @exception ArrayIndexOutOfBoundsException
* Copy back failed
* @exception ArrayStoreException
* Copy back failed
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
* @exception IllegalArgumentException
* - size is invalid
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Lget_val(int, String, String[] , int)}
**/
@Deprecated
public synchronized static native int H5Gget_linkval(int loc_id,
String name, int size, String[] value)
throws ArrayIndexOutOfBoundsException, ArrayStoreException,
HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* Returns number of objects in the group specified by its identifier
*
* @param loc_id
* Identifier of the group or the file
* @param num_obj
* Number of objects in the group
* @return positive value if successful; otherwise returns a negative value.
* @throws HDF5LibraryException
* @throws NullPointerException
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Gget_info(int)}
*/
@Deprecated
public synchronized static native int H5Gget_num_objs(int loc_id,
long[] num_obj) throws HDF5LibraryException, NullPointerException;
/**
* retrieves information of all objects under the group (name) located in
* the file or group specified by loc_id.
*
* @param loc_id
* IN: File or group identifier
* @param name
* IN: Name of group for which information is to be retrieved
* @param objNames
* OUT: Names of all objects under the group, name.
* @param objTypes
* OUT: Types of all objects under the group, name.
*
* @return the number of items found
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
*/
public synchronized static int H5Gget_obj_info_all(int loc_id, String name,
String[] oname, int[] otype, long[] ref)
throws HDF5LibraryException, NullPointerException
{
if (oname == null) {
throw new NullPointerException(
"H5Gget_obj_info_all(): name array is null");
}
return H5Gget_obj_info_all(loc_id, name, oname, otype, null, null, ref, HDF5Constants.H5_INDEX_NAME);
}
public synchronized static int H5Gget_obj_info_all(int loc_id, String name,
String[] oname, int[] otype, int[] ltype, long[] ref, int indx_type)
throws HDF5LibraryException, NullPointerException
{
return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, null, ref, indx_type, -1);
}
public synchronized static int H5Gget_obj_info_all(int loc_id, String name,
String[] oname, int[] otype, int[] ltype, long[] fno, long[] ref, int indx_type)
throws HDF5LibraryException, NullPointerException
{
return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, ref, oname.length, indx_type, -1);
}
public synchronized static int H5Gget_obj_info_full(int loc_id, String name,
String[] oname, int[] otype, int[] ltype, long[] fno, long[] ref, int indx_type, int indx_order)
throws HDF5LibraryException, NullPointerException
{
if (oname == null) {
throw new NullPointerException(
"H5Gget_obj_info_full(): name array is null");
}
if (otype == null) {
throw new NullPointerException(
"H5Gget_obj_info_full(): object type array is null");
}
if (oname.length == 0) {
throw new HDF5LibraryException(
"H5Gget_obj_info_full(): array size is zero");
}
if (oname.length != otype.length) {
throw new HDF5LibraryException(
"H5Gget_obj_info_full(): name and type array sizes are different");
}
if (ltype == null)
ltype = new int[otype.length];
if (fno == null)
fno = new long[ref.length];
if (indx_type < 0)
indx_type = HDF5Constants.H5_INDEX_NAME;
if (indx_order < 0)
indx_order = HDF5Constants.H5_ITER_INC;
return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, ref, oname.length, indx_type, indx_order);
}
private synchronized static native int H5Gget_obj_info_full(int loc_id,
String name, String[] oname, int[] otype, int[] ltype, long[] fno, long[] ref, int n, int indx_type, int indx_order)
throws HDF5LibraryException, NullPointerException;
/**
* H5Gget_obj_info_idx report the name and type of object with index 'idx'
* in a Group. The 'idx' corresponds to the index maintained by H5Giterate.
* Each link is returned, so objects with multiple links will be counted
* once for each link.
*
* @param loc_id
* IN: file or group ID.
* @param name
* IN: name of the group to iterate, relative to the loc_id
* @param idx
* IN: the index of the object to iterate.
* @param oname
* the name of the object [OUT]
* @param type
* the type of the object [OUT]
*
* @return non-negative if successful, -1 if not.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
*/
public synchronized static int H5Gget_obj_info_idx(int loc_id, String name,
int idx, String[] oname, int[] type)
throws HDF5LibraryException, NullPointerException
{
long default_buf_size = 4096;
String n[] = new String[1];
n[0] = new String("");
int grp_id = H5Gopen(loc_id, name);
long val = H5Gget_objname_by_idx(grp_id, idx, n, default_buf_size);
int type_code = H5Gget_objtype_by_idx(grp_id, idx);
oname[0] = new String(n[0]);
type[0] = type_code;
int ret = (new Long(val)).intValue();
return ret;
}
/*
* //////////////////////////////////////////////////////////////////////////
* /////// // // //Add these methods so that we don't need to call
* //in a loop to get information for all the object
* in a group, which takes //a lot of time to finish if the number of
* objects is more than 10,000 //
* ///////////////////////////////////////////
* //////////////////////////////////////
*/
/**
* retrieves information of all objects (recurvisely) under the group (name)
* located in the file or group specified by loc_id upto maximum specified
* by objMax.
*
* @param loc_id
* IN: File or group identifier
* @param name
* IN: Name of group for which information is to be retrieved
* @param objNames
* OUT: Names of all objects under the group, name.
* @param objTypes
* OUT: Types of all objects under the group, name.
* @param objMax
* IN: Maximum number of all objects under the group, name.
*
* @return the number of items found
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
*/
public synchronized static int H5Gget_obj_info_max(int loc_id,
String[] objNames, int[] objTypes, int[] lnkTypes, long[] ref, int objMax)
throws HDF5LibraryException, NullPointerException
{
if (objNames == null) {
throw new NullPointerException(
"H5Gget_obj_info_max(): name array is null");
}
if (objTypes == null) {
throw new NullPointerException(
"H5Gget_obj_info_max(): object type array is null");
}
if (lnkTypes == null) {
throw new NullPointerException(
"H5Gget_obj_info_max(): link type array is null");
}
if (objNames.length <= 0) {
throw new HDF5LibraryException(
"H5Gget_obj_info_max(): array size is zero");
}
if (objMax <= 0) {
throw new HDF5LibraryException(
"H5Gget_obj_info_max(): maximum array size is zero");
}
if (objNames.length != objTypes.length) {
throw new HDF5LibraryException(
"H5Gget_obj_info_max(): name and type array sizes are different");
}
return H5Gget_obj_info_max(loc_id, objNames, objTypes, lnkTypes, ref, objMax,
objNames.length);
}
private synchronized static native int H5Gget_obj_info_max(int loc_id,
String[] oname, int[] otype, int[] ltype, long[] ref, int amax, int n)
throws HDF5LibraryException, NullPointerException;
/**
* H5Gget_objinfo returns information about the specified object.
*
* @param loc_id
* IN: File, group, dataset, or datatype identifier.
* @param name
* IN: Name of the object for which status is being sought.
* @param follow_link
* IN: Link flag.
* @param fileno
* OUT: file id numbers.
* @param objno
* OUT: object id numbers.
* @param link_info
* OUT: link information.
*
*
* link_info[0] = nlink
* link_info[1] = type
* link_info[2] = linklen
*
* @param mtime
* OUT: modification time
*
* @return a non-negative value if successful, with the fields of link_info
* and mtime (if non-null) initialized.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name or array is null.
* @exception IllegalArgumentException
* - bad argument.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Lget_info(int, String, int) and #H5Oget_info(int)}
**/
@Deprecated
public synchronized static native int H5Gget_objinfo(int loc_id,
String name, boolean follow_link, long[] fileno, long[] objno,
int[] link_info, long[] mtime)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Gget_objinfo returns information about the specified object in an
* HDF5GroupInfo object.
*
* @param loc_id
* IN: File, group, dataset, or datatype identifier.
* @param name
* IN: Name of the object for which status is being sought.
* @param follow_link
* IN: Link flag.
* @param info
* OUT: the HDF5GroupInfo object to store the object infomation
*
* @return a non-negative value if successful, with the fields of
* HDF5GroupInfo object (if non-null) initialized.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
*
* @see ncsa.hdf.hdf5lib.HDF5GroupInfo See public synchronized static native
* int H5Gget_objinfo();
*
* @deprecated As of HDF5 1.8
**/
@Deprecated
public synchronized static int H5Gget_objinfo(int loc_id, String name,
boolean follow_link, HDF5GroupInfo info)
throws HDF5LibraryException, NullPointerException
{
int status = -1;
long[] fileno = new long[2];
long[] objno = new long[2];
int[] link_info = new int[3];
long[] mtime = new long[1];
status = H5Gget_objinfo(loc_id, name, follow_link, fileno, objno,
link_info, mtime);
if (status >= 0) {
info.setGroupInfo(fileno, objno, link_info[0], link_info[1],
mtime[0], link_info[2]);
}
return status;
}
/**
* Returns a name of an object specified by an index.
*
* @param group_id
* Group or file identifier
* @param idx
* Transient index identifying object
* @param name
* the object name
* @param size
* Name length
* @return the size of the object name if successful, or 0 if no name is
* associated with the group identifier. Otherwise returns a
* negative value
* @throws HDF5LibraryException
* @throws NullPointerException
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Lget_name_by_idx(int, String, int, int, long, int)}
*/
@Deprecated
public synchronized static native long H5Gget_objname_by_idx(int group_id,
long idx, String[] name, long size)
throws HDF5LibraryException, NullPointerException;
/**
* Returns the type of an object specified by an index.
*
* @param group_id
* Group or file identifier.
* @param idx
* Transient index identifying object.
* @return Returns the type of the object if successful. Otherwise returns a
* negative value
* @throws HDF5LibraryException
* @throws NullPointerException
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Oget_info(int)}
*/
@Deprecated
public synchronized static native int H5Gget_objtype_by_idx(int group_id,
long idx) throws HDF5LibraryException, NullPointerException;
/**
* H5Glink creates a new name for an already existing object.
*
* @param loc_id
* File, group, dataset, or datatype identifier.
* @param link_type
* Link type. Possible values are:
*
*
* @param current_name
* A name of the existing object if link is a hard link. Can be
* anything for the soft link.
* @param new_name
* New name for the object.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - current_name or name is null.
*
* @deprecated As of HDF5 1.8, replaced by
* {@link #H5Lcreate_hard(int, String, int, String, int, int)
* and #H5Lcreate_soft(String, int, String, int, int) }
**/
@Deprecated
public synchronized static native int H5Glink(int loc_id, int link_type,
String current_name, String new_name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Glink creates a new name for an already existing object.
*
* @deprecated As of HDF5 1.8
**/
@Deprecated
public synchronized static native int H5Glink2(int curr_loc_id,
String current_name, int link_type, int new_loc_id, String new_name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Gunlink removes an association between a name and an object.
*
* @param loc_id
* Identifier of the file containing the object.
* @param name
* Name of the object to unlink.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Ldelete(int, String, int)}
**/
@Deprecated
public synchronized static native int H5Gunlink(int loc_id, String name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Gmove renames an object within an HDF5 file. The original name, src, is
* unlinked from the group graph and the new name, dst, is inserted as an
* atomic operation. Both names are interpreted relative to loc_id, which is
* either a file or a group identifier.
*
* @param loc_id
* File or group identifier.
* @param src
* Object's original name.
* @param dst
* Object's new name.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - src or dst is null.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Lmove(int, String, int,String, int, int)}
**/
@Deprecated
public synchronized static native int H5Gmove(int loc_id, String src,
String dst) throws HDF5LibraryException, NullPointerException;
// Backward compatibility:
// These functions have been replaced by new HDF5 library calls.
// The interface is preserved as a convenience to existing code.
/**
* H5Gn_members report the number of objects in a Group. The 'objects'
* include everything that will be visited by H5Giterate. Each link is
* returned, so objects with multiple links will be counted once for each
* link.
*
* @param loc_id
* file or group ID.
* @param name
* name of the group to iterate, relative to the loc_id
*
* @return the number of members in the group or -1 if error.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
*/
public synchronized static long H5Gn_members_long(int loc_id, String name)
throws HDF5LibraryException, NullPointerException
{
int grp_id = H5Gopen(loc_id, name);
long n = -1;
try {
H5G_info_t info = H5.H5Gget_info(grp_id);
n = info.nlinks;
} finally {
H5Gclose(grp_id);
}
return n;
}
/**
* H5Gn_members report the number of objects in a Group. The 'objects'
* include everything that will be visited by H5Giterate. Each link is
* returned, so objects with multiple links will be counted once for each
* link.
*
* @param loc_id
* file or group ID.
* @param name
* name of the group to iterate, relative to the loc_id
*
* @return the number of members in the group or -1 if error.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
*/
public synchronized static int H5Gn_members(int loc_id, String name)
throws HDF5LibraryException, NullPointerException
{
return (int) H5Gn_members_long(loc_id, name);
}
/**
* H5Gopen opens an existing group with the specified name at the specified
* location, loc_id.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Gopen(int, String, int) }
*
* @param loc_id
* File or group identifier within which group is to be open.
* @param name
* Name of group to open.
*
* @return a valid group identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
@Deprecated
public static int H5Gopen(int loc_id, String name)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Gopen(loc_id, name);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Gopen(int loc_id, String name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Gopen opens an existing group, name, at the location specified by
* loc_id.
*
* @param loc_id
* IN: File or group identifier specifying the location of the
* group to be opened.
* @param name
* IN: Name of group to open.
* @param gapl_id
* IN: Identifier of group access property list. (No group access
* properties have been implemented at this time; use
* H5P_DEFAULT.)
*
* @return a valid group identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public static int H5Gopen(int loc_id, String name,
int gapl_id) throws HDF5LibraryException, NullPointerException
{
int id = _H5Gopen2(loc_id, name, gapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Gopen2(int loc_id, String name,
int gapl_id) throws HDF5LibraryException, NullPointerException;
//////////////////////////////////////////////////////////////
////
//H5I: HDF5 1.8 Identifier Interface API Functions //
////
//////////////////////////////////////////////////////////////
public synchronized static native int H5Iget_file_id(int obj_id)
throws HDF5LibraryException;
public synchronized static native long H5Iget_name(int obj_id,
String[] name, long size)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Iget_ref(int obj_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Idec_ref(int obj_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Iinc_ref(int obj_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Iget_type retrieves the type of the object identified by obj_id.
*
* @param obj_id
* IN: Object identifier whose type is to be determined.
*
* @return the object type if successful; otherwise H5I_BADID.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Iget_type(int obj_id)
throws HDF5LibraryException;
/**
* H5Iget_type_ref retrieves the reference count on an ID type. The reference count is used by the library to indicate when an ID type can be destroyed.
*
* @param type
* IN: The identifier of the type whose reference count is to be retrieved
*
* @return The current reference count on success, negative on failure.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Iget_type_ref(int type)
throws HDF5LibraryException;
/**
* H5Inmembers returns the number of identifiers of the identifier type specified in type.
*
* @param type
* IN: Identifier for the identifier type whose member count will be retrieved
*
* @return Number of identifiers of the specified identifier type
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Inmembers(int type)
throws HDF5LibraryException;
// //////////////////////////////////////////////////////////////////
// //
// New APIs for HDF5Index //
// October 10, 2005 //
// //////////////////////////////////////////////////////////////////
public synchronized static native int H5INcreate(String grp_name,
int grp_loc_id, int property_list, int data_loc_id,
String data_loc_name, String field_name, long max_mem_size);
public synchronized static native int H5INquery(int dset_id, String keys[],
Object ubounds, Object lbounds, int nkeys);
// //////////////////////////////////////////////////////////////////
// H5L: Link Interface Functions //
// //////////////////////////////////////////////////////////////////
/**
* H5Lcopy copies a link from one location to another.
*
* @param src_loc IN: Location identifier of the source link
* @param src_name IN: Name of the link to be copied
* @param dst_loc IN: Location identifier specifying the destination of the copy
* @param dst_name IN: Name to be assigned to the new copy
* @param lcpl_id IN: Link creation property list identifier
* @param lapl_id IN: Link access property list identifier
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native void H5Lcopy(int src_loc, String src_name, int dst_loc,
String dst_name, int lcpl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lcreate_external creates a new soft link to an external object, which is
* an object in a different HDF5 file from the location of the link.
*
* @param file_name IN: Name of the target file containing the target object.
* @param obj_name IN: Path within the target file to the target object.
* @param link_loc_id IN: The file or group identifier for the new link.
* @param link_name IN: The name of the new link.
* @param lcpl_id IN: Link creation property list identifier
* @param lapl_id IN: Link access property list identifier
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native void H5Lcreate_external(String file_name, String obj_name,
int link_loc_id, String link_name, int lcpl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lcreate_hard creates a new hard link to a pre-existing object in an HDF5 file.
*
* @param cur_loc IN: The file or group identifier for the target object.
* @param cur_name IN: Name of the target object, which must already exist.
* @param dst_loc IN: The file or group identifier for the new link.
* @param dst_name IN: The name of the new link.
* @param lcpl_id IN: Link creation property list identifier
* @param lapl_id IN: Link access property list identifier
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - cur_name or dst_name is null.
**/
public synchronized static native void H5Lcreate_hard(int cur_loc, String cur_name,
int dst_loc, String dst_name, int lcpl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lcreate_soft creates a new soft link to an object in an HDF5 file.
*
* @param link_target IN: Path to the target object, which is not required to exist.
* @param link_loc_id IN: The file or group identifier for the new link.
* @param link_name IN: The name of the new link.
* @param lcpl_id IN: Link creation property list identifier
* @param lapl_id IN: Link access property list identifier
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - link_name is null.
**/
public synchronized static native void H5Lcreate_soft(String link_target, int link_loc_id,
String link_name, int lcpl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Ldelete removes the link specified from a group.
*
* @param loc_id IN: Identifier of the file or group containing the object.
* @param name IN: Name of the link to delete.
* @param lapl_id IN: Link access property list identifier
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native void H5Ldelete(int loc_id, String name, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Ldelete_by_idx removes the nth link in a group according to the specified order
* and in the specified index.
*
* @param loc_id IN: File or group identifier specifying location of subject group
* @param group_name IN: Name of subject group
* @param idx_type IN: Index or field which determines the order
* @param order IN: Order within field or index
* @param n IN: Link for which to retrieve information
* @param lapl_id IN: Link access property list identifier
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - group_name is null.
**/
public synchronized static native void H5Ldelete_by_idx(int loc_id, String group_name,
int idx_type, int order, long n, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lexists checks if a link with a particular name exists in a group.
*
* @param loc_id IN: Identifier of the file or group to query.
* @param name IN: The name of the link to check.
* @param lapl_id IN: Link access property list identifier
*
* @return a boolean, true if the name exists, otherwise false.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native boolean H5Lexists(int loc_id, String name, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lget_info returns information about the specified link.
*
* @param loc_id IN: Identifier of the file or group.
* @param name IN: Name of the link for which information is being sought.
* @param lapl_id IN: Link access property list identifier
*
* @return a buffer(H5L_info_t) for the link information.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native H5L_info_t H5Lget_info(int loc_id, String name,
int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lget_info_by_idx opens a named datatype at the location specified
* by loc_id and return an identifier for the datatype.
*
* @param loc_id IN: File or group identifier specifying location of subject group
* @param group_name IN: Name of subject group
* @param idx_type IN: Type of index
* @param order IN: Order within field or index
* @param n IN: Link for which to retrieve information
* @param lapl_id IN: Link access property list identifier
*
* @return a buffer(H5L_info_t) for the link information.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - group_name is null.
**/
public synchronized static native H5L_info_t H5Lget_info_by_idx(int loc_id, String group_name,
int idx_type, int order, long n, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lget_name_by_idx retrieves name of the nth link in a group, according to
* the order within a specified field or index.
*
* @param loc_id IN: File or group identifier specifying location of subject group
* @param group_name IN: Name of subject group
* @param idx_type IN: Type of index
* @param order IN: Order within field or index
* @param n IN: Link for which to retrieve information
* @param lapl_id IN: Link access property list identifier
*
* @return a String for the link name.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - group_name is null.
**/
public synchronized static native String H5Lget_name_by_idx(int loc_id, String group_name,
int idx_type, int order, long n, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lget_val returns the link value of a symbolic link.
*
* @param loc_id IN: Identifier of the file or group containing the object.
* @param name IN: Name of the symbolic link.
* @param link_value OUT: Path of the symbolic link, or the file_name and path of an external file.
* @param lapl_id IN: Link access property list identifier
*
* @return the link type
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native int H5Lget_val(int loc_id, String name, String[] link_value, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lget_val_by_idx retrieves value of the nth link in a group, according to the order within an index.
*
* @param loc_id IN: File or group identifier specifying location of subject group
* @param group_name IN: Name of subject group
* @param idx_type IN: Type of index
* @param order IN: Order within field or index
* @param n IN: Link for which to retrieve information
* @param link_value OUT: Path of the symbolic link, or the file_name and path of an external file.
* @param lapl_id IN: Link access property list identifier
*
* @return the link type
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - group_name is null.
**/
public synchronized static native int H5Lget_val_by_idx(int loc_id, String group_name,
int idx_type, int order, long n, String[] link_value, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Literate iterates through links in a group.
*
* @param grp_id IN: Identifier specifying subject group
* @param idx_type IN: Type of index
* @param order IN: Order of iteration within index
* @param idx IN: Iteration position at which to start
* @param op IN: Callback function passing data regarding the link to the calling application
* @param op_data IN: User-defined pointer to data required by the application for its processing of the link
*
* @return returns the return value of the first operator that returns a positive value, or zero if all members were
* processed with no operator returning non-zero.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Literate(int grp_id,
int idx_type, int order,
long idx, H5L_iterate_cb op, H5L_iterate_t op_data)
throws HDF5LibraryException;
/**
* H5Literate_by_name iterates through links in a group.
*
* @param grp_id IN: Identifier specifying subject group
* @param group_name IN: Name of subject group
* @param idx_type IN: Type of index
* @param order IN: Order of iteration within index
* @param idx IN: Iteration position at which to start
* @param op IN: Callback function passing data regarding the link to the calling application
* @param op_data IN: User-defined pointer to data required by the application for its processing of the link
* @param lapl_id IN: Link access property list identifier
*
* @return returns the return value of the first operator that returns a positive value, or zero if all members were
* processed with no operator returning non-zero.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - group_name is null.
**/
public synchronized static native int H5Literate_by_name(int loc_id, String group_name,
int idx_type, int order, long idx,
H5L_iterate_cb op, H5L_iterate_t op_data, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lmove renames a link within an HDF5 file.
*
* @param src_loc IN: Original file or group identifier.
* @param src_name IN: Original link name.
* @param dst_loc IN: Destination file or group identifier.
* @param dst_name IN: New link name.
* @param lcpl_id IN: Link creation property list identifier to be associated with the new link.
* @param lapl_id IN: Link access property list identifier to be associated with the new link.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native void H5Lmove(int src_loc, String src_name, int dst_loc,
String dst_name, int lcpl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Lvisit recursively visits all links starting from a specified group.
*
* @param grp_id IN: Identifier specifying subject group
* @param idx_type IN: Type of index
* @param order IN: Order of iteration within index
* @param op IN: Callback function passing data regarding the link to the calling application
* @param op_data IN: User-defined pointer to data required by the application for its processing of the link
*
* @return returns the return value of the first operator that returns a positive value, or zero if all members were
* processed with no operator returning non-zero.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Lvisit(int grp_id, int idx_type, int order,
H5L_iterate_cb op, H5L_iterate_t op_data)
throws HDF5LibraryException;
/**
* H5Lvisit_by_name recursively visits all links starting from a specified group.
*
* @param loc_id IN: Identifier specifying subject group
* @param group_name IN: Name of subject group
* @param idx_type IN: Type of index
* @param order IN: Order of iteration within index
* @param op IN: Callback function passing data regarding the link to the calling application
* @param op_data IN: User-defined pointer to data required by the application for its processing of the link
*
* @return returns the return value of the first operator that returns a positive value, or zero if all members were
* processed with no operator returning non-zero.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - group_name is null.
**/
public synchronized static native int H5Lvisit_by_name(int loc_id, String group_name,
int idx_type, int order, H5L_iterate_cb op,
H5L_iterate_t op_data, int lapl_id)
throws HDF5LibraryException, NullPointerException;
//////////////////////////////////////////////////////////////
////
//H5O: HDF5 1.8 Object Interface API Functions //
////
//////////////////////////////////////////////////////////////
/**
* H5Oclose closes the group, dataset, or named datatype specified.
*
* @param object_id IN: Object identifier
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Oclose(int object_id) throws HDF5LibraryException
{
if (object_id < 0)
throw new HDF5LibraryException("Negative ID");;
OPEN_IDS.removeElement(object_id);
return _H5Oclose(object_id);
}
private synchronized static native int _H5Oclose(int object_id)
throws HDF5LibraryException;
/**
* H5Ocopy copies the group, dataset or named datatype specified from the file or
* group specified by source location to the destination location.
*
* @param src_loc_id IN: Object identifier indicating the location of the source object to be copied
* @param src_name IN: Name of the source object to be copied
* @param dst_loc_id IN: Location identifier specifying the destination
* @param dst_name IN: Name to be assigned to the new copy
* @param ocpypl_id IN: Object copy property list
* @param lcpl_id IN: Link creation property list for the new hard link
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native void H5Ocopy(int src_loc_id, String src_name, int dst_loc_id,
String dst_name, int ocpypl_id, int lcpl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Oget_comment retrieves the comment for the specified object.
*
* @param obj_id IN: File or group identifier
*
* @return the comment
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native String H5Oget_comment(int obj_id)
throws HDF5LibraryException;
/**
* H5Oset_comment sets the comment for the specified object.
*
* @param obj_id IN: Identifier of the target object
* @param comment IN: The new comment.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native void H5Oset_comment(int obj_id, String comment)
throws HDF5LibraryException;
/**
* H5Oget_comment_by_name retrieves the comment for an object.
*
* @param loc_id IN: Identifier of a file, group, dataset, or named datatype.
* @param name IN: Relative name of the object whose comment is to be set or reset.
* @param lapl_id IN: Link access property list identifier.
*
* @return the comment
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native String H5Oget_comment_by_name(int loc_id, String name, int lapl_id)
throws HDF5LibraryException, NullPointerException;
//long H5Oget_comment_by_name(int loc_id, String name, String comment, long bufsize, int lapl_id);
/**
* H5Oset_comment_by_name sets the comment for the specified object.
*
* @param loc_id IN: Identifier of a file, group, dataset, or named datatype.
* @param name IN: Relative name of the object whose comment is to be set or reset.
* @param comment IN: The new comment.
* @param lapl_id IN: Link access property list identifier.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native void H5Oset_comment_by_name(int loc_id, String name,
String comment, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Oget_info retrieves the metadata for an object specified by an identifier.
*
* @param loc_id IN: Identifier for target object
*
* @return object information
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native H5O_info_t H5Oget_info(int loc_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Oget_info_by_idx retrieves the metadata for an object, identifying the object by an index position.
*
* @param loc_id IN: File or group identifier
* @param group_name IN: Name of group, relative to loc_id, in which object is located
* @param idx_type IN: Type of index by which objects are ordered
* @param order IN: Order of iteration within index
* @param n IN: Object to open
* @param lapl_id IN: Access property list identifier for the link pointing to the object (Not currently used; pass as H5P_DEFAULT.)
*
* @return object information
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native H5O_info_t H5Oget_info_by_idx(int loc_id, String group_name,
int idx_type, int order, long n, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and relative name.
*
* @param loc_id IN: File or group identifier specifying location of group in which object is located
* @param name IN: Relative name of group
* @param lapl_id IN: Access property list identifier for the link pointing to the object (Not currently used; pass as H5P_DEFAULT.)
*
* @return object information
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native H5O_info_t H5Oget_info_by_name(int loc_id, String name, int lapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Olink creates a new hard link to an object in an HDF5 file.
*
* @param obj_id IN: Object to be linked.
* @param new_loc_id IN: File or group identifier specifying location at which object is to be linked.
* @param name IN: Relative name of link to be created.
* @param lcpl_id IN: Link creation property list identifier.
* @param lapl_id IN: Access property list identifier.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native void H5Olink(int obj_id, int new_loc_id, String new_name,
int lcpl_id, int lapl_id)
throws HDF5LibraryException, NullPointerException;
///**
//* H5Odecr_refcount decrements the hard link reference count for an object.
//*
//* @param object_id IN: Object identifier
//*
//* @return none
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//**/
//
//public synchronized static native void H5Odecr_refcount(int object_id)
// throws HDF5LibraryException;
///**
//* H5Oincr_refcount increments the hard link reference count for an object.
//*
//* @param object_id IN: Object identifier
//*
//* @return none
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//**/
//public synchronized static native void H5Oincr_refcount(int object_id)
// throws HDF5LibraryException;
/**
* H5Oopen opens a group, dataset, or named datatype specified by a location and a path name.
*
* @param loc_id IN: File or group identifier
* @param name IN: Relative path to the object
* @param lapl_id IN: Access property list identifier for the link pointing to the object
*
* @return an object identifier for the opened object
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public static int H5Oopen(int loc_id, String name, int lapl_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Oopen(loc_id, name, lapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Oopen(int loc_id, String name,
int lapl_id) throws HDF5LibraryException, NullPointerException;
//
///**
//* H5Oopen_by_addr opens a group, dataset, or named datatype using its address within an HDF5 file.
//*
//* @param loc_id IN: File or group identifier
//* @param addr IN: Object's address in the file
//*
//* @return an object identifier for the opened object
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//**/
//public synchronized static native int H5Oopen_by_addr(int loc_id, long addr)
// throws HDF5LibraryException;
//
///**
//* H5Oopen_by_idx opens the nth object in the group specified.
//*
//* @param loc_id IN: File or group identifier
//* @param group_name IN: Name of group, relative to loc_id, in which object is located
//* @param idx_type IN: Type of index by which objects are ordered
//* @param order IN: Order of iteration within index
//* @param n IN: Object to open
//* @param lapl_id IN: Access property list identifier for the link pointing to the object
//*
//* @return an object identifier for the opened object
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//* @exception NullPointerException - group_name is null.
//**/
//public synchronized static native int H5Oopen_by_idx(int loc_id, String group_name,
// H5_INDEX idx_type, H5_ITER order, long n, int lapl_id)
// throws HDF5LibraryException, NullPointerException;
////Prototype for H5Ovisit/H5Ovisit_by_name() operator
//public interface H5O_iterate_t extends Callback
//{
// int callback(int obj, String name, H5O_info_t info,
// Pointer op_data);
//}
/**
* H5Ovisit recursively visits all objects accessible from a specified object.
*
* @param obj_id IN: Identifier of the object at which the recursive iteration begins.
* @param idx_type IN: Type of index
* @param order IN: Order of iteration within index
* @param op IN: Callback function passing data regarding the object to the calling application
* @param op_data IN: User-defined pointer to data required by the application for its processing of the object
*
* @return returns the return value of the first operator that returns a positive value, or zero if all members were
processed with no operator returning non-zero.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native int H5Ovisit(int obj_id, int idx_type, int order,
H5O_iterate_cb op, H5O_iterate_t op_data)
throws HDF5LibraryException, NullPointerException;
/**
* H5Ovisit_by_name recursively visits all objects starting from a specified object.
*
* @param loc_id IN: File or group identifier
* @param obj_name IN: Relative path to the object
* @param idx_type IN: Type of index
* @param order IN: Order of iteration within index
* @param op IN: Callback function passing data regarding the object to the calling application
* @param op_data IN: User-defined pointer to data required by the application for its processing of the object
* @param lapl_id IN: Link access property list identifier
*
* @return returns the return value of the first operator that returns a positive value, or zero if all members
were processed with no operator returning non-zero.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native int H5Ovisit_by_name(int loc_id, String obj_name,
int idx_type, int order, H5O_iterate_cb op,
H5O_iterate_t op_data, int lapl_id)
throws HDF5LibraryException, NullPointerException;
// ////////////////////////////////////////////////////////////
// //
// H5P: Property List Interface Functions //
// //
// ////////////////////////////////////////////////////////////
public synchronized static native boolean H5Pall_filters_avail(int dcpl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pclose terminates access to a property list.
*
* @param plist
* IN: Identifier of the property list to terminate access to.
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Pclose(int plist) throws HDF5LibraryException
{
if (plist < 0)
throw new HDF5LibraryException("Negative ID");;
OPEN_IDS.removeElement(plist);
return _H5Pclose(plist);
}
private synchronized static native int _H5Pclose(int plist)
throws HDF5LibraryException;
/**
* Closes an existing property list class
*
* @param plid
* IN: Property list class to close
* @return a non-negative value if successful; a negative value if failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Pclose_class(int plid)
throws HDF5LibraryException;
/**
* H5Pcopy copies an existing property list to create a new property list.
*
* @param plist
* IN: Identifier of property list to duplicate.
*
* @return a property list identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Pcopy(int plist) throws HDF5LibraryException
{
int id = _H5Pcopy(plist);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Pcopy(int plist)
throws HDF5LibraryException;
/**
* H5Pcopy_prop copies a property from one property list or class to another
*
* @param dst_id
* IN: Identifier of the destination property list or class
* @param src_id
* IN: Identifier of the source property list or class
* @param name
* IN: Name of the property to copy
* @return a non-negative value if successful; a negative value if failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Pcopy_prop(int dst_id, int src_id,
String name) throws HDF5LibraryException;
/**
* H5Pcreate creates a new property as an instance of some property list
* class.
*
* @param type
* IN: The type of property list to create.
*
* @return a property list identifier (plist) if successful; otherwise Fail
* (-1).
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Pcreate(int type) throws HDF5LibraryException
{
int id = _H5Pcreate(type);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Pcreate(int type)
throws HDF5LibraryException;
//hid_t H5Pcreate_class( hid_t parent_class, const char *name, H5P_cls_create_func_t create, void *create_data, H5P_cls_copy_func_t copy, void *copy_data, H5P_cls_close_func_t close, void *close_data )
/**
* H5Pequal determines if two property lists or classes are equal
*
* @param plid1
* IN: First property object to be compared
* @param plid2
* IN: Second property object to be compared
* @return positive value if equal; zero if unequal, a negative value if
* failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Pequal(int plid1, int plid2)
throws HDF5LibraryException;
public static boolean H5P_equal(int plid1, int plid2)
throws HDF5LibraryException
{
if(H5Pequal(plid1, plid2)==1) return true;
return false;
}
/**
* H5Pexist determines whether a property exists within a property list or
* class
*
* @param plid
* IN: Identifier for the property to query
* @param name
* IN: Name of property to check for
* @return a positive value if the property exists in the property object;
* zero if the property does not exist; a negative value if failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Pexist(int plid, String name)
throws HDF5LibraryException;
public synchronized static native int H5Pfill_value_defined(int plist_id,
int[] status) throws HDF5LibraryException, NullPointerException;
/**
* H5Pget retrieves a copy of the value for a property in a property list
* (support integer only)
*
* @param plid
* IN: Identifier of property object to query
* @param name
* IN: Name of property to query
* @return value for a property if successful; a negative value if failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Pget(int plid, String name)
throws HDF5LibraryException;
/**
* Sets a property list value (support integer only)
*
* @param plid
* IN: Property list identifier to modify
* @param name
* IN: Name of property to modify
* @param value
* IN: value to set the property to
* @return a non-negative value if successful; a negative value if failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Pset(int plid, String name,
int value) throws HDF5LibraryException;
/**
* H5Pget_alignment retrieves the current settings for alignment properties
* from a file access property list.
*
* @param plist
* IN: Identifier of a file access property list.
* @param alignment
* OUT: threshold value and alignment value.
*
*
* alignment[0] = threshold // threshold value
* alignment[1] = alignment // alignment value
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - aligment array is null.
* @exception IllegalArgumentException
* - aligment array is invalid.
**/
public synchronized static native int H5Pget_alignment(int plist,
long[] alignment)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Pset_alignment sets the alignment properties of a file access property
* list so that any file object >= THRESHOLD bytes will be aligned on an
* address which is a multiple of ALIGNMENT.
*
* @param plist
* IN: Identifier for a file access property list.
* @param threshold
* IN: Threshold value.
* @param alignment
* IN: Alignment value.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_alignment(int plist,
long threshold, long alignment) throws HDF5LibraryException;
public synchronized static native int H5Pget_alloc_time(int plist_id,
int[] alloc_time) throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_alloc_time(int plist_id,
int alloc_time) throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_attr_creation_order retrieves the settings for tracking and indexing attribute creation order on an object
* @param ocpl_id IN: Object (group or dataset) creation property list identifier
*
* @return Flags specifying whether to track and index attribute creation order
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pget_attr_creation_order(int ocpl_id)
throws HDF5LibraryException;
/**
* H5Pset_attr_creation_order sets flags specifying whether to track and index attribute creation order on an object.
* @param ocpl_id IN: Object creation property list identifier
* @param crt_order_flags IN: Flags specifying whether to track and index attribute creation order
*
* @return Returns a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pset_attr_creation_order(int ocpl_id, int crt_order_flags)
throws HDF5LibraryException;
/**
* H5Pget_attr_phase_change retrieves attribute storage phase change thresholds.
* @param ocpl_id IN: : Object (dataset or group) creation property list identifier
* @param attributes
* The maximun and minimum no. of attributes
* to be stored.
*
*
* attributes[0] = The maximum number of attributes to be stored in compact storage
* attributes[1] = The minimum number of attributes to be stored in dense storage
*
*
* @return Returns a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - size is null.
*
**/
public synchronized static native int H5Pget_attr_phase_change(int ocpl_id, int []attributes)
throws HDF5LibraryException, NullPointerException;
//herr_t H5Pset_attr_phase_change( hid_t ocpl_id, unsigned max_compact, unsigned min_dense )
/**
* H5Pget_btree_ratio Get the B-tree split ratios for a dataset transfer
* property list.
*
* @param plist_id
* IN Dataset transfer property list
* @param left
* OUT split ratio for leftmost nodes
* @param right
* OUT split ratio for righttmost nodes
* @param middle
* OUT split ratio for all other nodes
*
* @return non-negative if succeed
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - an input array is null.
**/
public synchronized static native int H5Pget_btree_ratios(int plist_id,
double[] left, double[] middle, double[] right)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_btree_ratio Sets B-tree split ratios for a dataset transfer
* property list. The split ratios determine what percent of children go in
* the first node when a node splits.
*
* @param plist_id
* IN Dataset transfer property list
* @param left
* IN split ratio for leftmost nodes
* @param right
* IN split ratio for righttmost nodes
* @param middle
* IN split ratio for all other nodes
*
* @return non-negative if succeed
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_btree_ratios(int plist_id,
double left, double middle, double right)
throws HDF5LibraryException;
/**
* HH5Pget_buffer gets type conversion and background buffers. Returns
* buffer size, in bytes, if successful; otherwise 0 on failure.
*
* @param plist
* Identifier for the dataset transfer property list.
* @param tconv
* byte array of application-allocated type conversion buffer.
* @param bkg
* byte array of application-allocated background buffer.
*
* @return buffer size, in bytes, if successful; otherwise 0 on failure
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - plist is invalid.
**/
public synchronized static native int H5Pget_buffer(int plist,
byte[] tconv, byte[] bkg)
throws HDF5LibraryException, IllegalArgumentException;
public synchronized static native long H5Pget_buffer_size(int plist)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pset_buffer sets type conversion and background buffers. status to TRUE
* or FALSE.
*
* Given a dataset transfer property list, H5Pset_buffer sets the maximum
* size for the type conversion buffer and background buffer and optionally
* supplies pointers to application-allocated buffers. If the buffer size is
* smaller than the entire amount of data being transferred between the
* application and the file, and a type conversion buffer or background
* buffer is required, then strip mining will be used.
*
* Note that there are minimum size requirements for the buffer. Strip
* mining can only break the data up along the first dimension, so the
* buffer must be large enough to accommodate a complete slice that
* encompasses all of the remaining dimensions. For example, when strip
* mining a 100x200x300 hyperslab of a simple data space, the buffer must be
* large enough to hold 1x200x300 data elements. When strip mining a
* 100x200x300x150 hyperslab of a simple data space, the buffer must be
* large enough to hold 1x200x300x150 data elements.
*
* If tconv and/or bkg are null pointers, then buffers will be allocated and
* freed during the data transfer.
*
* @param plist
* Identifier for the dataset transfer property list.
* @param size
* Size, in bytes, of the type conversion and background buffers.
* @param tconv
* byte array of application-allocated type conversion buffer.
* @param bkg
* byte array of application-allocated background buffer.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - plist is invalid.
**/
public synchronized static native void H5Pset_buffer_size(int plist, long size)
throws HDF5LibraryException, IllegalArgumentException;
/**
* Retrieves the maximum possible number of elements in the meta data cache
* and the maximum possible number of bytes and the RDCC_W0 value in the raw
* data chunk cache.
*
* @param plist IN: Identifier of the file access property list.
* @param mdc_nelmts IN/OUT: No longer used, will be ignored.
* @param rdcc_nelmts IN/OUT: Number of elements (objects) in the raw data chunk cache.
* @param rdcc_nbytes IN/OUT: Total size of the raw data chunk cache, in bytes.
* @param rdcc_w0 IN/OUT: Preemption policy.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - an array is null.
**/
public synchronized static native int H5Pget_cache(int plist,
int[] mdc_nelmts, long[] rdcc_nelmts, long[] rdcc_nbytes,
double[] rdcc_w0) throws HDF5LibraryException, NullPointerException;
/**
* @deprecated As of HDF5 1.8, replaced by {@link #H5Pget_cache(int, int[], long[], long[], double[]) }
* because of possible loss of precision
**/
@Deprecated
public static int H5Pget_cache(int plist,
int[] mdc_nelmts, int[] rdcc_nelmts, int[] rdcc_nbytes,
double[] rdcc_w0) throws HDF5LibraryException, NullPointerException
{
long[] rdcc_nelmts_l = {rdcc_nelmts[0]};
long[] rdcc_nbytes_l = {rdcc_nbytes[0]};
int retval = H5Pget_cache(plist, mdc_nelmts, rdcc_nelmts_l, rdcc_nbytes_l, rdcc_w0);
rdcc_nelmts[0] = (int)rdcc_nelmts_l[0];
rdcc_nbytes[0] = (int)rdcc_nbytes_l[0];
return retval;
}
/**
* H5Pset_cache sets the number of elements (objects) in the meta data cache
* and the total number of bytes in the raw data chunk cache.
*
* @param plist IN: Identifier of the file access property list.
* @param mdc_nelmts IN: No longer used, will be ignored.
* @param rdcc_nelmts IN: Number of elements (objects) in the raw data chunk cache.
* @param rdcc_nbytes IN: Total size of the raw data chunk cache, in bytes.
* @param rdcc_w0 IN: Preemption policy.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_cache(int plist,
int mdc_nelmts, long rdcc_nelmts, long rdcc_nbytes, double rdcc_w0)
throws HDF5LibraryException;
public synchronized static native int H5Pget_char_encoding(int plist_id)
throws HDF5LibraryException;
public synchronized static native void H5Pset_char_encoding(int plist_id, int encoding)
throws HDF5LibraryException;
/**
* H5Pget_chunk retrieves the size of chunks for the raw data of a chunked
* layout dataset.
*
* @param plist
* IN: Identifier of property list to query.
* @param max_ndims
* IN: Size of the dims array.
* @param dims
* OUT: Array to store the chunk dimensions.
*
* @return chunk dimensionality successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - dims array is null.
* @exception IllegalArgumentException
* - max_ndims <=0
**/
public synchronized static native int H5Pget_chunk(int plist,
int max_ndims, long[] dims)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Pset_chunk sets the size of the chunks used to store a chunked layout
* dataset.
*
* @param plist
* IN: Identifier for property list to query.
* @param ndims
* IN: The number of dimensions of each chunk.
* @param dim
* IN: An array containing the size of each chunk.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - dims array is null.
* @exception IllegalArgumentException
* - dims <=0
**/
public synchronized static native int H5Pset_chunk(int plist, int ndims,
byte[] dim)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
public synchronized static int H5Pset_chunk(int plist, int ndims, long[] dim)
throws HDF5Exception, NullPointerException,
IllegalArgumentException
{
if (dim == null) {
return -1;
}
HDFArray theArray = new HDFArray(dim);
byte[] thedims = theArray.byteify();
int retVal = H5Pset_chunk(plist, ndims, thedims);
thedims = null;
theArray = null;
return retVal;
}
/**
* Retrieves the maximum possible number of elements in the meta data cache
* and the maximum possible number of bytes and the RDCC_W0 value in the raw
* data chunk cache on a per-datset basis.
*
* @param dapl_id IN: Identifier of the dataset access property list.
* @param rdcc_nslots IN/OUT: Number of elements (objects) in the raw data chunk cache.
* @param rdcc_nbytes IN/OUT: Total size of the raw data chunk cache, in bytes.
* @param rdcc_w0 IN/OUT: Preemption policy.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - an array is null.
**/
public synchronized static native void H5Pget_chunk_cache(int dapl_id,
long[] rdcc_nslots, long[] rdcc_nbytes, double[] rdcc_w0)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_chunk_cache sets the number of elements (objects) in the meta data cache
* and the total number of bytes in the raw data chunk cache on a per-datset basis.
*
* @param dapl_id IN: Identifier of the datset access property list.
* @param rdcc_nslots IN: Number of elements (objects) in the raw data chunk cache.
* @param rdcc_nbytes IN: Total size of the raw data chunk cache, in bytes.
* @param rdcc_w0 IN: Preemption policy.
*
* @return none
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Pset_chunk_cache(int dapl_id,
long rdcc_nslots, long rdcc_nbytes, double rdcc_w0)
throws HDF5LibraryException;
/**
* H5Pget_class returns the property list class for the property list
* identified by the plist parameter.
*
* @param plist
* IN: Identifier of property list to query.
* @return a property list class if successful. Otherwise returns
* H5P_NO_CLASS (-1).
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pget_class(int plist)
throws HDF5LibraryException;
/**
* H5Pget_class_name retrieves the name of a generic property list class
*
* @param plid
* IN: Identifier of property object to query
* @return name of a property list if successful; null if failed
* @throws HDF5LibraryException
*/
public synchronized static native String H5Pget_class_name(int plid)
throws HDF5LibraryException;
/**
* H5Pget_class_parent retrieves an identifier for the parent class of a
* property class
*
* @param plid
* IN: Identifier of the property class to query
* @return a valid parent class object identifier if successful; a negative
* value if failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Pget_class_parent(int plid)
throws HDF5LibraryException;
/**
* H5Pget_copy_object retrieves the properties to be used when an object is copied.
* @param ocp_plist_id IN: Object copy property list identifier
*
* @return Copy option(s) set in the object copy property list
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pget_copy_object(int ocp_plist_id)
throws HDF5LibraryException;
/**
* H5Pset_copy_object Sets properties to be used when an object is copied.
* @param ocp_plist_id IN: Object copy property list identifier
* @param copy_options IN: Copy option(s) to be set
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_copy_object(int ocp_plist_id, int copy_options)
throws HDF5LibraryException;
/**
* H5Pget_create_intermediate_group determines whether property is set to enable creating missing intermediate groups.
* @param lcpl_id IN: Link creation property list identifier
*
* @return Boolean true or false
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native boolean H5Pget_create_intermediate_group(int lcpl_id)
throws HDF5LibraryException;
/**
* H5Pset_create_intermediate_group specifies in property list whether to create missing intermediate groups
* @param lcpl_id IN: Link creation property list identifier
* @param crt_intermed_group IN: Flag specifying whether to create intermediate groups upon the creation of an object
*
* @return a non-negative valule if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pset_create_intermediate_group(int lcpl_id, boolean crt_intermed_group)
throws HDF5LibraryException;
/**
* H5Pget_data_transform retrieves the data transform expression previously set in the dataset transfer property list plist_id by H5Pset_data_transform.
* @param plist_id IN: Identifier of the property list or class
* @param size IN: Number of bytes of the transform expression to copy to
* @param expression OUT: A data transform expression
*
* @return The size of the transform expression if successful; 0(zero) if no transform expression exists. Otherwise returns a negative value.
*
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception IllegalArgumentException - Size is <= 0.
*
**/
public synchronized static native long H5Pget_data_transform( int plist_id, String[] expression, long size)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pset_data_transform sets a data transform expression
* @param plist_id IN: Identifier of the property list or class
* @param expression IN: Pointer to the null-terminated data transform expression
*
* @return a non-negative valule if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - expression is null.
*
**/
public synchronized static native int H5Pset_data_transform(int plist_id, String expression)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_driver returns the identifier of the low-level file driver
* associated with the file access property list or data transfer
* property list plid.
*
* @param plid
* IN: File access or data transfer property list identifier.
* @return a valid low-level driver identifier if successful; a negative value if failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Pget_driver(int plid)
throws HDF5LibraryException;
//herr_t H5Pset_driver( hid_t plist_id, hid_t new_driver_id, const void *new_driver_info )
//void *H5Pget_driver_info( hid_t plist_id )
//herr_t H5Pget_dxpl_mpio( hid_t dxpl_id, H5FD_mpio_xfer_t *xfer_mode )
//herr_t H5Pset_dxpl_mpio( hid_t dxpl_id, H5FD_mpio_xfer_t xfer_mode )
//herr_t H5Pset_dxpl_mpio_chunk_opt (hid_t dxpl_id, H5FD_mpio_chunk_opt_t opt_mode)
//herr_t H5Pset_dxpl_mpio_chunk_opt_num (hid_t dxpl_id, unsigned num_chunk_per_proc)
//herr_t H5Pset_dxpl_mpio_chunk_opt_ratio (hid_t dxpl_id, unsigned percent_proc_per_chunk)
//herr_t H5Pset_dxpl_mpio_collective_opt (hid_t dxpl_id, H5FD_mpio_collective_opt_t opt_mode)
public synchronized static native void H5Pget_dxpl_multi(int dxpl_id, int[] memb_dxpl)
throws HDF5LibraryException, NullPointerException;
public synchronized static native void H5Pset_dxpl_multi(int dxpl_id, int[] memb_dxpl)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pget_edc_check(int plist)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_edc_check(int plist, int check)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_elink_acc_flags retrieves the external link traversal file access flag from the specified link access property list.
* @param lapl_id IN: Link access property list identifier
*
* @return File access flag for link traversal.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pget_elink_acc_flags(int lapl_id)
throws HDF5LibraryException;
/**
* H5Pset_elink_acc_flags Sets the external link traversal file access flag in a link access property list.
* @param lapl_id IN: Link access property list identifier
* @param flags IN: The access flag for external link traversal.
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception IllegalArgumentException - Invalid Flag values.
*
**/
public synchronized static native int H5Pset_elink_acc_flags(int lapl_id, int flags)
throws HDF5LibraryException, IllegalArgumentException;
//herr_t H5Pget_elink_cb( hid_t lapl_id, H5L_elink_traverse_t *func, void **op_data )
//herr_t H5Pset_elink_cb( hid_t lapl_id, H5L_elink_traverse_t func, void *op_data )
/**
* H5Pget_elink_fapl Retrieves the file access property list identifier associated with
* the link access property list.
*
* @param lapl_id IN: Link access property list identifier
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public static int H5Pget_elink_fapl(int lapl_id)
throws HDF5LibraryException
{
int id = _H5Pget_elink_fapl(lapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Pget_elink_fapl(int lapl_id)
throws HDF5LibraryException;
/**
* H5Pset_elink_fapl sets a file access property list for use in accessing a
* file pointed to by an external link.
*
* @param lapl_id IN: Link access property list identifier
* @param fapl_id IN: File access property list identifier
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pset_elink_fapl(int lapl_id, int fapl_id)
throws HDF5LibraryException;
/**
* H5Pget_elink_file_cache_size retrieves the size of the external link open file cache.
* @param fapl_id IN: File access property list identifier
*
* @return External link open file cache size in number of files.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pget_elink_file_cache_size(int fapl_id)
throws HDF5LibraryException;
/**
* H5Pset_elink_file_cache_size sets the number of files that can be held open in an external link open file cache.
* @param fapl_id IN: File access property list identifier
* @param efc_size IN: External link open file cache size in number of files.
*
* @return none.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_elink_file_cache_size(int fapl_id, int efc_size)
throws HDF5LibraryException;
/**
* H5Pget_elink_prefix Retrieves prefix applied to external link paths.
* @param lapl_id IN: Link access property list identifier
* @param prefix OUT: Prefix applied to external link paths
*
* @return If successful, returns a non-negative value specifying the size in bytes of the prefix without the NULL terminator;
* otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - prefix is null.
*
**/
public synchronized static native long H5Pget_elink_prefix(int lapl_id, String[] prefix)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_elink_prefix Sets prefix to be applied to external link paths.
* @param lapl_id IN: Link access property list identifier
* @param prefix IN: Prefix to be applied to external link paths
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - prefix is null.
*
**/
public synchronized static native int H5Pset_elink_prefix(int lapl_id, String prefix)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_est_link_info Queries data required to estimate required local heap or object header size.
* @param gcpl_id IN: Group creation property list identifier
* @param link_info
* Estimated number of links to be inserted into group
* And the estimated average length of link names
*
*
* link_info[0] = Estimated number of links to be inserted into group
* link_info[1] = Estimated average length of link names
*
*
* @return Returns a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - link_info is null.
*
**/
public synchronized static native int H5Pget_est_link_info(int gcpl_id, int []link_info)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_est_link_info Sets estimated number of links and length of link names in a group.
* @param gcpl_id IN: Group creation property list identifier
* @param est_num_entries IN: Estimated number of links to be inserted into group
* @param est_name_len IN: Estimated average length of link names
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception IllegalArgumentException - Invalid values to est_num_entries and est_name_len.
*
**/
public synchronized static native int H5Pset_est_link_info(int gcpl_id, int est_num_entries, int est_name_len)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_external returns information about an external file.
*
* @param plist
* IN: Identifier of a dataset creation property list.
* @param idx
* IN: External file index.
* @param name_size
* IN: Maximum length of name array.
* @param name
* OUT: Name of the external file.
* @param size
* OUT: the offset value and the size of the external file data.
*
*
* size[0] = offset // a location to return an offset value
* size[1] = size // a location to return the size of
* // the external file data.
*
*
* @return a non-negative value if successful
*
* @exception ArrayIndexOutOfBoundsException
* Fatal error on Copyback
* @exception ArrayStoreException
* Fatal error on Copyback
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name or size is null.
* @exception IllegalArgumentException
* - name_size <= 0 .
*
**/
public synchronized static native int H5Pget_external(int plist, int idx,
long name_size, String[] name, long[] size)
throws ArrayIndexOutOfBoundsException, ArrayStoreException,
HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Pset_external adds an external file to the list of external files.
*
* @param plist
* IN: Identifier of a dataset creation property list.
* @param name
* IN: Name of an external file.
* @param offset
* IN: Offset, in bytes, from the beginning of the file to the
* location in the file where the data starts.
* @param size
* IN: Number of bytes reserved in the file for the data.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native int H5Pset_external(int plist,
String name, long offset, long size)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_external_count returns the number of external files for the
* specified dataset.
*
* @param plist
* IN: Identifier of a dataset creation property list.
*
* @return the number of external files if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pget_external_count(int plist)
throws HDF5LibraryException;
public synchronized static native long H5Pget_family_offset(int fapl_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_family_offset(int fapl_id,
long offset) throws HDF5LibraryException, NullPointerException;
public synchronized static native void H5Pget_fapl_core(int fapl_id,
long[] increment, boolean[] backing_store)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_fapl_core(int fapl_id,
long increment, boolean backing_store)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_fapl_direct Retrieve direct I/O settings.
* @param fapl_id IN: File access property list identifier
* @param info[0] = alignment OUT: Required memory alignment boundary
* @param info[1] = block_size OUT: File system block size
* @param info[2] = cbuf_size OUT: Copy buffer size
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pget_fapl_direct(int fapl_id, long[]info) throws HDF5LibraryException;
/**
* H5Pset_fapl_direct Sets up use of the direct I/O driver.
* @param fapl_id IN: File access property list identifier
* @param alignment IN: Required memory alignment boundary
* @param block_size IN: File system block size
* @param cbuf_size IN: Copy buffer size
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pset_fapl_direct(int fapl_id, long alignment, long block_size, long cbuf_size)
throws HDF5LibraryException;
public synchronized static native int H5Pget_fapl_family(int fapl_id,
long[] memb_size, int[] memb_fapl_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_fapl_family(int fapl_id,
long memb_size, int memb_fapl_id)
throws HDF5LibraryException, NullPointerException;
//herr_t H5Pget_fapl_mpio( int fapl_id, MPI_Comm *comm, MPI_Info *info )
//herr_t H5Pset_fapl_mpio( int fapl_id, MPI_Comm comm, MPI_Info info )
//herr_t H5Pget_fapl_mpiposix( int fapl_id, MPI_Comm *comm, hbool_t *use_gpfs_hints )
//herr_t H5Pset_fapl_mpiposix( int fapl_id, MPI_Comm comm, hbool_t use_gpfs_hints )
/**
* H5Pget_fapl_multi Sets up use of the multi I/O driver.
* @param fapl_id IN: File access property list identifier
* @param memb_map IN: Maps memory usage types to other memory usage types.
* @param memb_fapl IN: Property list for each memory usage type.
* @param memb_name IN: Name generator for names of member files.
* @param memb_addr IN: The offsets within the virtual address space, from 0 (zero) to HADDR_MAX, at which each type of data storage begins.
*
* @return a boolean value; Allows read-only access to incomplete file sets when TRUE.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - an array is null.
*
**/
public synchronized static native boolean H5Pget_fapl_multi(int fapl_id, int[] memb_map,
int[] memb_fapl, String[] memb_name, long[] memb_addr)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_fapl_multi Sets up use of the multi I/O driver.
* @param fapl_id IN: File access property list identifier
* @param memb_map IN: Maps memory usage types to other memory usage types.
* @param memb_fapl IN: Property list for each memory usage type.
* @param memb_name IN: Name generator for names of member files.
* @param memb_addr IN: The offsets within the virtual address space, from 0 (zero) to HADDR_MAX, at which each type of data storage begins.
* @param relax IN: Allows read-only access to incomplete file sets when TRUE.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - an array is null.
*
**/
public synchronized static native void H5Pset_fapl_multi(int fapl_id, int[] memb_map,
int[] memb_fapl, String[] memb_name, long[] memb_addr, boolean relax)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pget_fclose_degree(int plist_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_fclose_degree(int plist,
int degree) throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pget_fill_time(int plist_id,
int[] fill_time) throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_fill_time(int plist_id,
int fill_time) throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_fill_value queries the fill value property of a dataset creation
* property list.
*
* @param plist_id
* IN: Property list identifier.
* @param type_id
* IN: The datatype identifier of value.
* @param value
* IN: The fill value.
*
* @return a non-negative value if successful
*
**/
public synchronized static native int H5Pget_fill_value(int plist_id,
int type_id, byte[] value) throws HDF5Exception;
/**
* H5Pget_fill_value queries the fill value property of a dataset creation
* property list.
*
* @param plist_id
* IN: Property list identifier.
* @param type_id
* IN: The datatype identifier of value.
* @param obj
* IN: The fill value.
*
* @return a non-negative value if successful
*
**/
public synchronized static int H5Pget_fill_value(int plist_id, int type_id,
Object obj) throws HDF5Exception
{
HDFArray theArray = new HDFArray(obj);
byte[] buf = theArray.emptyBytes();
int status = H5Pget_fill_value(plist_id, type_id, buf);
if (status >= 0) {
obj = theArray.arrayify(buf);
}
return status;
}
/**
* H5Pset_fill_value sets the fill value for a dataset creation property
* list.
*
* @param plist_id
* IN: Property list identifier.
* @param type_id
* IN: The datatype identifier of value.
* @param value
* IN: The fill value.
*
* @return a non-negative value if successful
*
* @exception HDF5Exception
* - Error converting data array
**/
public synchronized static native int H5Pset_fill_value(int plist_id,
int type_id, byte[] value) throws HDF5Exception;
/**
* H5Pset_fill_value sets the fill value for a dataset creation property
* list.
*
* @param plist_id
* IN: Property list identifier.
* @param type_id
* IN: The datatype identifier of value.
* @param obj
* IN: The fill value.
*
* @return a non-negative value if successful
*
* @exception HDF5Exception
* - Error converting data array
**/
public synchronized static int H5Pset_fill_value(int plist_id, int type_id,
Object obj) throws HDF5Exception
{
HDFArray theArray = new HDFArray(obj);
byte[] buf = theArray.byteify();
int retVal = H5Pset_fill_value(plist_id, type_id, buf);
buf = null;
theArray = null;
return retVal;
}
/**
* H5Pget_filter returns information about a filter, specified by its filter
* number, in a filter pipeline, specified by the property list with which
* it is associated.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Pget_filter(int, int, int[], int[], int[], int, String[], int[]) }
*
* @param plist
* IN: Property list identifier.
* @param filter_number
* IN: Sequence number within the filter pipeline of the filter
* for which information is sought.
* @param flags
* OUT: Bit vector specifying certain general properties of the
* filter.
* @param cd_nelmts
* IN/OUT: Number of elements in cd_values
* @param cd_values
* OUT: Auxiliary data for the filter.
* @param namelen
* IN: Anticipated number of characters in name.
* @param name
* OUT: Name of the filter.
*
* @return the filter identification number if successful. Otherwise returns
* H5Z_FILTER_ERROR (-1).
*
* @exception ArrayIndexOutOfBoundsException
* Fatal error on Copyback
* @exception ArrayStoreException
* Fatal error on Copyback
* @exception NullPointerException
* - name or an array is null.
*
**/
@Deprecated
public synchronized static native int H5Pget_filter(int plist, int filter_number, int[] flags,
int[] cd_nelmts, int[] cd_values, int namelen, String[] name)
throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException,
NullPointerException;
/**
* H5Pget_filter returns information about a filter, specified by its filter
* number, in a filter pipeline, specified by the property list with which
* it is associated.
*
* @param plist IN: Property list identifier.
* @param filter_number IN: Sequence number within the filter pipeline of the filter
* for which information is sought.
* @param flags OUT: Bit vector specifying certain general properties of the
* filter.
* @param cd_nelmts IN/OUT: Number of elements in cd_values
* @param cd_values OUT: Auxiliary data for the filter.
* @param namelen IN: Anticipated number of characters in name.
* @param name OUT: Name of the filter.
* @param filter_config OUT:A bit field encoding the returned filter information
*
* @return the filter identification number if successful. Otherwise returns
* H5Z_FILTER_ERROR (-1).
*
* @exception ArrayIndexOutOfBoundsException
* Fatal error on Copyback
* @exception ArrayStoreException
* Fatal error on Copyback
* @exception NullPointerException
* - name or an array is null.
*
**/
public static int H5Pget_filter(int plist, int filter_number, int[] flags, long[] cd_nelmts,
int[] cd_values, long namelen, String[] name, int[] filter_config)
throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException,
NullPointerException
{
return H5Pget_filter2(plist, filter_number, flags, cd_nelmts, cd_values, namelen,
name, filter_config);
}
/**
* H5Pget_filter2 returns information about a filter, specified by its filter
* number, in a filter pipeline, specified by the property list with which
* it is associated.
*
* @see public static int H5Pget_filter(int plist, int filter_number, int[] flags,
* int[] cd_nelmts, int[] cd_values, int namelen, String[] name, int[] filter_config)
*
**/
private synchronized static native int H5Pget_filter2(int plist, int filter_number, int[] flags,
long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config)
throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException,
NullPointerException;
/**
* H5Pset_filter adds the specified filter and corresponding properties to
* the end of an output filter pipeline.
*
* @param plist
* IN: Property list identifier.
* @param filter
* IN: Filter to be added to the pipeline.
* @param flags
* IN: Bit vector specifying certain general properties of the
* filter.
* @param cd_nelmts
* IN: Number of elements in cd_values
* @param cd_values
* IN: Auxiliary data for the filter.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_filter(int plist, int filter,
int flags, long cd_nelmts, int[] cd_values)
throws HDF5LibraryException;
//herr_t H5Pset_filter_callback(hid_t plist, H5Z_filter_func_t func, void *op_data)
/**
* H5Pget_filter_by_id returns information about the filter specified in filter_id, a
* filter identifier. plist_id must be a dataset or group creation property list and
* filter_id must be in the associated filter pipeline. The filter_id and flags parameters
* are used in the same manner as described in the discussion of H5Pset_filter. Aside from
* the fact that they are used for output, the parameters cd_nelmts and cd_values[] are
* used in the same manner as described in the discussion of H5Pset_filter. On input, the
* cd_nelmts parameter indicates the number of entries in the cd_values[] array allocated
* by the calling program; on exit it contains the number of values defined by the filter.
* On input, the namelen parameter indicates the number of characters allocated for the
* filter name by the calling program in the array name[]. On exit name[] contains the name
* of the filter with one character of the name in each element of the array. If the filter
* specified in filter_id is not set for the property list, an error will be returned and
* H5Pget_filter_by_id1 will fail.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Pget_filter_by_id(int, int, int[], int[], int[], int, String[], int[]) }
*
* @param plist_id IN: Property list identifier.
* @param filter_id IN: Filter identifier.
* @param flags OUT: Bit vector specifying certain general properties of the
* filter.
* @param cd_nelmts IN/OUT: Number of elements in cd_values
* @param cd_values OUT: Auxiliary data for the filter.
* @param namelen IN: Anticipated number of characters in name.
* @param name OUT: Name of the filter.
*
* @return the filter identification number if successful. Otherwise returns
* H5Z_FILTER_ERROR (-1).
*
* @exception ArrayIndexOutOfBoundsException
* Fatal error on Copyback
* @exception ArrayStoreException
* Fatal error on Copyback
* @exception NullPointerException
* - name or an array is null.
*
**/
@Deprecated
public synchronized static native int H5Pget_filter_by_id(int plist_id,
int filter_id, int[] flags, long[] cd_nelmts, int[] cd_values,
long namelen, String[] name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_filter_by_id returns information about the filter specified in filter_id, a
* filter identifier. plist_id must be a dataset or group creation property list and
* filter_id must be in the associated filter pipeline. The filter_id and flags parameters
* are used in the same manner as described in the discussion of H5Pset_filter. Aside from
* the fact that they are used for output, the parameters cd_nelmts and cd_values[] are
* used in the same manner as described in the discussion of H5Pset_filter. On input, the
* cd_nelmts parameter indicates the number of entries in the cd_values[] array allocated
* by the calling program; on exit it contains the number of values defined by the filter.
* On input, the namelen parameter indicates the number of characters allocated for the
* filter name by the calling program in the array name[]. On exit name[] contains the name
* of the filter with one character of the name in each element of the array. If the filter
* specified in filter_id is not set for the property list, an error will be returned and
* H5Pget_filter_by_id1 will fail.
*
* @param plist_id IN: Property list identifier.
* @param filter_id IN: Filter identifier.
* @param flags OUT: Bit vector specifying certain general properties of the
* filter.
* @param cd_nelmts IN/OUT: Number of elements in cd_values
* @param cd_values OUT: Auxiliary data for the filter.
* @param namelen IN: Anticipated number of characters in name.
* @param name OUT: Name of the filter.
* @param filter_config OUT:A bit field encoding the returned filter information
*
* @return the filter identification number if successful. Otherwise returns
* H5Z_FILTER_ERROR (-1).
*
* @exception ArrayIndexOutOfBoundsException
* Fatal error on Copyback
* @exception ArrayStoreException
* Fatal error on Copyback
* @exception NullPointerException
* - name or an array is null.
*
**/
public static int H5Pget_filter_by_id(int plist_id,
int filter_id, int[] flags, long[] cd_nelmts, int[] cd_values,
long namelen, String[] name, int[] filter_config)
throws ArrayIndexOutOfBoundsException, ArrayStoreException,
HDF5LibraryException, NullPointerException
{
return H5Pget_filter_by_id2(plist_id, filter_id, flags, cd_nelmts, cd_values,
namelen, name, filter_config);
}
/**
* H5Pget_filter_by_id2 returns information about a filter, specified by its filter
* id, in a filter pipeline, specified by the property list with which
* it is associated.
*
* @see public static int H5Pget_filter_by_id(int plist,
int filter_id, int[] flags, int[] cd_nelmts, int[] cd_values,
int namelen, String[] name, int[] filter_config)
**/
public synchronized static native int H5Pget_filter_by_id2(int plist_id,
int filter_id, int[] flags, long[] cd_nelmts, int[] cd_values,
long namelen, String[] name, int[] filter_config)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_gc_references Returns the current setting for the garbage
* collection refernces property from a file access property list.
*
* libver[0] = The earliest version of the library that will be used for writing objects
* libver[1] = The latest version of the library that will be used for writing objects.
*
*
* @return Returns a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - size is null.
*
**/
public synchronized static native int H5Pget_libver_bounds(int fapl_id, int []libver)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_libver_bounds Sets bounds on library versions, and indirectly format versions, to be used when creating objects
* @param fapl_id IN: File access property list identifier
* @param low IN: The earliest version of the library that will be used for writing objects
* @param high IN: The latest version of the library that will be used for writing objects.
*
*
* @return Returns a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception IllegalArgumentException - Argument is Illegal
*
**/
public synchronized static native int H5Pset_libver_bounds(int fapl_id, int low, int high)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_link_creation_order queries the group creation property list, gcpl_id, and returns a flag indicating whether link creation order is tracked and/or indexed in a group.
* @param gcpl_id IN: Group creation property list identifier
*
* @return crt_order_flags -Creation order flag(s)
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pget_link_creation_order(int gcpl_id)
throws HDF5LibraryException;
/**
* H5Pset_link_creation_order Sets flags in a group creation property list, gcpl_id, for tracking and/or indexing links on creation order.
* @param gcpl_id IN: Group creation property list identifier
* @param crt_order_flags IN: Creation order flag(s)
*
*
* @return Returns a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pset_link_creation_order(int gcpl_id, int crt_order_flags)
throws HDF5LibraryException;
/**
* H5Pget_link_phase_change Queries the settings for conversion between compact and dense groups.
* @param gcpl_id IN: Group creation property list identifier
* @param links
* The max. no. of compact links & the min. no. of dense
* links, which are used for storing groups
*
*
* links[0] = The maximum number of links for compact storage
* links[1] = The minimum number of links for dense storage
*
*
* @return Returns a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - size is null.
*
**/
public synchronized static native int H5Pget_link_phase_change(int gcpl_id, int []links)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_link_phase_change Sets the parameters for conversion between compact and dense groups.
* @param gcpl_id IN: Group creation property list identifier
* @param max_compact IN: Maximum number of links for compact storage(Default: 8)
* @param min_dense IN: Minimum number of links for dense storage(Default: 6)
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception IllegalArgumentException - Invalid values of max_compact and min_dense.
*
**/
public synchronized static native int H5Pset_link_phase_change(int gcpl_id, int max_compact, int min_dense)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_local_heap_size_hint Retrieves the anticipated size of the local heap for original-style groups.
* @param gcpl_id IN: Group creation property list identifier
*
* @return size_hint, the anticipated size of local heap
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native long H5Pget_local_heap_size_hint(int gcpl_id)
throws HDF5LibraryException;
/**
* H5Pset_local_heap_size_hint Specifies the anticipated maximum size of a local heap.
* @param gcpl_id IN: Group creation property list identifier
* @param size_hint IN: Anticipated maximum size in bytes of local heap
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pset_local_heap_size_hint(int gcpl_id, long size_hint)
throws HDF5LibraryException;
/**
* H5Pget_mdc_config gets the initial metadata cache configuration contained in a
* file access property list and loads it into the instance of H5AC_cache_config_t
* pointed to by the config_ptr parameter. This configuration is used when the file is opened.
*
* @param plist_id IN: Identifier of the file access property list.
*
* @return A buffer(H5AC_cache_config_t) for the current metadata cache configuration information
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native H5AC_cache_config_t H5Pget_mdc_config(int plist_id)
throws HDF5LibraryException;
public synchronized static native void H5Pset_mdc_config(int plist_id, H5AC_cache_config_t config_ptr)
throws HDF5LibraryException;
/**
* H5Pget_meta_block_size the current metadata block size setting.
* @param fapl_id IN: File access property list identifier
*
* @return the minimum size, in bytes, of metadata block allocations.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native long H5Pget_meta_block_size(int fapl_id)
throws HDF5LibraryException;
/**
* H5Pset_meta_block_size sets the minimum metadata block size.
* @param fapl_id IN: File access property list identifier
* @param size IN: Minimum size, in bytes, of metadata block allocations.
*
* @return none.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_meta_block_size(int fapl_id, long size)
throws HDF5LibraryException;
//herr_t H5Pget_multi_type ( hid_t fapl_id, H5FD_mem_t *type )
//herr_t H5Pset_multi_type ( hid_t fapl_id, H5FD_mem_t type )
/**
* H5Pget_nfilters returns the number of filters defined in the filter
* pipeline associated with the property list plist.
*
* @param plist
* IN: Property list identifier.
*
* @return the number of filters in the pipeline if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pget_nfilters(int plist)
throws HDF5LibraryException;
/**
* H5Pget_nlinks retrieves the maximum number of soft or user-defined link traversals allowed, nlinks, before the library assumes it has found a cycle and aborts the traversal. This value is retrieved from the link access property list lapl_id.
* @param lapl_id IN: File access property list identifier
*
* @return Returns a Maximum number of links to traverse.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native long H5Pget_nlinks(int lapl_id)
throws HDF5LibraryException;
/**
* H5Pset_nlinks sets the maximum number of soft or user-defined link traversals allowed, nlinks, before the library assumes it has found a cycle and aborts the traversal. This value is set in the link access property list lapl_id.
* @param fapl_id IN: File access property list identifier
* @param nlinks IN: Maximum number of links to traverse
*
* @return Returns a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception IllegalArgumentException - Argument is Illegal
*
**/
public synchronized static native int H5Pset_nlinks(int lapl_id, long nlinks)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_nprops retrieves the number of properties in a property list or
* class
*
* @param plid
* IN: Identifier of property object to query
* @return number of properties if successful; a negative value if failed
* @throws HDF5LibraryException
*/
public synchronized static native long H5Pget_nprops(int plid)
throws HDF5LibraryException;
/**
* H5Pget_preserve checks the status of the dataset transfer property list.
*
* @deprecated As of HDF5 1.8, compound datatype field preservation is now core functionality in the HDF5 Library.
*
* @param plist
* IN: Identifier for the dataset transfer property list.
*
* @return TRUE or FALSE if successful; otherwise returns a negative value
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
@Deprecated
public synchronized static native int H5Pget_preserve(int plist)
throws HDF5LibraryException;
/**
* H5Pset_preserve sets the dataset transfer property list status to TRUE or
* FALSE.
*
* @deprecated As of HDF5 1.8, compound datatype field preservation is now core functionality in the HDF5 Library.
*
* @param plist
* IN: Identifier for the dataset transfer property list.
* @param status
* IN: Status of for the dataset transfer property list.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - plist is invalid.
**/
@Deprecated
public synchronized static native int H5Pset_preserve(int plist,
boolean status)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_obj_track_times queries the object creation property list, ocpl_id,
* to determine whether object times are being recorded.
*
* @param ocpl_id IN: Object creation property list identifier
*
* @return TRUE or FALSE, specifying whether object times are being recorded
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native boolean H5Pget_obj_track_times(int ocpl_id)
throws HDF5LibraryException;
/**
* H5Pset_obj_track_times sets a property in the object creation property list, ocpl_id,
* that governs the recording of times associated with an object.
*
* @param ocpl_id IN: Object creation property list identifier
*
* @param track_times IN: TRUE or FALSE, specifying whether object times are to be tracked
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_obj_track_times(int ocpl_id, boolean track_times)
throws HDF5LibraryException;
/**
* H5Pget_shared_mesg_index Retrieves the configuration settings for a shared message index.
* @param fcpl_id IN: File creation property list identifier
* @param index_num IN: Index being configured.
* @param mesg_info
* The message type and minimum message size
*
*
* mesg_info[0] = Types of messages that may be stored in this index.
* mesg_info[1] = Minimum message size.
*
*
* @return Returns a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - mesg_info is null.
* @exception IllegalArgumentException - Invalid value of nindexes
*
**/
public synchronized static native int H5Pget_shared_mesg_index(int fcpl_id, int index_num, int []mesg_info)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Pset_shared_mesg_index Configures the specified shared object header message index
* @param fcpl_id IN: File creation property list identifier.
* @param index_num IN: Index being configured.
* @param mesg_type_flags IN: Types of messages that should be stored in this index.
* @param min_mesg_size IN: Minimum message size.
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception IllegalArgumentException - Invalid value of nindexes
*
**/
public synchronized static native int H5Pset_shared_mesg_index(int fcpl_id, int index_num, int mesg_type_flags, int min_mesg_size)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_shared_mesg_nindexes retrieves number of shared object header message indexes in file creation property list.
* @param fcpl_id IN: : File creation property list identifier
*
* @return nindexes, the number of shared object header message indexes available in files created with this property list
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pget_shared_mesg_nindexes(int fcpl_id)
throws HDF5LibraryException;
/**
* H5Pset_shared_mesg_nindexes sets the number of shared object header message indexes in the specified file creation property list.
* @param plist_id IN: File creation property list
* @param nindexes IN: Number of shared object header message indexes to be available in files created with this property list
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception IllegalArgumentException - Invalid value of nindexes
*
**/
public synchronized static native int H5Pset_shared_mesg_nindexes(int plist_id, int nindexes)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_shared_mesg_phase_change retrieves shared object header message phase change information.
* @param fcpl_id IN: : File creation property list identifier
* @param size
* The threshold values for storage of shared object header
* message indexes in a file.
*
*
* size[0] = Threshold above which storage of a shared object header message index shifts from list to B-tree
* size[1] = Threshold below which storage of a shared object header message index reverts to list format
*
*
* @return Returns a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - size is null.
*
**/
public synchronized static native int H5Pget_shared_mesg_phase_change(int fcpl_id, int []size)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_shared_mesg_phase_change sets shared object header message storage phase change thresholds.
* @param fcpl_id IN: File creation property list identifier
* @param max_list IN: Threshold above which storage of a shared object header message index shifts from list to B-tree
* @param min_btree IN: Threshold below which storage of a shared object header message index reverts to list format
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception IllegalArgumentException - Invalid values of max_list and min_btree.
*
**/
public synchronized static native int H5Pset_shared_mesg_phase_change(int fcpl_id, int max_list, int min_btree)
throws HDF5LibraryException, IllegalArgumentException;
public synchronized static native long H5Pget_sieve_buf_size(int fapl_id)
throws HDF5LibraryException;
public synchronized static native void H5Pset_sieve_buf_size(int fapl_id, long size)
throws HDF5LibraryException;
/**
* H5Pget_size retrieves the size of a property's value in bytes
*
* @param plid
* IN: Identifier of property object to query
* @param name
* IN: Name of property to query
* @return size of a property's value if successful; a negative value if
* failed
* @throws HDF5LibraryException
*/
public synchronized static native long H5Pget_size(int plid, String name)
throws HDF5LibraryException;
/**
* H5Pget_sizes retrieves the size of the offsets and lengths used in an
* HDF5 file. This function is only valid for file creation property lists.
*
* @param plist
* IN: Identifier of property list to query.
* @param size
* OUT: the size of the offsets and length.
*
*
* size[0] = sizeof_addr // offset size in bytes
* size[1] = sizeof_size // length size in bytes
*
* @return a non-negative value with the sizes initialized; if successful;
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - size is null.
* @exception IllegalArgumentException
* - size is invalid.
**/
public synchronized static native int H5Pget_sizes(int plist, long[] size)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Pset_sizes sets the byte size of the offsets and lengths used to
* address objects in an HDF5 file.
*
* @param plist
* IN: Identifier of property list to modify.
* @param sizeof_addr
* IN: Size of an object offset in bytes.
* @param sizeof_size
* IN: Size of an object length in bytes.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_sizes(int plist,
int sizeof_addr, int sizeof_size) throws HDF5LibraryException;
/**
* H5Pget_small_data_block_size retrieves the size of a block of small data
* in a file creation property list.
*
* @param plist
* IN: Identifier for property list to query.
* @param size
* OUT: Pointer to location to return block size.
*
* @return a non-negative value and the size of the user block; if
* successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - size is null.
**/
public synchronized static native int H5Pget_small_data_block_size(
int plist, long[] size)
throws HDF5LibraryException, NullPointerException;
public synchronized static native long H5Pget_small_data_block_size_long(
int plist)
throws HDF5LibraryException;
/**
* H5Pset_small_data_block_size reserves blocks of size bytes for the
* contiguous storage of the raw data portion of small datasets.
*
* @param plist
* IN: Identifier of property list to modify.
* @param size
* IN: Size of the blocks in bytes.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_small_data_block_size(
int plist, long size) throws HDF5LibraryException;
/**
* H5Pget_sym_k retrieves the size of the symbol table B-tree 1/2 rank and
* the symbol table leaf node 1/2 size.
*
* @param plist
* IN: Property list to query.
* @param size
* OUT: the symbol table's B-tree 1/2 rank and leaf node 1/2
* size.
*
*
* size[0] = ik // the symbol table's B-tree 1/2 rank
* size[1] = lk // leaf node 1/2 size
*
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - size is null.
* @exception IllegalArgumentException
* - size is invalid.
**/
public synchronized static native int H5Pget_sym_k(int plist, int[] size)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Pset_sym_k sets the size of parameters used to control the symbol table
* nodes.
*
* @param plist
* IN: Identifier for property list to query.
* @param ik
* IN: Symbol table tree rank.
* @param lk
* IN: Symbol table node size.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_sym_k(int plist, int ik, int lk)
throws HDF5LibraryException;
//herr_t H5Pget_type_conv_cb(hid_t plist, H5T_conv_except_func_t *func, void **op_data)
//herr_t H5Pset_type_conv_cb( hid_t plist, H5T_conv_except_func_t func, void *op_data)
/**
* H5Pget_userblock retrieves the size of a user block in a file creation
* property list.
*
* @param plist
* IN: Identifier for property list to query.
* @param size
* OUT: Pointer to location to return user-block size.
*
* @return a non-negative value and the size of the user block; if
* successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - size is null.
**/
public synchronized static native int H5Pget_userblock(int plist,
long[] size) throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_userblock sets the user block size of a file creation property
* list.
*
* @param plist
* IN: Identifier of property list to modify.
* @param size
* IN: Size of the user-block in bytes.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_userblock(int plist, long size)
throws HDF5LibraryException;
/**
* H5Pget_version retrieves the version information of various objects for a
* file creation property list.
*
* @param plist
* IN: Identifier of the file creation property list.
* @param version_info
* OUT: version information.
*
*
* version_info[0] = boot // boot block version number
* version_info[1] = freelist // global freelist version
* version_info[2] = stab // symbol tabl version number
* version_info[3] = shhdr // hared object header version
*
* @return a non-negative value, with the values of version_info
* initialized, if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - version_info is null.
* @exception IllegalArgumentException
* - version_info is illegal.
**/
public synchronized static native int H5Pget_version(int plist, int[] version_info)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
//herr_t H5Pget_vlen_mem_manager(hid_t plist, H5MM_allocate_t *alloc, void **alloc_info, H5MM_free_t *free, void **free_info )
//herr_t H5Pset_vlen_mem_manager(hid_t plist, H5MM_allocate_t alloc, void *alloc_info, H5MM_free_t free, void *free_info )
//herr_t H5Pinsert( hid_t plid, const char *name, size_t size, void *value, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_close_func_t close )
//herr_t H5Pinsert( hid_t plid, const char *name, size_t size, void *value, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close ) [2]
//herr_t H5Pinsert1( hid_t plid, const char *name, size_t size, void *value, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_close_func_t close )
//herr_t H5Pinsert2( hid_t plid, const char *name, size_t size, void *value, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close )
/**
* H5Pisa_class checks to determine whether a property list is a member of
* the specified class
*
* @param plist
* IN: Identifier of the property list
* @param pclass
* IN: Identifier of the property class
* @return a positive value if equal; zero if unequal; a negative value if
* failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Pisa_class(int plist, int pclass)
throws HDF5LibraryException;
//int H5Piterate( hid_t id, int * idx, H5P_iterate_t iter_func, void * iter_data )
public synchronized static native int H5Pmodify_filter(int plist,
int filter, int flags, long cd_nelmts, int[] cd_values)
throws HDF5LibraryException, NullPointerException;
// herr_t H5Pregister( hid_t class, const char * name, size_t size, void * default, H5P_prp_create_func_t create, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_close_func_t close ) [1]
// herr_t H5Pregister( hid_t class, const char * name, size_t size, void * default, H5P_prp_create_func_t create, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close ) [2]
//herr_t H5Pregister1( hid_t class, const char * name, size_t size, void * default, H5P_prp_create_func_t create, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_close_func_t close )
//herr_t H5Pregister2( hid_t class, const char * name, size_t size, void * default, H5P_prp_create_func_t create, H5P_prp_set_func_t set, H5P_prp_get_func_t get, H5P_prp_delete_func_t delete, H5P_prp_copy_func_t copy, H5P_prp_compare_func_t compare, H5P_prp_close_func_t close )
/**
* H5Punregister removes a property from a property list class
*
* @param plid
* IN: Property list class from which to remove permanent
* property
* @param name
* IN: Name of property to remove
* @return a non-negative value if successful; a negative value if failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Punregister(int plid, String name)
throws HDF5LibraryException;
/**
* H5Premove removes a property from a property list
*
* @param plid
* IN: Identifier of the property list to modify
* @param name
* IN: Name of property to remove
* @return a non-negative value if successful; a negative value if failed
* @throws HDF5LibraryException
*/
public synchronized static native int H5Premove(int plid, String name)
throws HDF5LibraryException;
public synchronized static native int H5Premove_filter(int obj_id,
int filter) throws HDF5LibraryException;
/**
* H5Pset_deflate sets the compression method for a dataset.
*
* @param plist
* IN: Identifier for the dataset creation property list.
* @param level
* IN: Compression level.
*
* @return non-negative if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_deflate(int plist, int level)
throws HDF5LibraryException;
/**
* H5Pset_fapl_log Sets up the logging virtual file driver (H5FD_LOG) for use.
* H5Pset_fapl_log modifies the file access property list to use the logging driver, H5FD_LOG.
* The logging virtual file driver (VFD) is a clone of the standard SEC2 (H5FD_SEC2) driver
* with additional facilities for logging VFD metrics and activity to a file.
*
* @deprecated As of HDF5 1.8.7, replaced by {@link #H5Pset_fapl_log(int, String, long, int)}
*
* @param fapl_id IN: File access property list identifier.
* @param logfile IN: logfile is the name of the file in which the logging entries are to be recorded.
* @param flags IN: Flags specifying the types of logging activity.
* @param buf_size IN: The size of the logging buffers, in bytes.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - logfile is null.
**/
@Deprecated
public static int H5Pset_fapl_log(int fapl_id,
String logfile, int flags, int buf_size)
throws HDF5LibraryException, NullPointerException
{
H5Pset_fapl_log(fapl_id, logfile, (long)flags, (long)buf_size);
return 1;
}
/**
* H5Pset_fapl_log Sets up the logging virtual file driver (H5FD_LOG) for use.
* H5Pset_fapl_log modifies the file access property list to use the logging driver, H5FD_LOG.
* The logging virtual file driver (VFD) is a clone of the standard SEC2 (H5FD_SEC2) driver
* with additional facilities for logging VFD metrics and activity to a file.
*
* @param fapl_id IN: File access property list identifier.
* @param logfile IN: logfile is the name of the file in which the logging entries are to be recorded.
* @param flags IN: Flags specifying the types of logging activity.
* @param buf_size IN: The size of the logging buffers, in bytes.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - logfile is null.
**/
public synchronized static native void H5Pset_fapl_log(int fapl_id,
String logfile, long flags, long buf_size)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_fapl_sec2(int fapl_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native void H5Pset_fapl_split(int fapl_id,
String meta_ext, int meta_plist_id, String raw_ext, int raw_plist_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_fapl_stdio(int fapl_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_fapl_windows(int fapl_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_fletcher32(int plist)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_nbit Sets up the use of the N-Bit filter.
* @param plist_id IN: Dataset creation property list identifier.
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pset_nbit(int plist_id)
throws HDF5LibraryException;
/**
* H5Pset_scaleoffset sets the Scale-Offset filter for a dataset.
* @param plist_id IN: Dataset creation property list identifier.
* @param scale_type IN: Flag indicating compression method.
* @param scale_factor IN: Parameter related to scale.
*
* @return a non-negative value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception IllegalArgumentException - Invalid arguments
*
**/
public synchronized static native int H5Pset_scaleoffset(int plist_id, int scale_type, int scale_factor)
throws HDF5LibraryException, IllegalArgumentException;
public synchronized static native int H5Pset_shuffle(int plist_id)
throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Pset_szip(int plist,
int options_mask, int pixels_per_block)
throws HDF5LibraryException, NullPointerException;
//////////////////////////////////////////////////////////////
////
//H5R: HDF5 1.8 Reference API Functions //
////
//////////////////////////////////////////////////////////////
private synchronized static native int H5Rcreate(byte[] ref, int loc_id,
String name, int ref_type, int space_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Rcreate creates the reference, ref, of the type specified in ref_type,
* pointing to the object name located at loc_id.
*
* @param loc_id
* IN: Location identifier used to locate the object being
* pointed to.
* @param name
* IN: Name of object at location loc_id.
* @param ref_type
* IN: Type of reference.
* @param space_id
* IN: Dataspace identifier with selection.
*
* @return the reference (byte[]) if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - an input array is null.
* @exception IllegalArgumentException
* - an input array is invalid.
**/
public synchronized static byte[] H5Rcreate(int loc_id, String name,
int ref_type, int space_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException
{
/* These sizes are correct for HDF5.1.2 */
int ref_size = 8;
if (ref_type == HDF5Constants.H5R_DATASET_REGION) {
ref_size = 12;
}
byte rbuf[] = new byte[ref_size];
/* will raise an exception if fails */
H5Rcreate(rbuf, loc_id, name, ref_type, space_id);
return rbuf;
}
/**
* Given a reference to some object, H5Rdereference opens that object and
* return an identifier.
*
* @param dataset
* IN: Dataset containing reference object.
* @param ref_type
* IN: The reference type of ref.
* @param ref
* IN: reference to an object
*
* @return valid identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - output array is null.
* @exception IllegalArgumentException
* - output array is invalid.
**/
public static int H5Rdereference(int dataset, int ref_type, byte[] ref)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException
{
int id = _H5Rdereference(dataset, ref_type, ref);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Rdereference(int dataset,
int ref_type, byte[] ref)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Rget_name retrieves a name for the object identified by ref.
* @param loc_id IN: Identifier for the dataset containing the reference or for the group that dataset is in.
* @param ref_type IN: Type of reference.
* @param ref IN: An object or dataset region reference.
* @param name OUT: A name associated with the referenced object or dataset region.
* @param size IN: The size of the name buffer.
*
* @return Returns the length of the name if successful, returning 0 (zero) if no name is associated with the identifier. Otherwise returns a negative value.
*
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - size is null.
* @exception IllegalArgumentException - Argument is illegal.
*
**/
public synchronized static native long H5Rget_name( int loc_id, int ref_type, byte[] ref, String[] name, long size)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/*
* [NOTE: This function is only supported in HDF5 Releases 1.4.x. It has
* been replaced in Release 1.6 by the function H5Rget_obj_type public
* synchronized static native int H5Rget_object_type(int loc_id, byte ref[])
* throws HDF5LibraryException, NullPointerException,
* IllegalArgumentException;
*/
/**
* Given a reference to an object ref, H5Rget_obj_type returns the type of
* the object pointed to.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Rget_obj_type(int, int, byte[], int[]) }
*
* @param loc_id
* IN: loc_id of the reference object.
* @param ref_type
* IN: Type of reference to query. *
* @param ref
* IN: the reference
*
* @return a valid object type if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - array is null.
* @exception IllegalArgumentException
* - array is invalid.
**/
@Deprecated
public synchronized static native int H5Rget_obj_type(int loc_id,
int ref_type, byte ref[])
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Rget_obj_type Given a reference to an object ref, H5Rget_obj_type returns the type of
* the object pointed to.
*
* @param loc_id IN: loc_id of the reference object.
* @param ref_type IN: Type of reference to query.
* @param ref IN: the reference
* @param obj_type OUT:Type of referenced object
*
* @return Returns the object type, which is the same as obj_type[0]. The return value is
* the same as the HDF5 1.6 version.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - array is null.
* @exception IllegalArgumentException
* - array is invalid.
**/
public static int H5Rget_obj_type(int loc_id,
int ref_type, byte ref[], int [] obj_type)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException
{
return H5Rget_obj_type2(loc_id, ref_type, ref, obj_type);
}
/**
* H5Rget_obj_type2 Retrieves the type of object that an object reference points to.
*
* @see public static int H5Rget_obj_type(int loc_id, int ref_type, byte ref[], int [] obj_type)
**/
private synchronized static native int H5Rget_obj_type2(int loc_id,
int ref_type, byte ref[], int [] obj_type)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* Given a reference to an object ref, H5Rget_region creates a copy of the
* dataspace of the dataset pointed to and defines a selection in the copy
* which is the region pointed to.
*
* @param loc_id
* IN: loc_id of the reference object.
* @param ref_type
* IN: The reference type of ref.
* @param ref
* OUT: the reference to the object and region
*
* @return a valid identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - output array is null.
* @exception IllegalArgumentException
* - output array is invalid.
**/
public static int H5Rget_region(int loc_id, int ref_type, byte[] ref)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException
{
int id = _H5Rget_region(loc_id, ref_type, ref);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Rget_region(int loc_id,
int ref_type, byte[] ref)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
//////////////////////////////////////////////////////////////
// //
//H5S: Dataspace Interface Functions //
// //
//////////////////////////////////////////////////////////////
/**
* H5Sclose releases a dataspace.
*
* @param space_id
* Identifier of dataspace to release.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Sclose(int space_id) throws HDF5LibraryException
{
if (space_id < 0)
throw new HDF5LibraryException("Negative ID");;
OPEN_IDS.removeElement(space_id);
return _H5Sclose(space_id);
}
private synchronized static native int _H5Sclose(int space_id)
throws HDF5LibraryException;
/**
* H5Scopy creates a new dataspace which is an exact copy of the dataspace
* identified by space_id.
*
* @param space_id
* Identifier of dataspace to copy.
* @return a dataspace identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Scopy(int space_id) throws HDF5LibraryException
{
int id = _H5Scopy(space_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Scopy(int space_id)
throws HDF5LibraryException;
/**
* H5Screate creates a new dataspace of a particular type.
*
* @param type IN: The type of dataspace to be created.
* @return a dataspace identifier
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Screate(int type) throws HDF5LibraryException
{
int id = _H5Screate(type);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Screate(int type)
throws HDF5LibraryException;
/**
* H5Screate_simple creates a new simple data space and opens
* it for access.
*
* @param rank IN: Number of dimensions of dataspace.
* @param dims IN: An array of the size of each dimension.
* @param maxdims IN: An array of the maximum size of each dimension.
*
* @return a dataspace identifier
*
* @exception HDF5Exception - Error from the HDF-5 Library.
* @exception NullPointerException - dims or maxdims is null.
**/
public static int H5Screate_simple(int rank, long[] dims, long[] maxdims)
throws HDF5Exception, NullPointerException
{
int id = _H5Screate_simple(rank, dims, maxdims);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Screate_simple(int rank, long[] dims,
long[] maxdims) throws HDF5Exception, NullPointerException;
/**
* @deprecated use H5Screate_simple(int rank, long[] dims, long[] maxdims)
**/
@Deprecated
public static int H5Screate_simple(int rank, byte[] dims, byte[] maxdims)
throws HDF5Exception, NullPointerException
{
ByteBuffer dimsbb = ByteBuffer.wrap(dims);
long[] ladims = (dimsbb.asLongBuffer()).array();
ByteBuffer maxdimsbb = ByteBuffer.wrap(maxdims);
long[] lamaxdims = (maxdimsbb.asLongBuffer()).array();
int id = _H5Screate_simple(rank, ladims, lamaxdims);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
/**
* H5Sdecode reconstructs the HDF5 data space object and returns a
* new object handle for it.
*
* @param buf IN: Buffer for the data space object to be decoded.
*
* @return a new object handle
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - buf is null.
**/
public synchronized static native int H5Sdecode(byte[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Sencode converts a data space description into binary form in a buffer.
*
* @param obj_id IN: Identifier of the object to be encoded.
*
* @return the buffer for the object to be encoded into.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native byte[] H5Sencode(int obj_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Sextent_copy copies the extent from source_space_id to dest_space_id.
* This action may change the type of the dataspace.
*
* @param dest_space_id
* IN: The identifier for the dataspace from which the extent is
* copied.
* @param source_space_id
* IN: The identifier for the dataspace to which the extent is
* copied.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Sextent_copy(int dest_space_id,
int source_space_id) throws HDF5LibraryException;
/**
* H5Sextent_equal determines whether the dataspace extents of two dataspaces,
* space1_id and space2_id, are equal.
*
* @param first_space_id
* IN: The identifier for the first dataspace.
* @param second_space_id
* IN: The identifier for the seconddataspace.
*
* @return true if successful, else false
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native boolean H5Sextent_equal(int first_space_id,
int second_space_id) throws HDF5LibraryException;
/**
* H5Sget_select_bounds retrieves the coordinates of the bounding box
* containing the current selection and places them into user-supplied
* buffers.
*
* <"start" coordinate>, immediately followed by
* <"opposite" corner coordinate>, followed by
* the next "start" and "opposite" coordinates,
* etc.
* until all of the selected blocks have been listed.
*
*
* @param spaceid
* Identifier of dataspace to release.
* @param startblock
* first block to retrieve
* @param numblocks
* number of blocks to retrieve
* @param buf
* returns blocks startblock to startblock+num-1, each block is
* rank * 2 (corners) longs.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - buf is null.
**/
public synchronized static native int H5Sget_select_hyper_blocklist(
int spaceid, long startblock, long numblocks, long[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the
* current dataspace selection.
*
* @param spaceid
* Identifier of dataspace to release.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native long H5Sget_select_hyper_nblocks(
int spaceid) throws HDF5LibraryException;
/**
* H5Sget_select_npoints determines the number of elements in the current
* selection of a dataspace.
*
* @param space_id IN: Identifier of the dataspace object to query
*
* @return the number of elements in the selection if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native long H5Sget_select_npoints(int space_id)
throws HDF5LibraryException;
/**
* H5Sget_select_type retrieves the type of selection currently defined for the dataspace space_id.
*
* @param space_id IN: Identifier of the dataspace object to query
*
* @return the dataspace selection type if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Sget_select_type(int space_id)
throws HDF5LibraryException;
/**
* H5Sget_simple_extent_dims returns the size and maximum sizes of each
* dimension of a dataspace through the dims and maxdims parameters.
*
* @param space_id IN: Identifier of the dataspace object to query
* @param dims OUT: Pointer to array to store the size of each dimension.
* @param maxdims OUT: Pointer to array to store the maximum size of each
* dimension.
*
* @return the number of dimensions in the dataspace if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - dims or maxdims is null.
**/
public synchronized static native int H5Sget_simple_extent_dims(
int space_id, long[] dims, long[] maxdims)
throws HDF5LibraryException, NullPointerException;
/**
* H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a
* dataspace.
*
* @param space_id IN: Identifier of the dataspace
*
* @return the number of dimensions in the dataspace if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Sget_simple_extent_ndims(
int space_id) throws HDF5LibraryException;
/**
* H5Sget_simple_extent_npoints determines the number of elements in a
* dataspace.
*
* @param space_id
* ID of the dataspace object to query
* @return the number of elements in the dataspace if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native long H5Sget_simple_extent_npoints(
int space_id) throws HDF5LibraryException;
/**
* H5Sget_simple_extent_type queries a dataspace to determine the current
* class of a dataspace.
*
* @param space_id
* Dataspace identifier.
*
* @return a dataspace class name if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Sget_simple_extent_type(int space_id)
throws HDF5LibraryException;
/**
* H5Sis_simple determines whether a dataspace is a simple dataspace.
*
* @param space_id
* Identifier of the dataspace to query
*
* @return true if is a simple dataspace
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native boolean H5Sis_simple(int space_id)
throws HDF5LibraryException;
/**
* H5Soffset_simple sets the offset of a simple dataspace space_id.
*
* @param space_id
* IN: The identifier for the dataspace object to reset.
* @param offset
* IN: The offset at which to position the selection.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - offset array is null.
**/
public synchronized static native int H5Soffset_simple(int space_id,
byte[] offset) throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Soffset_simple(int space_id, long[] offset)
throws HDF5Exception, NullPointerException
{
if (offset == null) {
return -1;
}
HDFArray theArray = new HDFArray(offset);
byte[] theArr = theArray.byteify();
int retVal = H5Soffset_simple(space_id, theArr);
theArr = null;
theArray = null;
return retVal;
}
/**
* H5Sselect_all selects the entire extent of the dataspace space_id.
*
* @param space_id
* IN: The identifier of the dataspace to be selected.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Sselect_all(int space_id)
throws HDF5LibraryException;
/**
* H5Sselect_elements selects array elements to be included in the selection
* for the space_id dataspace.
*
* @param space_id
* Identifier of the dataspace.
* @param op
* operator specifying how the new selection is combined.
* @param num_elements
* Number of elements to be selected.
* @param coord
* A 2-dimensional array specifying the coordinates of the
* elements.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
private synchronized static native int H5Sselect_elements(int space_id,
int op, int num_elements, byte[] coord)
throws HDF5LibraryException, NullPointerException;
/**
* H5Sselect_elements selects array elements to be included in the selection
* for the space_id dataspace.
*
* @param space_id
* Identifier of the dataspace.
* @param op
* operator specifying how the new selection is combined.
* @param num_elements
* Number of elements to be selected.
* @param coord2D
* A 2-dimensional array specifying the coordinates of the
* elements.
*
* @return a non-negative value if successful
*
* @exception HDF5Exception
* - Error in the data conversion
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - cord array is
**/
public synchronized static int H5Sselect_elements(int space_id, int op,
int num_elements, long[][] coord2D)
throws HDF5Exception, HDF5LibraryException, NullPointerException
{
if (coord2D == null) {
return -1;
}
HDFArray theArray = new HDFArray(coord2D);
byte[] coord = theArray.byteify();
int retVal = H5Sselect_elements(space_id, op, num_elements, coord);
coord = null;
theArray = null;
return retVal;
}
///**
//* H5Sselect_hyperslab selects a hyperslab region to add to
//* the current selected region for the dataspace specified
//* by space_id. The start, stride, count, and block arrays
//* must be the same size as the rank of the dataspace.
//*
//* @param space_id IN: Identifier of dataspace selection to modify
//* @param op IN: Operation to perform on current selection.
//* @param start IN: Offset of start of hyperslab
//* @param count IN: Number of blocks included in hyperslab.
//* @param stride IN: Hyperslab stride.
//* @param block IN: Size of block in hyperslab.
//*
//* @return none
//*
//* @exception HDF5LibraryException - Error from the HDF-5 Library.
//* @exception NullPointerException - an input array is null.
//* @exception IllegalArgumentException - an input array is invalid.
//**/
//public synchronized static native void H5Sselect_hyperslab(int space_id, H5S_SELECT_OPER op,
// long start[], long _stride[], long count[], long _block[])
// throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
//public synchronized static native int H5Scombine_hyperslab(int space_id, H5S_SELECT_OPER op,
// const long start[], const long _stride[],
// const long count[], const long _block[])
// throws HDF5LibraryException, NullPointerException;
//public synchronized static native int H5Sselect_select(int space1_id, H5S_SELECT_OPER op,
// int space2_id)
// throws HDF5LibraryException, NullPointerException;
//public synchronized static native int H5Scombine_select(int space1_id, H5S_SELECT_OPER op,
// int space2_id)
// throws HDF5LibraryException, NullPointerException;
/**
* H5Sselect_hyperslab selects a hyperslab region to add to the current
* selected region for the dataspace specified by space_id. The start,
* stride, count, and block arrays must be the same size as the rank of the
* dataspace.
*
* @param space_id
* IN: Identifier of dataspace selection to modify
* @param op
* IN: Operation to perform on current selection.
* @param start
* IN: Offset of start of hyperslab
* @param stride
* IN: Hyperslab stride.
* @param count
* IN: Number of blocks included in hyperslab.
* @param block
* IN: Size of block in hyperslab.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - an input array is null.
* @exception NullPointerException
* - an input array is invalid.
**/
public synchronized static int H5Sselect_hyperslab(int space_id,
int op, byte[] start, byte[] stride, byte[] count, byte[] block)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException
{
ByteBuffer startbb = ByteBuffer.wrap(start);
long[] lastart = (startbb.asLongBuffer()).array();
ByteBuffer stridebb = ByteBuffer.wrap(stride);
long[] lastride = (stridebb.asLongBuffer()).array();
ByteBuffer countbb = ByteBuffer.wrap(count);
long[] lacount = (countbb.asLongBuffer()).array();
ByteBuffer blockbb = ByteBuffer.wrap(block);
long[] lablock = (blockbb.asLongBuffer()).array();
return H5Sselect_hyperslab(space_id, op, lastart, lastride, lacount, lablock);
}
public synchronized static native int H5Sselect_hyperslab(int space_id, int op,
long[] start, long[] stride, long[] count, long[] block)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Sselect_none resets the selection region for the dataspace space_id to
* include no elements.
*
* @param space_id
* IN: The identifier of the dataspace to be reset.
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Sselect_none(int space_id)
throws HDF5LibraryException;
/**
* H5Sselect_valid verifies that the selection for the dataspace.
*
* @param space_id
* The identifier for the dataspace in which the selection is
* being reset.
*
* @return true if the selection is contained within the extent and FALSE if
* it is not or is an error.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native boolean H5Sselect_valid(int space_id)
throws HDF5LibraryException;
/**
* H5Sset_extent_none removes the extent from a dataspace and sets the type
* to H5S_NONE.
*
* @param space_id
* The identifier for the dataspace from which the extent is to
* be removed.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Sset_extent_none(int space_id)
throws HDF5LibraryException;
/**
* H5Sset_extent_simple sets or resets the size of an existing dataspace.
*
* @param space_id
* Dataspace identifier.
* @param rank
* Rank, or dimensionality, of the dataspace.
* @param current_size
* Array containing current size of dataspace.
* @param maximum_size
* Array containing maximum size of dataspace.
*
* @return a dataspace identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Sset_extent_simple(int space_id,
int rank, long[] current_size, long[] maximum_size)
throws HDF5LibraryException, NullPointerException;
public synchronized static int H5Sset_extent_simple(int space_id,
int rank, byte[] current_size, byte[] maximum_size)
throws HDF5LibraryException, NullPointerException
{
ByteBuffer csbb = ByteBuffer.wrap(current_size);
long[] lacs = (csbb.asLongBuffer()).array();
ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size);
long[] lamaxs = (maxsbb.asLongBuffer()).array();
return H5Sset_extent_simple(space_id, rank, lacs, lamaxs);
}
//////////////////////////////////////////////////////////////
////
//H5T: Datatype Interface Functions //
////
//////////////////////////////////////////////////////////////
/**
* H5Tarray_create creates a new array datatype object.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Tarray_create(int, int, long[])}
*
* @param base IN: Datatype identifier for the array base datatype.
* @param rank IN: Rank of the array.
* @param dims IN: Size of each array dimension.
* @param perms IN: Dimension permutation. (Currently not implemented.)
*
* @return a valid datatype identifier
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - dims is null.
**/
@Deprecated
public static int H5Tarray_create(int base, int rank, int[] dims,
int[] perms) throws HDF5LibraryException, NullPointerException
{
int id = _H5Tarray_create(base, rank, dims, perms);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Tarray_create(int base, int rank,
int[] dims, int[] perms)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tarray_create creates a new array datatype object.
*
* @param base_id IN: Datatype identifier for the array base datatype.
* @param ndims IN: Rank of the array.
* @param dim IN: Size of each array dimension.
*
* @return a valid datatype identifier
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - dim is null.
**/
public static int H5Tarray_create(int base_id, int ndims, long[] dim)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Tarray_create2(base_id, ndims, dim);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Tarray_create2(int base_id, int ndims, long[] dim)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tclose releases a datatype.
*
* @param type_id IN: Identifier of datatype to release.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Tclose(int type_id) throws HDF5LibraryException
{
if (type_id < 0)
throw new HDF5LibraryException("Negative ID");;
OPEN_IDS.removeElement(type_id);
return _H5Tclose(type_id);
}
private synchronized static native int _H5Tclose(int type_id)
throws HDF5LibraryException;
/**
* H5Tcommit commits a transient datatype (not immutable) to a file, turned
* it into a named datatype.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Tcommit(int, String, int, int, int, int)}
*
* @param loc_id IN: Location identifier.
* @param name IN: Name given to committed datatype.
* @param type_id IN: Identifier of datatype to be committed.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
@Deprecated
public static int H5Tcommit(int loc_id, String name,
int type) throws HDF5LibraryException, NullPointerException
{
return H5Tcommit1(loc_id, name, type);
}
public synchronized static native int H5Tcommit1(int loc_id, String name,
int type) throws HDF5LibraryException, NullPointerException;
/**
* H5Tcommit saves a transient datatype as an immutable named datatype in a file.
*
* @param loc_id IN: Location identifier.
* @param name IN: Name given to committed datatype.
* @param type_id IN: Identifier of datatype to be committed.
* @param lcpl_id IN: Link creation property list.
* @param tcpl_id IN: Datatype creation property list.
* @param tapl_id IN: Datatype access property list.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native void H5Tcommit(int loc_id, String name, int type_id, int lcpl_id,
int tcpl_id, int tapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tcommit_anon commits a transient datatype (not immutable) to a file,
* turning it into a named datatype with the specified creation and property lists.
*
* @param loc_id IN: Location identifier.
* @param type_id IN: Identifier of datatype to be committed.
* @param tcpl_id IN: Datatype creation property list.
* @param tapl_id IN: Datatype access property list.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tcommit_anon(int loc_id, int type_id, int tcpl_id, int tapl_id)
throws HDF5LibraryException;
/**
* H5Tcommitted queries a type to determine whether the type specified by
* the type identifier is a named type or a transient type.
*
* @param type_id IN: Identifier of datatype.
*
* @return true the datatype has been committed
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native boolean H5Tcommitted(int type)
throws HDF5LibraryException;
/**
* H5Tcompiler_conv finds out whether the library's conversion function from
* type src_id to type dst_id is a compiler (hard) conversion.
*
* @param src_id IN: Identifier of source datatype.
* @param dst_id IN: Identifier of destination datatype.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tcompiler_conv(int src_id, int dst_id)
throws HDF5LibraryException;
/**
** H5Tconvert converts nelmts elements from the type specified by the src_id identifier to type dst_id.
*
* @param src_id IN: Identifier of source datatype.
* @param dst_id IN: Identifier of destination datatype.
* @param nelmts IN: Size of array buf.
* @param buf IN: Array containing pre- and post-conversion values.
* @param background IN: Optional background buffer.
* @param plist_id IN: Dataset transfer property list identifier.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - buf is null.
**/
public synchronized static native void H5Tconvert(int src_id, int dst_id, long nelmts, byte[] buf,
byte[] background, int plist_id)
throws HDF5LibraryException, NullPointerException;
// int H5Tconvert(int src_id, int dst_id, long nelmts, Pointer buf, Pointer background, int plist_id);
/**
* H5Tcopy copies an existing datatype. The returned type is
* always transient and unlocked.
*
* @param type_id IN: Identifier of datatype to copy. Can be a datatype
* identifier, a predefined datatype (defined in
* H5Tpublic.h), or a dataset Identifier.
*
* @return a datatype identifier if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Tcopy(int type_id) throws HDF5LibraryException
{
int id = _H5Tcopy(type_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Tcopy(int type_id)
throws HDF5LibraryException;
/**
* H5Tcreate creates a new dataype of the specified class with the specified
* number of bytes.
*
* @param type IN: Class of datatype to create.
* @param size IN: The number of bytes in the datatype to create.
*
* @return datatype identifier if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Tcreate(int dclass, int size)
throws HDF5LibraryException
{
return H5Tcreate(dclass, (long)size);
}
/**
* H5Tcreate creates a new dataype of the specified class with
* the specified number of bytes.
*
* @param type IN: Class of datatype to create.
* @param size IN: The number of bytes in the datatype to create.
*
* @return datatype identifier
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Tcreate(int type, long size)
throws HDF5LibraryException
{
int id = _H5Tcreate(type, size);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Tcreate(int type, long size)
throws HDF5LibraryException;
/**
* H5Tdecode reconstructs the HDF5 data type object and
* returns a new object handle for it.
*
* @param buf IN: Buffer for the data type object to be decoded.
*
* @return a new object handle
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - buf is null.
**/
public synchronized static native int H5Tdecode(byte[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tdetect_class determines whether the datatype specified in dtype_id contains
* any datatypes of the datatype class specified in dtype_class.
*
* @param type_id IN: Identifier of datatype to query.
* @param cls IN: Identifier of datatype cls.
*
* @return true if the datatype specified in dtype_id contains any datatypes of the datatype class
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native boolean H5Tdetect_class(int type_id, int cls)
throws HDF5LibraryException;
/**
* H5Tencode converts a data type description into binary form in a buffer.
*
* @param obj_id IN: Identifier of the object to be encoded.
* @param buf OUT: Buffer for the object to be encoded into.
* If the provided buffer is NULL, only the
* size of buffer needed is returned.
* @param nalloc IN: The size of the allocated buffer.
*
* @return the size needed for the allocated buffer.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - buf is null.
**/
public synchronized static native int H5Tencode(int obj_id, byte[] buf, long nalloc)
throws HDF5LibraryException, NullPointerException;
///**
// * H5Tencode converts a data type description into binary form in a buffer.
// *
// * @param obj_id IN: Identifier of the object to be encoded.
// *
// * @return the buffer for the object to be encoded into.
// *
// * @exception HDF5LibraryException - Error from the HDF-5 Library.
// **/
//public synchronized static native byte[] H5Tencode(int obj_id)
//throws HDF5LibraryException;
/**
* H5Tenum_create creates a new enumeration datatype based on the specified
* base datatype, parent_id, which must be an integer type.
*
* @param base_id IN: Identifier of the parent datatype to release.
*
* @return the datatype identifier for the new enumeration datatype
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Tenum_create(int base_id) throws HDF5LibraryException
{
int id = _H5Tenum_create(base_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Tenum_create(int base_id)
throws HDF5LibraryException;
/**
* H5Tenum_insert inserts a new enumeration datatype member
* into an enumeration datatype.
*
* @param type IN: Identifier of datatype.
* @param name IN: The name of the member
* @param value IN: The value of the member, data of the correct type
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native void H5Tenum_insert(int type, String name, byte[] value)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tenum_insert inserts a new enumeration datatype member into an
* enumeration datatype.
*
* @param type IN: Identifier of datatype.
* @param name IN: The name of the member
* @param value IN: The value of the member, data of the correct type
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public static int H5Tenum_insert(int type, String name,
int[] value) throws HDF5LibraryException, NullPointerException
{
return H5Tenum_insert_int(type, name, value);
}
public static int H5Tenum_insert(int type, String name,
int value) throws HDF5LibraryException, NullPointerException
{
int[] val = { value };
return H5Tenum_insert_int(type, name, val);
}
private synchronized static native int H5Tenum_insert_int(int type, String name,
int[] value) throws HDF5LibraryException, NullPointerException;
/**
* H5Tenum_nameof finds the symbol name that corresponds
* to the specified value of the enumeration datatype type.
*
* @param type IN: Identifier of datatype.
* @param value IN: The value of the member, data of the correct
* @param size IN: The probable length of the name
*
* @return the symbol name.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - value is null.
**/
public synchronized static native String H5Tenum_nameof(int type, byte[] value, long size)
throws HDF5LibraryException, NullPointerException;
//int H5Tenum_nameof(int type, Pointer value, Buffer name/* out */, long size);
/**
* H5Tenum_nameof finds the symbol name that corresponds to the specified
* value of the enumeration datatype type.
*
* @param type IN: Identifier of datatype.
* @param value IN: The value of the member, data of the correct
* @param name OUT: The name of the member
* @param size IN: The max length of the name
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public static int H5Tenum_nameof(int type, int[] value,
String[] name, int size)
throws HDF5LibraryException, NullPointerException
{
return H5Tenum_nameof_int(type, value, name, size);
}
private synchronized static native int H5Tenum_nameof_int(int type, int[] value,
String[] name, int size)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tenum_valueof finds the value that corresponds to
* the specified name of the enumeration datatype type.
*
* @param type IN: Identifier of datatype.
* @param name IN: The name of the member
* @param value OUT: The value of the member
*
* @return the value of the enumeration datatype.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tenum_valueof(int type, String name, byte[] value)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tenum_valueof finds the value that corresponds to the specified name of
* the enumeration datatype type.
*
* @param type IN: Identifier of datatype.
* @param name IN: The name of the member
* @param value OUT: The value of the member
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public static int H5Tenum_valueof(int type,
String name, int[] value)
throws HDF5LibraryException, NullPointerException
{
return H5Tenum_valueof_int(type, name, value);
}
private synchronized static native int H5Tenum_valueof_int(int type,
String name, int[] value)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tequal determines whether two datatype identifiers refer
* to the same datatype.
*
* @param type_id1 IN: Identifier of datatype to compare.
* @param type_id2 IN: Identifier of datatype to compare.
*
* @return true if the datatype identifiers refer to the
* same datatype, else false.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native boolean H5Tequal(int type_id1,
int type_id2) throws HDF5LibraryException;
//public interface H5T_conv_t extends Callback {
//int callback(int src_id, int dst_id, H5T_cdata_t cdata, long nelmts,
//long buf_stride, long bkg_stride, Pointer buf, Pointer bkg,
//int dset_xfer_plist);
//}
//
////Exception handler. If an exception like overflow happenes during
////conversion,
////this function is called if it's registered through H5Pset_type_conv_cb.
//public interface H5T_conv_except_func_t extends Callback {
//int callback(H5T_conv_except_t except_type, int src_id, int dst_id,
//Pointer src_buf, Pointer dst_buf, Pointer user_data);
//}
//H5T_conv_t H5Tfind(int src_id, int dst_id, H5T_cdata_t *pcdata);
/**
* H5Tget_array_dims returns the sizes of the dimensions of the specified array datatype object.
*
* @deprecated As of HDF5 1.8
*
* @param type_id IN: Datatype identifier of array object.
* @param dims OUT: Sizes of array dimensions.
* @param perm[] OUT: Dimension permutations. (This parameter is not used.)
*
* @return the non-negative number of dimensions of the array type
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - dims is null.
**/
@Deprecated
public synchronized static native int H5Tget_array_dims(int dt, int[] dims,
int[] perms) throws HDF5LibraryException, NullPointerException;
/**
* H5Tget_array_dims returns the sizes of the dimensions of the specified array datatype object.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Tget_array_dims(int, long[])}
*
* @param type_id IN: Datatype identifier of array object.
* @param dims OUT: Sizes of array dimensions.
* @param perm OUT: Dimension permutation. (Currently not implemented.)
*
* @return the non-negative number of dimensions of the array type
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
@Deprecated
public static int H5Tget_array_dims(int type_id, long[] dims, int[] perm)
throws HDF5LibraryException, NullPointerException
{
return H5Tget_array_dims1(type_id, dims, perm);
}
/**
* H5Tget_array_dims1 returns the sizes of the dimensions of the specified array datatype object.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Tget_array_dims2(int, long[])}
*
* @see public static int H5Tget_array_dims(int type_id, long[] dims, int[] perm)
**/
@Deprecated
private synchronized static native int H5Tget_array_dims1(int type_id, long[] dims, int[] perm)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tget_array_dims returns the sizes of the dimensions of the specified array datatype object.
*
* @param type_id IN: Datatype identifier of array object.
* @param dims OUT: Sizes of array dimensions.
*
* @return the non-negative number of dimensions of the array type
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - dims is null.
**/
public static int H5Tget_array_dims(int type_id, long[] dims)
throws HDF5LibraryException, NullPointerException
{
return H5Tget_array_dims2(type_id, dims);
}
/**
* H5Tget_array_dims2 returns the sizes of the dimensions of the specified array datatype object.
*
* @see public static int H5Tget_array_dims(int type_id, long[] dims)
**/
public synchronized static native int H5Tget_array_dims2(int type_id, long[] dims)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tget_array_ndims returns the rank, the number of dimensions, of an array datatype object.
*
* @param type_id IN: Datatype identifier of array object.
*
* @return the rank of the array
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_array_ndims(int type_id)
throws HDF5LibraryException;
/**
* H5Tget_class returns the datatype class identifier.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return datatype class identifier if successful; otherwise H5T_NO_CLASS(-1).
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_class(int type_id)
throws HDF5LibraryException;
/**
* H5Tget_class_name returns the datatype class identifier.
*
* @param class_id IN: Identifier of class from H5Tget_class.
*
* @return class name if successful; otherwise H5T_NO_CLASS.
*
**/
public static String H5Tget_class_name(int class_id)
{
String retValue = null;
if(HDF5Constants.H5T_INTEGER==class_id) /*integer types */
retValue = "H5T_INTEGER";
else if(HDF5Constants.H5T_FLOAT==class_id) /*floating-point types */
retValue = "H5T_FLOAT";
else if(HDF5Constants.H5T_TIME==class_id) /*date and time types */
retValue = "H5T_TIME";
else if(HDF5Constants.H5T_STRING==class_id) /*character string types */
retValue = "H5T_STRING";
else if(HDF5Constants.H5T_BITFIELD==class_id) /*bit field types */
retValue = "H5T_BITFIELD";
else if(HDF5Constants.H5T_OPAQUE==class_id) /*opaque types */
retValue = "H5T_OPAQUE";
else if(HDF5Constants.H5T_COMPOUND==class_id) /*compound types */
retValue = "H5T_COMPOUND";
else if(HDF5Constants.H5T_REFERENCE==class_id)/*reference types */
retValue = "H5T_REFERENCE";
else if(HDF5Constants.H5T_ENUM==class_id) /*enumeration types */
retValue = "H5T_ENUM";
else if(HDF5Constants.H5T_VLEN==class_id) /*Variable-Length types */
retValue = "H5T_VLEN";
else if(HDF5Constants.H5T_ARRAY==class_id) /*Array types */
retValue = "H5T_ARRAY";
else
retValue = "H5T_NO_CLASS";
return retValue;
}
/**
* H5Tget_create_plist returns a property list identifier for the datatype
* creation property list associated with the datatype specified by type_id.
*
* @param type_id IN: Identifier of datatype.
*
* @return a datatype property list identifier.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_create_plist(int type_id)
throws HDF5LibraryException;
/**
* H5Tget_cset retrieves the character set type of a string datatype.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return a valid character set type if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_cset(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_cset the character set to be used.
*
* @param type_id IN: Identifier of datatype to modify.
* @param cset IN: Character set type.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tset_cset(int type_id, int cset)
throws HDF5LibraryException;
/**
* H5Tget_ebias retrieves the exponent bias of a floating-point type.
*
* @param type_id
* Identifier of datatype to query.
*
* @return the bias if successful; otherwise 0.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_ebias(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_ebias sets the exponent bias of a floating-point type.
*
* @param type_id
* Identifier of datatype to set.
* @param ebias
* Exponent bias value.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Tset_ebias(int type_id, int ebias)
throws HDF5LibraryException
{
H5Tset_ebias(type_id, (long)ebias);
return 0;
}
/**
* H5Tget_ebias retrieves the exponent bias of a
* floating-point type.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return the bias
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native long H5Tget_ebias_long(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_ebias sets the exponent bias of a floating-point type.
*
* @param type_id IN: Identifier of datatype to set.
* @param ebias IN: Exponent bias value.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tset_ebias(int type_id, long ebias)
throws HDF5LibraryException;
/**
* H5Tget_fields retrieves information about the locations of
* the various bit fields of a floating point datatype.
*
* @param type_id IN: Identifier of datatype to query.
* @param fields OUT: location of size and bit-position.
*
*
*
* @return none.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - fields is null.
* @exception IllegalArgumentException - fields array is invalid.
**/
public synchronized static native void H5Tget_fields(int type_id, long[] fields)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Tget_fields retrieves information about the locations of the various
* bit fields of a floating point datatype.
*
* @param type_id IN: Identifier of datatype to query.
* @param fields OUT: location of size and bit-position.
*
*
* fields[0] = spos OUT: location to return size of in bits.
* fields[1] = epos OUT: location to return exponent bit-position.
* fields[2] = esize OUT: location to return size of exponent in bits.
* fields[3] = mpos OUT: location to return mantissa bit-position.
* fields[4] = msize OUT: location to return size of mantissa in bits.
*
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - fields is null.
* @exception IllegalArgumentException - fields array is invalid.
**/
public static int H5Tget_fields(int type_id, int[] fields)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException
{
return H5Tget_fields_int(type_id, fields);
}
private synchronized static native int H5Tget_fields_int(int type_id,
int[] fields)
throws HDF5LibraryException, NullPointerException,
IllegalArgumentException;
/**
* H5Tset_fields sets the locations and sizes of the various
* floating point bit fields.
*
* @param type_id IN: Identifier of datatype to set.
* @param spos IN: Size position.
* @param epos IN: Exponent bit position.
* @param esize IN: Size of exponent in bits.
* @param mpos IN: Mantissa bit position.
* @param msize IN: Size of mantissa in bits.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tset_fields(int type_id, long spos, long epos, long esize, long mpos, long msize)
throws HDF5LibraryException;
/**
* H5Tset_fields sets the locations and sizes of the various floating point
* bit fields.
*
* @param type_id
* Identifier of datatype to set.
* @param spos
* Size position.
* @param epos
* Exponent bit position.
* @param esize
* Size of exponent in bits.
* @param mpos
* Mantissa bit position.
* @param msize
* Size of mantissa in bits.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Tset_fields(int type_id, int spos,
int epos, int esize, int mpos, int msize)
throws HDF5LibraryException
{
H5Tset_fields(type_id, (long)spos, (long)epos, (long)esize,
(long)mpos, (long)msize);
return 0;
}
/**
* H5Tget_inpad retrieves the internal padding type for unused bits in
* floating-point datatypes.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return a valid padding type if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_inpad(int type_id)
throws HDF5LibraryException;
/**
* If any internal bits of a floating point type are unused (that is, those
* significant bits which are not part of the sign, exponent, or mantissa),
* then H5Tset_inpad will be filled according to the value of the padding
* value property inpad.
*
* @param type_id IN: Identifier of datatype to modify.
* @param inpad IN: Padding type.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tset_inpad(int type_id, int inpad)
throws HDF5LibraryException;
/**
* H5Tget_member_class returns the datatype of the specified member.
*
* @param type_id IN: Datatype identifier of compound object.
* @param membno IN: Compound object member number.
*
* @return the identifier of a copy of the datatype of the field if successful;
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_member_class(int type_id,
int membno) throws HDF5LibraryException;
/**
* H5Tget_member_index retrieves the index of a field of a compound
* datatype.
*
* @param type_id IN: Identifier of datatype to query.
* @param field_name IN: Field name of the field index to retrieve.
*
* @return if field is defined, the index; else negative.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_member_index(int type_id, String field_name);
/**
* H5Tget_member_name retrieves the name of a field of a compound datatype or
* an element of an enumeration datatype.
*
* @param type_id IN: Identifier of datatype to query.
* @param field_idx IN: Field index (0-based) of the field name to retrieve.
*
* @return a valid pointer to the name if successful; otherwise null.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native String H5Tget_member_name(int type_id, int field_idx);
/**
* H5Tget_member_offset returns the byte offset of the specified member of
* the compound datatype. This is the byte offset in the HDF-5 file/library,
* NOT the offset of any Java object which might be mapped to this data
* item.
*
* @param type_id IN: Identifier of datatype to query.
* @param membno IN: Field index (0-based) of the field type to retrieve.
*
* @return the offset of the member.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native long H5Tget_member_offset(int type_id,
int membno) throws HDF5LibraryException;
/**
* H5Tget_member_type returns the datatype of the specified member.
*
* @param type_id IN: Identifier of datatype to query.
* @param field_idx IN: Field index (0-based) of the field type to retrieve.
*
* @return the identifier of a copy of the datatype of the field if
* successful;
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Tget_member_type(int type_id, int field_idx)
throws HDF5LibraryException
{
int id = _H5Tget_member_type(type_id, field_idx);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Tget_member_type(int type_id,
int field_idx) throws HDF5LibraryException;
/**
* H5Tget_member_value returns the value of the enumeration datatype member memb_no.
*
* @param type_id IN: Datatype identifier for the enumeration datatype.
* @param membno IN: Number of the enumeration datatype member.
* @param value OUT: The value of the member
*
* @return none.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - value is null.
**/
public synchronized static native void H5Tget_member_value(int type_id, int membno, byte[] value)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tget_member_value returns the value of the enumeration datatype member
* memb_no.
*
* @param type_id IN: Identifier of datatype.
* @param membno IN: The name of the member
* @param value OUT: The value of the member
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - value is null.
**/
public static int H5Tget_member_value(int type_id,
int membno, int[] value)
throws HDF5LibraryException, NullPointerException
{
return H5Tget_member_value_int(type_id, membno, value);
}
private synchronized static native int H5Tget_member_value_int(int type_id,
int membno, int[] value)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tget_native_type returns the equivalent native datatype for the datatype specified in type_id.
*
* @param type_id IN: Identifier of datatype to query.
* Direction of search is assumed to be in ascending order.
*
* @return the native datatype identifier for the specified dataset datatype.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static int H5Tget_native_type(int tid)
throws HDF5LibraryException
{
return H5Tget_native_type(tid, HDF5Constants.H5T_DIR_ASCEND);
}
/**
* H5Tget_native_type returns the equivalent native datatype for the datatype specified in type_id.
*
* @param type_id IN: Identifier of datatype to query.
* @param direction IN: Direction of search.
*
* @return the native datatype identifier for the specified dataset datatype.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Tget_native_type(int tid, int direction)
throws HDF5LibraryException
{
int id = _H5Tget_native_type(tid, direction);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Tget_native_type(int tid,
int direction) throws HDF5LibraryException;
/**
* H5Tget_nmembers retrieves the number of fields a compound datatype has.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return number of members datatype has if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_nmembers(int type_id)
throws HDF5LibraryException;
/**
* H5Tget_norm retrieves the mantissa normalization of a floating-point
* datatype.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return a valid normalization type if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_norm(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_norm sets the mantissa normalization of a floating-point datatype.
*
* @param type_id IN: Identifier of datatype to set.
* @param norm IN: Mantissa normalization type.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tset_norm(int type_id, int norm)
throws HDF5LibraryException;
/**
* H5Tget_offset retrieves the bit offset of the first significant bit.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return a positive offset value if successful; otherwise 0.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_offset(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_offset sets the bit offset of the first significant bit.
*
* @param type_id
* Identifier of datatype to set.
* @param offset
* Offset of first significant bit.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Tset_offset(int type_id, int offset)
throws HDF5LibraryException
{
H5Tset_offset(type_id, (long)offset);
return 0;
}
/**
* H5Tset_offset sets the bit offset of the first significant bit.
*
* @param type_id IN: Identifier of datatype to set.
* @param offset IN: Offset of first significant bit.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tset_offset(int type_id, long offset)
throws HDF5LibraryException;
/**
* H5Tget_order returns the byte order of an atomic datatype.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return a byte order constant if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_order(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_order sets the byte ordering of an atomic datatype.
*
* @param type_id IN: Identifier of datatype to set.
* @param order IN: Byte ordering constant.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tset_order(int type_id, int order)
throws HDF5LibraryException;
/**
* H5Tget_pad retrieves the padding type of the least and most-significant
* bit padding.
*
* @param type_id IN: Identifier of datatype to query.
* @param pad OUT: locations to return least-significant and
* most-significant bit padding type.
*
*
* pad[0] = lsb // least-significant bit padding type
* pad[1] = msb // most-significant bit padding type
*
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - pad is null.
**/
public synchronized static native int H5Tget_pad(int type_id, int[] pad)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tset_pad sets the least and most-significant bits padding types.
*
* @param type_id IN: Identifier of datatype to set.
* @param lsb IN: Padding type for least-significant bits.
* @param msb IN: Padding type for most-significant bits.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tset_pad(int type_id, int lsb,
int msb) throws HDF5LibraryException;
/**
* H5Tget_precision returns the precision of an atomic datatype.
*
* @param type_id
* Identifier of datatype to query.
*
* @return the number of significant bits if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_precision(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_precision sets the precision of an atomic datatype.
*
* @param type_id
* Identifier of datatype to set.
* @param precision
* Number of bits of precision for datatype.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Tset_precision(int type_id,
int precision) throws HDF5LibraryException
{
H5Tset_precision(type_id, (long)precision);
return 0;
}
/**
* H5Tget_precision returns the precision of an atomic datatype.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return the number of significant bits if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native long H5Tget_precision_long(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_precision sets the precision of an atomic datatype.
*
* @param type_id IN: Identifier of datatype to set.
* @param precision IN: Number of bits of precision for datatype.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tset_precision(int type_id, long precision)
throws HDF5LibraryException;
/**
* H5Tget_sign retrieves the sign type for an integer type.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return a valid sign type if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_sign(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_sign sets the sign proprety for an integer type.
*
* @param type_id IN: Identifier of datatype to set.
* @param sign IN: Sign type.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tset_sign(int type_id, int sign)
throws HDF5LibraryException;
/**
* H5Tget_size returns the size of a datatype in bytes.
*
* @param type_id
* Identifier of datatype to query.
*
* @return the size of the datatype in bytes if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_size(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_size sets the total size in bytes, size, for an atomic datatype
* (this operation is not permitted on compound datatypes).
*
* @param type_id
* Identifier of datatype to change size.
* @param size
* Size in bytes to modify datatype.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static int H5Tset_size(int type_id, int size)
throws HDF5LibraryException
{
H5Tset_size(type_id, (long)size);
return 0;
}
/**
* H5Tget_size returns the size of a datatype in bytes.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return the size of the datatype in bytes
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native long H5Tget_size_long(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_size sets the total size in bytes, size, for an
* atomic datatype (this operation is not permitted on
* compound datatypes).
*
* @param type_id IN: Identifier of datatype to change size.
* @param size IN: Size in bytes to modify datatype.
*
* @return none
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tset_size(int type_id, long size)
throws HDF5LibraryException;
/**
* H5Tget_strpad retrieves the string padding method for a string datatype.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return a valid string padding type if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_strpad(int type_id)
throws HDF5LibraryException;
/**
* H5Tset_strpad defines the storage mechanism for the string.
*
* @param type_id IN: Identifier of datatype to modify.
* @param strpad IN: String padding type.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tset_strpad(int type_id, int strpad)
throws HDF5LibraryException;
/**
* H5Tget_super returns the type from which TYPE is derived.
*
* @param type IN: Identifier of datatype.
*
* @return the parent type
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public static int H5Tget_super(int type) throws HDF5LibraryException
{
int id = _H5Tget_super(type);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Tget_super(int type)
throws HDF5LibraryException;
/**
* H5Tget_tag returns the tag associated with datatype type_id.
*
* @param type IN: Identifier of datatype.
*
* @return the tag
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native String H5Tget_tag(int type)
throws HDF5LibraryException;
/**
* H5Tset_tag tags an opaque datatype type_id with a unique ASCII identifier
* tag.
*
* @param type IN: Datatype identifier for the opaque datatype to be tagged.
* @param tag IN: Descriptive ASCII string with which the opaque datatype is to be tagged.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tset_tag(int type, String tag)
throws HDF5LibraryException;
/**
* H5Tinsert adds another member to the compound datatype type_id.
*
* @param type_id IN: Identifier of compound datatype to modify.
* @param name IN: Name of the field to insert.
* @param offset IN: Offset in memory structure of the field to insert.
* @param field_id IN: Datatype identifier of the field to insert.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public synchronized static native int H5Tinsert(int type_id, String name,
long offset, int field_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tis_variable_str determines whether the datatype identified in type_id is a variable-length string.
*
* @param type_id IN: Identifier of datatype to query.
*
* @return true if type_id is a variable-length string.
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native boolean H5Tis_variable_str(int type_id)
throws HDF5LibraryException;
/**
* H5Tlock locks the datatype specified by the type_id identifier, making it
* read-only and non-destrucible.
*
* @param type_id IN: Identifier of datatype to lock.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tlock(int type_id)
throws HDF5LibraryException;
/**
* H5Topen opens a named datatype at the location specified
* by loc_id and return an identifier for the datatype.
*
* @deprecated As of HDF5 1.8, replaced by {@link #H5Topen(int, String, int)}
*
* @param loc_id IN: A file, group, or datatype identifier.
* @param name IN: A datatype name, defined within the file or group identified by loc_id.
*
* @return a named datatype identifier if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
@Deprecated
public static int H5Topen(int loc_id, String name)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Topen(loc_id, name);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Topen(int loc_id, String name)
throws HDF5LibraryException, NullPointerException;
/**
* H5Topen opens a named datatype at the location specified
* by loc_id and return an identifier for the datatype.
*
* @param loc_id IN: A file, group, or datatype identifier.
* @param name IN: A datatype name, defined within the file or group identified by loc_id.
* @param tapl_id IN: Datatype access property list.
*
* @return a named datatype identifier if successful
*
* @exception HDF5LibraryException - Error from the HDF-5 Library.
* @exception NullPointerException - name is null.
**/
public static int H5Topen(int loc_id, String name, int tapl_id)
throws HDF5LibraryException, NullPointerException
{
int id = _H5Topen2(loc_id, name, tapl_id);
if (id > 0)
OPEN_IDS.addElement(id);
return id;
}
private synchronized static native int _H5Topen2(int loc_id, String name, int tapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Tpack recursively removes padding from within a compound datatype to
* make it more efficient (space-wise) to store that data.
*