* 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(long fid, long filetype, long memtype, long memspace, * void * data); ** *
* where ``void *'' means that the data may be any valid numeric type, and is a contiguous block of bytes that is the * data for a multi-dimensional array. The other parameters describe the dimensions, rank, and datatype of the array on * disk (source) and in memory (destination). *
* For Java, this ``ANY'' is a problem, as the type of data must always be declared. Furthermore, multidimensional * arrays are definitely not 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(long fid, long filetype, long memtype, long memspace, Object data); ** OPEN_IDS.addElement(id); * and the parameter data can be any multi-dimensional array of numbers, such as float[][], or int[][][], or * Double[][]. *
* 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: * *
* long data_type = HDF5CDataTypes.JH5T_NATIVE_INT; ** * The Java application uses both types of constants the same way, the only difference is that the * HDF5CDataTypes may have different values on different platforms. *
* Error handling and Exceptions *
* The HDF5 error API (H5E) manages the behavior of the error stack in the 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(). * * @return a non-negative value if successful */ public synchronized static native int H5error_off(); /** * Turn on error handling. By default, the C library prints the error stack of the HDF-5 C library on stdout. This * behavior may be reenabled by calling H5error_on(). */ public synchronized static native void H5error_on(); /** * 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. * *
* 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;
/**
* H5set_free_list_limits
* Sets limits on the different kinds of free lists. Setting a value
* of -1 for a limit means no limit of that type. These limits are global
* for the entire library. Each "global" limit only applies to free lists
* of that type, so if an application sets a limit of 1 MB on each of the
* global lists, up to 3 MB of total storage might be allocated (1MB on
* each of regular, array and block type lists).
*
* The settings for block free lists are duplicated to factory free lists.
* Factory free list limits cannot be set independently currently.
*
* @param reg_global_lim
* The limit on all "regular" free list memory used
* @param reg_list_lim
* The limit on memory used in each "regular" free list
* @param arr_global_lim
* The limit on all "array" free list memory used
* @param arr_list_lim
* The limit on memory used in each "array" free list
* @param blk_global_lim
* The limit on all "block" free list memory used
* @param blk_list_lim
* The limit on memory used in each "block" free list
* @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 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;
/**
* H5export_dataset is a utility function to save data in a file.
*
* @param file_export_name
* The file name to export data into.
* @param file_name
* The name of the HDF5 file containing the dataset.
* @param object_path
* The full path of the dataset to be exported.
* @param binary_order
* 99 - export data as text.
* 1 - export data as binary Native Order.
* 2 - export data as binary Little Endian.
* 3 - export data as binary Big Endian.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5export_dataset(String file_export_name, String file_name,
String object_path, int binary_order) throws HDF5LibraryException;
/**
* H5is_library_threadsafe Checks to see if the library was built with thread-safety enabled.
*
* @return true if hdf5 library implements threadsafe
*
**/
private synchronized static native boolean H5is_library_threadsafe();
// /////// unimplemented ////////
// herr_t H5free_memory(void *mem);
// void *H5allocate_memory(size_t size, hbool_t clear);
// void *H5resize_memory(void *mem, size_t size);
// ////////////////////////////////////////////////////////////
// //
// 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(long attr_id) throws HDF5LibraryException {
if (attr_id < 0)
return 0; // throw new HDF5LibraryException("Negative ID");;
log.trace("OPEN_IDS: H5Aclose remove {}", attr_id);
OPEN_IDS.remove(attr_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
return _H5Aclose(attr_id);
}
private synchronized static native int _H5Aclose(long 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 destination attribute
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*/
public synchronized static native int H5Acopy(long src_aid, long dst_aid) throws HDF5LibraryException;
/**
* 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 long H5Acreate(long loc_id, String attr_name, long type_id, long space_id, long acpl_id, long aapl_id)
throws HDF5LibraryException, NullPointerException {
long id = _H5Acreate2(loc_id, attr_name, type_id, space_id, acpl_id, aapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5A create add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
/**
* H5Acreate2 an attribute, attr_name, which is attached to the object specified by the identifier loc_id.
*
* @see public static long H5Acreate( long loc_id, String attr_name, long type_id, long space_id, long acpl_id, long
* aapl_id )
**/
private synchronized static native long _H5Acreate2(long loc_id, String attr_name, long type_id, long space_id,
long acpl_id, long 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 long H5Acreate_by_name(long loc_id, String obj_name, String attr_name, long type_id, long space_id,
long acpl_id, long aapl_id, long lapl_id) throws HDF5LibraryException, NullPointerException {
long id = _H5Acreate_by_name(loc_id, obj_name, attr_name, type_id, space_id, acpl_id, aapl_id, lapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Acreate_by_name add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Acreate_by_name(long loc_id, String obj_name, String attr_name,
long type_id, long space_id, long acpl_id, long aapl_id, long 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(long 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
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - obj_name is null.
**/
public synchronized static native void H5Adelete_by_idx(long loc_id, String obj_name, int idx_type, int order,
long n, long 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(long loc_id, String obj_name, String attr_name, long 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(long 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(long loc_id, String obj_name, String attr_name,
long 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(long 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(long loc_id, String obj_name, int idx_type,
int order, long n, long 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(long loc_id, String obj_name, String attr_name,
long 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.
*
* @return String for Attribute name.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native String H5Aget_name(long attr_id)
throws HDF5LibraryException;
/**
* 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 HDF5 Library.
* @exception NullPointerException
* - obj_name is null.
**/
public synchronized static native String H5Aget_name_by_idx(long attr_id, String obj_name, int idx_type, int order,
long n, long lapl_id) throws HDF5LibraryException, NullPointerException;
/**
* 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 long H5Aget_space(long attr_id) throws HDF5LibraryException
{
long id = _H5Aget_space(attr_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aget_space add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Aget_space(long 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(long 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 long H5Aget_type(long attr_id) throws HDF5LibraryException
{
long id = _H5Aget_type(attr_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aget_type add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Aget_type(long 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: Identifier 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 long H5Aopen(long obj_id, String attr_name, long aapl_id)
throws HDF5LibraryException, NullPointerException
{
long id = _H5Aopen(obj_id, attr_name, aapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aopen add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Aopen(long obj_id, String attr_name, long 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 long H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, int order, long n, long aapl_id,
long lapl_id) throws HDF5LibraryException, NullPointerException
{
long id = _H5Aopen_by_idx(loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aopen_by_idx add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, int order,
long n, long aapl_id, long 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 long H5Aopen_by_name(long loc_id, String obj_name, String attr_name, long aapl_id, long lapl_id)
throws HDF5LibraryException, NullPointerException
{
long id = _H5Aopen_by_name(loc_id, obj_name, attr_name, aapl_id, lapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aopen_by_name add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Aopen_by_name(long loc_id, String obj_name, String attr_name,
long aapl_id, long lapl_id) 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 buffer 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
* Buffer to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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(long attr_id, long mem_type_id, byte[] obj, boolean isCriticalPinning)
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 buffer 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
* 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 int H5Aread(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException
{
return H5Aread(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer 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
* 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 int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException
{
return H5Aread(attr_id, mem_type_id, obj, true);
}
/**
* 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.
* @param isCriticalPinning
* request lock on data reference.
*
* @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 buffer is null. See public synchronized static native int H5Aread( )
**/
public synchronized static int H5Aread(long attr_id, long mem_type_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("H5Aread: data is not an array"));
}
String cname = dataClass.getName();
is1D = (cname.lastIndexOf('[') == cname.indexOf('['));
char dname = cname.charAt(cname.lastIndexOf("[") + 1);
log.trace("H5Aread: cname={} is1D={} dname={}", cname, is1D, dname);
if (is1D && (dname == 'B')) {
log.trace("H5Aread_dname_B");
status = H5Aread(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning);
}
else if (is1D && (dname == 'S')) {
log.trace("H5Aread_dname_S");
status = H5Aread_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning);
}
else if (is1D && (dname == 'I')) {
log.trace("H5Aread_dname_I");
status = H5Aread_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning);
}
else if (is1D && (dname == 'J')) {
log.trace("H5Aread_dname_J");
status = H5Aread_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning);
}
else if (is1D && (dname == 'F')) {
log.trace("H5Aread_dname_F");
status = H5Aread_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning);
}
else if (is1D && (dname == 'D')) {
log.trace("H5Aread_dname_D");
status = H5Aread_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning);
}
else if ((H5.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) &&
(is1D && (dataClass.getComponentType() == String.class))) ||
H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
log.trace("H5Aread_reg_ref");
status = H5Aread_reg_ref(attr_id, mem_type_id, (String[]) obj);
}
else if (is1D && (dataClass.getComponentType() == String.class)) {
log.trace("H5Aread_string type");
status = H5Aread_string(attr_id, mem_type_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();
log.trace("H5Aread_else");
// This will raise an exception if there is an error
status = H5Aread(attr_id, mem_type_id, buf, isCriticalPinning);
// No exception: status really ought to be OK
if (status >= 0) {
obj = theArray.arrayify(buf);
}
// clean up these: assign 'null' as hint to gc()
buf = null;
theArray = null;
}
return status;
}
/**
* 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 buffer of double 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
* Buffer of double to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning)
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 buffer of double 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
* Buffer of double 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 int H5Aread_double(long attr_id, long mem_type_id, double[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Aread_double(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer of float 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
* Buffer of float to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning)
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 buffer of float 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
* Buffer of float 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 int H5Aread_float(long attr_id, long mem_type_id, float[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Aread_float(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer of int 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
* Buffer of int to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning)
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 buffer of int 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
* Buffer of int 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 int H5Aread_int(long attr_id, long mem_type_id, int[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Aread_int(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer of long 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
* Buffer of long to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning)
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 buffer of long 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
* Buffer of long 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 int H5Aread_long(long attr_id, long mem_type_id, long[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Aread_long(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer of String 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
* Buffer of String 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 H5Aread_reg_ref(long attr_id, long mem_type_id, String[] 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 buffer of short 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
* Buffer of short to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
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 buffer of shortfrom 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
* Buffer of short 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 int H5Aread_short(long attr_id, long mem_type_id, short[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Aread_short(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer of variable-lenght 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
* Buffer of variable-lenght 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 H5AreadVL(long attr_id, long mem_type_id, Object[] 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 buffer of String 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
* Buffer of String 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 H5Aread_string(long attr_id, long mem_type_id, String[] 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 buffer of variable-lenght strings 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
* Buffer of variable-lenght strings 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 H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] 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 buffer of string 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
* Buffer of string 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 H5AreadComplex(long attr_id, long 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(long 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(long loc_id, String obj_name, String old_attr_name,
String new_attr_name, long 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: Buffer with data to be written to the file.
* @param isCriticalPinning
* IN: request lock on data reference.
*
* @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(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning)
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: 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
* - data is null.
**/
public synchronized static int H5Awrite(long attr_id, long mem_type_id, byte[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Awrite(attr_id, mem_type_id, buf, true);
}
/**
* 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 obj
* IN: 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
* - data is null.
**/
public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj)
throws HDF5Exception, HDF5LibraryException, NullPointerException
{
return H5Awrite(attr_id, mem_type_id, obj, true);
}
/**
* 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.
* @param isCriticalPinning
* request lock on data reference.
*
* @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 H5Awrite(long attr_id, long mem_type_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("H5Dwrite: 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 = H5Awrite(attr_id, mem_type_id, (byte[]) obj, isCriticalPinning);
}
else if (is1D && (dname == 'S')) {
status = H5Awrite_short(attr_id, mem_type_id, (short[]) obj, isCriticalPinning);
}
else if (is1D && (dname == 'I')) {
status = H5Awrite_int(attr_id, mem_type_id, (int[]) obj, isCriticalPinning);
}
else if (is1D && (dname == 'J')) {
status = H5Awrite_long(attr_id, mem_type_id, (long[]) obj, isCriticalPinning);
}
else if (is1D && (dname == 'F')) {
status = H5Awrite_float(attr_id, mem_type_id, (float[]) obj, isCriticalPinning);
}
else if (is1D && (dname == 'D')) {
status = H5Awrite_double(attr_id, mem_type_id, (double[]) obj, isCriticalPinning);
}
else if (is1D && (dataClass.getComponentType() == String.class)) {
log.trace("H5Dwrite_string type");
status = H5Awrite_string(attr_id, mem_type_id, (String[]) obj);
}
else {
HDFArray theArray = new HDFArray(obj);
byte[] buf = theArray.byteify();
status = H5Awrite(attr_id, mem_type_id, buf);
buf = null;
theArray = null;
}
return status;
}
/**
* 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 buffer of double 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: Buffer of double with data to be written to the file.
* @param isCriticalPinning
* IN: request lock on data reference.
*
* @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_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning)
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 buffer of double 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: Buffer of double 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
* - data is null.
**/
public synchronized static int H5Awrite_double(long attr_id, long mem_type_id, double[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Awrite_double(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer of float 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: Buffer of float with data to be written to the file.
* @param isCriticalPinning
* IN: request lock on data reference.
*
* @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_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning)
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 buffer of float 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: Buffer of float 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
* - data is null.
**/
public synchronized static int H5Awrite_float(long attr_id, long mem_type_id, float[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Awrite_float(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer of int 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: Buffer of int with data to be written to the file.
* @param isCriticalPinning
* IN: request lock on data reference.
*
* @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(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning)
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 buffer of int 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: Buffer of int 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
* - data is null.
**/
public synchronized static int H5Awrite_int(long attr_id, long mem_type_id, int[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Awrite_int(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer of long 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: Buffer of long with data to be written to the file.
* @param isCriticalPinning
* IN: request lock on data reference.
*
* @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_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning)
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 buffer of long 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: Buffer of long 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
* - data is null.
**/
public synchronized static int H5Awrite_long(long attr_id, long mem_type_id, long[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Awrite_long(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer of short 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: Buffer of short with data to be written to the file.
* @param isCriticalPinning
* IN: request lock on data reference.
*
* @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_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
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 buffer of short 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: Buffer of short 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
* - data is null.
**/
public synchronized static int H5Awrite_short(long attr_id, long mem_type_id, short[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Awrite_short(attr_id, mem_type_id, buf, true);
}
/**
* 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 buffer of string 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: Buffer of string 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
* - data is null.
**/
public synchronized static native int H5Awrite_string(long attr_id, long mem_type_id, String[] 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 buffer of variable-lenght 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: Buffer of variable-lenght 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
* - data is null.
**/
public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Awrite_VLStrings writes a variable length String dataset, specified by its identifier attr_id, from
* the application memory buffer buffer of variable-lenght strings into the file.
*
* ---- contributed by Rosetta Biosoftware
*
* @param attr_id
* Identifier of the attribute read from.
* @param mem_type_id
* Identifier of the memory datatype.
* @param buf
* Buffer of variable-lenght strings 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 H5Awrite_VLStrings(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Aget_create_plist retrieves a copy of the attribute creation property list identifier.
*
* @param attr_id
* IN: Identifier of an attribute.
*
* @return identifier for the attribute's creation property list if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public static long H5Aget_create_plist(long attr_id)
throws HDF5LibraryException
{
long id = _H5Aget_create_plist(attr_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Aget_create_plist add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Aget_create_plist(long attr_id) throws HDF5LibraryException;
/**
* H5Aiterate2 iterates over the attributes attached to a dataset, named datatype, or group, as
* specified by obj_id. For each attribute, user-provided data, op_data, with additional information
* as defined below, is passed to a user-defined function, op, which operates on that attribute.
*
* @param loc_id
* IN: Identifier for object to which attributes are attached; may be group, dataset, or named datatype.
* @param idx_type
* IN: The type of index specified by idx_type can be one of the following:
* H5_INDEX_NAME An alpha-numeric index by attribute name.
* H5_INDEX_CRT_ORDER An index by creation order.
* @param order
* IN: The order in which the index is to be traversed, as specified by order, can be one of the following:
* H5_ITER_INC Iteration is from beginning to end, i.e., a top-down iteration
* incrementing the index position at each step.
* H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration
* decrementing the index position at each step.
* H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided
* as to the order, but HDF5 ensures that each element in the index will be
* visited if the iteration completes successfully.
* @param idx
* IN/OUT: Initial and returned offset within index.
* @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 H5Aiterate(long loc_id, int idx_type, int order, long idx,
H5A_iterate_cb op, H5A_iterate_t op_data) throws HDF5LibraryException, NullPointerException;
/**
* H5Aiterate_by_name iterates over the attributes attached to the dataset or group specified with loc_id
* and obj_name. For each attribute, user-provided data, op_data, with additional information as defined
* below, is passed to a user-defined function, op, which operates on that attribute.
*
* @param loc_id
* IN: Identifier for object to which attributes are attached; may be group, dataset, or named datatype.
* @param obj_name
* IN: Name of object, relative to location.
* @param idx_type
* IN: The type of index specified by idx_type can be one of the following:
* H5_INDEX_NAME An alpha-numeric index by attribute name.
* H5_INDEX_CRT_ORDER An index by creation order.
* @param order
* IN: The order in which the index is to be traversed, as specified by order, can be one of the following:
* H5_ITER_INC Iteration is from beginning to end, i.e., a top-down iteration
* incrementing the index position at each step.
* H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration
* decrementing the index position at each step.
* H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided
* as to the order, but HDF5 ensures that each element in the index will be
* visited if the iteration completes successfully.
* @param idx
* IN/OUT: Initial and returned offset within index.
* @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.
* @param lapl_id
* IN: Link access property list
*
* @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 H5Aiterate_by_name(long loc_id, String obj_name, int idx_type,
int order, long idx, H5A_iterate_cb op, H5A_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException;
// ////////////////////////////////////////////////////////////
// //
// H5AC: Cache Interface Functions //
// //
// ////////////////////////////////////////////////////////////
// No public Functions
// ////////////////////////////////////////////////////////////
// //
// H5B: B-link-tree Interface Functions //
// //
// ////////////////////////////////////////////////////////////
// No public Functions
// ////////////////////////////////////////////////////////////
// //
// H5B2: v2 B-tree Interface Functions //
// //
// ////////////////////////////////////////////////////////////
// No public Functions
// ////////////////////////////////////////////////////////////
// //
// H5C: Cache Interface Functions //
// //
// ////////////////////////////////////////////////////////////
// No public Functions
// ////////////////////////////////////////////////////////////
// //
// H5D: Datasets Interface Functions //
// //
// ////////////////////////////////////////////////////////////
/**
* 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
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*/
public synchronized static native int H5Dcopy(long src_did, long dst_did) throws HDF5LibraryException;
/**
* 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(long dataset_id) throws HDF5LibraryException {
if (dataset_id < 0)
return 0; // throw new HDF5LibraryException("Negative ID");
log.trace("OPEN_IDS: H5Dclose remove {}", dataset_id);
OPEN_IDS.remove(dataset_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
return _H5Dclose(dataset_id);
}
private synchronized static native int _H5Dclose(long dataset_id) throws HDF5LibraryException;
/**
* 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 long H5Dcreate(long loc_id, String name, long type_id, long space_id, long lcpl_id, long dcpl_id,
long dapl_id) throws HDF5LibraryException, NullPointerException {
long id = _H5Dcreate2(loc_id, name, type_id, space_id, lcpl_id, dcpl_id, dapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Dcreate add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
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 long _H5Dcreate2(long loc_id, String name, long type_id, long space_id,
long lcpl_id, long dcpl_id, long 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 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 long H5Dcreate_anon(long loc_id, long type_id, long space_id, long dcpl_id, long dapl_id)
throws HDF5LibraryException {
long id = _H5Dcreate_anon(loc_id, type_id, space_id, dcpl_id, dapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Dcreate_anon add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Dcreate_anon(long loc_id, long type_id, long space_id, long dcpl_id,
long dapl_id) throws HDF5LibraryException;
/**
* 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_id
* IN: Dataspace describing memory buffer and containing the selection to be filled.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - buf is null.
**/
public synchronized static native void H5Dfill(byte[] fill, long fill_type, byte[] buf, long buf_type, long space_id)
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 long H5Dget_access_plist(long 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 long H5Dget_create_plist(long dataset_id) throws HDF5LibraryException {
long id = _H5Dget_create_plist(dataset_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Dget_create_plist add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Dget_create_plist(long 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(long 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 long H5Dget_space(long dataset_id) throws HDF5LibraryException {
long id = _H5Dget_space(dataset_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Dget_space add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Dget_space(long 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(long dset_id) throws HDF5LibraryException;
/**
* 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(long 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 long H5Dget_type(long dataset_id) throws HDF5LibraryException {
long id = _H5Dget_type(dataset_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Dget_type add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Dget_type(long dataset_id) throws HDF5LibraryException;
/**
* 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_id
* 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[] buf, long buf_type, long space_id, 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.
*
* @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 long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException, NullPointerException
{
long id = _H5Dopen2(loc_id, name, dapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Dopen add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
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 long _H5Dopen2(long loc_id, String name, long 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 obj
* Buffer to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, byte[] obj, boolean isCriticalPinning) 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 int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long 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);
}
/**
* 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 obj
* 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 int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long 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.
* @param isCriticalPinning
* request lock on data reference.
*
* @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(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long 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);
log.trace("H5Dread: cname={} is1D={} dname={}", cname, is1D, dname);
if (is1D && (dname == 'B')) {
log.trace("H5Dread_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')) {
log.trace("H5Dread_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')) {
log.trace("H5Dread_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')) {
log.trace("H5Dread_dname_J");
status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj,
isCriticalPinning);
}
else if (is1D && (dname == 'F')) {
log.trace("H5Dread_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')) {
log.trace("H5Dread_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.H5Tdetect_class(mem_type_id, HDF5Constants.H5T_REFERENCE) &&
(is1D && (dataClass.getComponentType() == String.class))) ||
H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) {
log.trace("H5Dread_reg_ref");
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)) {
log.trace("H5Dread_string type");
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();
log.trace("H5Dread_else");
// 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;
}
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of type double.
*
* @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 of type double to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_double(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of type double.
*
* @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 of double 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 int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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);
}
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of float.
*
* @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 of float to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_float(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of float.
*
* @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 of float 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 int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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);
}
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of int.
*
* @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 of int to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException,
NullPointerException;
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of int.
*
* @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 of int 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 int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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);
}
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of long.
*
* @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 of long to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_long(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException,
NullPointerException;
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of long.
*
* @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 of long 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 int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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);
}
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of string.
*
* @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 of string 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_reg_ref(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException;
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of short.
*
* @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 of short to store data read from the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_short(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of short.
*
* @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 of short 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 int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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);
}
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of variable-lenght.
*
* @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 of variable-lenght 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 H5DreadVL(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException;
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of string.
*
* @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 of string 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_string(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException;
/**
* H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application
* memory buffer of variable-lenght strings.
*
* @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 of variable-lenght strings 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_VLStrings(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - size is null.
**/
public synchronized static native void H5Dset_extent(long dset_id, long size[]) throws HDF5LibraryException,
NullPointerException;
/**
* 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 dset_id, long type_id, long space_id)
throws HDF5LibraryException;
/**
* H5Dvlen_reclaim reclaims buffer used for VL data.
*
* @param type_id
* Identifier of the datatype.
* @param space_id
* Identifier of the dataspace.
* @param xfer_plist_id
* Identifier of a transfer property list for this I/O operation.
* @param buf
* Buffer with data to be reclaimed.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - buf is null.
*
* @deprecated As of HDF5 1.12.0 in favor of H5Treclaim
**/
@Deprecated
public synchronized static native int H5Dvlen_reclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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.
* @param isCriticalPinning
* request lock on data reference.
*
* @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(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, byte[] buf, boolean isCriticalPinning) throws HDF5LibraryException,
NullPointerException;
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long 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);
}
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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
* 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 int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long 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.
* @param isCriticalPinning
* request lock on data reference.
*
* @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(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id,
long 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("H5Dwrite: 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);
}
else if (is1D && (dataClass.getComponentType() == String.class)) {
log.trace("H5Dwrite_string type");
status = H5Dwrite_string(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;
}
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of double with data to be written to the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_double(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of double 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 int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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);
}
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of float with data to be written to the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_float(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of float 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 int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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);
}
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of int with data to be written to the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException,
NullPointerException;
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of int 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 int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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);
}
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of long with data to be written to the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_long(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException,
NullPointerException;
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of long 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 int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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);
}
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of short with data to be written to the file.
* @param isCriticalPinning
* request lock on data reference.
*
* @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_short(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException;
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of short 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 int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long 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);
}
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of string 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_string(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException;
/**
* H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer
* 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 of variable-length 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 H5DwriteVL(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException;
/**
* H5Dwrite_VLStrings writes a (partial) variable length String dataset, specified by its identifier dataset_id, from
* the application memory buffer buf into the file.
*
* ---- contributed by Rosetta Biosoftware
*
* @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_VLStrings(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException;
/**
* H5Dflush causes all buffers associated with a dataset to be immediately flushed to disk without removing the
* data from the cache.
*
* @param dset_id
* IN: Identifier of the dataset to be flushed.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Dflush(long dset_id) throws HDF5LibraryException;
/**
* H5Drefresh causes all buffers associated with a dataset to be cleared and immediately re-loaded with updated
* contents from disk. This function essentially closes the dataset, evicts all metadata associated with it
* from the cache, and then re-opens the dataset. The reopened dataset is automatically re-registered with the same ID.
*
* @param dset_id
* IN: Identifier of the dataset to be refreshed.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Drefresh(long dset_id) throws HDF5LibraryException;
// /////// unimplemented ////////
// herr_t H5Ddebug(hid_t dset_id);
// herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes);
// herr_t H5Dformat_convert(hid_t dset_id);
// herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
// herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id,
// size_t dst_buf_size, void *dst_buf, H5D_gather_func_t op, void *op_data);
// herr_t H5Dscatter(H5D_scatter_func_t op, void *op_data, hid_t type_id, hid_t dst_space_id, void *dst_buf);
// ////////////////////////////////////////////////////////////
// //
// 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(long stack_id) throws HDF5LibraryException;
/**
* H5Eclear clears the error stack for the current thread. H5Eclear can fail if there are problems initializing the
* 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. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static void H5Eclear(long stack_id) throws HDF5LibraryException { H5Eclear2(stack_id); } /** * 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. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eclear2(long stack_id) 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. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eclose_msg(long 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. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eclose_stack(long 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 long H5Ecreate_msg(long 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. * * @return an error stack identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Ecreate_stack() throws HDF5LibraryException; /** * 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(long class_id) throws HDF5LibraryException, NullPointerException; /** * H5Eget_current_stack copies the current error stack and returns an error stack identifier for the new copy. * * @return an error stack identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long 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. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eset_current_stack(long 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_list * 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(long msg_id, int[] type_list) 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(long stack_id) throws HDF5LibraryException, NullPointerException; /** * 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. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eprint2(long stack_id, Object stream) throws HDF5LibraryException; /** * 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. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Epop(long stack_id, long count) throws HDF5LibraryException; /** * H5Epush pushes a new error record onto the error stack specified by estack_id. * * @param stack_id * IN: Error stack identifier. * @param file * IN: Name of the file in which the error was detected. * @param func * IN: Name of the function in which the error was detected. * @param line * IN: Line number within the file at which the error was detected. * @param cls_id * IN: Error class identifier. * @param maj_id * IN: Major error identifier. * @param min_id * IN: Minor error identifier. * @param msg * IN: Error description string. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - file, func, or msg is null. **/ public static void H5Epush(long stack_id, String file, String func, int line, long cls_id, long maj_id, long min_id, String msg) throws HDF5LibraryException, NullPointerException { H5Epush2(stack_id, file, func, line, cls_id, maj_id, min_id, msg); } /** * H5Epush2 pushes a new error record onto the error stack specified by estack_id. * * @param stack_id * IN: Error stack identifier. * @param file * IN: Name of the file in which the error was detected. * @param func * IN: Name of the function in which the error was detected. * @param line * IN: Line number within the file at which the error was detected. * @param cls_id * IN: Error class identifier. * @param maj_id * IN: Major error identifier. * @param min_id * IN: Minor error identifier. * @param msg * IN: Error description string. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - file, func, or msg is null. **/ public synchronized static native void H5Epush2(long stack_id, String file, String func, int line, long cls_id, long maj_id, long min_id, String msg) throws HDF5LibraryException, NullPointerException; /** * 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 long 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. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eunregister_class(long class_id) throws HDF5LibraryException; /** * H5Ewalk walks the error stack specified by estack_id for the current thread and calls the * function specified in func for each error along the way. * * @param stack_id * IN: Error stack identifier. * @param direction * IN: Direction in which the error stack is to be walked. * @param func * IN: Function to be called for each error encountered. * @param client_data * IN: Data to be passed with func. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - func is null. **/ public static void H5Ewalk(long stack_id, long direction, H5E_walk_cb func, H5E_walk_t client_data) throws HDF5LibraryException, NullPointerException { H5Ewalk2(stack_id, direction, func, client_data); } /** * H5Ewalk2 walks the error stack specified by estack_id for the current thread and calls the * function specified in func for each error along the way. * * @param stack_id * IN: Error stack identifier. * @param direction * IN: Direction in which the error stack is to be walked. * @param func * IN: Function to be called for each error encountered. * @param client_data * IN: Data to be passed with func. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - func is null. **/ public synchronized static native void H5Ewalk2(long stack_id, long direction, H5E_walk_cb func, H5E_walk_t client_data) throws HDF5LibraryException, NullPointerException; // /////// unimplemented //////// // public interface H5E_auto2_t extends Callback // { // int callback(int estack, Pointer client_data); // } // int H5Eget_auto(long estack_id, H5E_auto2_t func, PointerByReference client_data); // { // return H5Eget_auto2(estack_id, func, client_data); // } // int H5Eget_auto2(long estack_id, H5E_auto2_t func, PointerByReference client_data); // int H5Eset_auto(long estack_id, H5E_auto2_t func, Pointer client_data); // { // return H5Eset_auto2(estack_id, func, client_data); // } // int H5Eset_auto2(long estack_id, H5E_auto2_t func, Pointer client_data); // public static void H5Epush(long err_stack, String file, String func, int line, // long cls_id, long maj_id, long min_id, String msg, ...) // { // H5Epush2(err_stack, file, func, line, cls_id, maj_id, min_id, msg, ...); // } // public synchronized static native void H5Epush2(long err_stack, String file, String func, int line, // long cls_id, long maj_id, long min_id, String msg, ...); // //////////////////////////////////////////////////////////// // // // 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(long file_id) throws HDF5LibraryException { if (file_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; log.trace("OPEN_IDS: H5Fclose remove {}", file_id); OPEN_IDS.remove(file_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); return _H5Fclose(file_id); } private synchronized static native int _H5Fclose(long 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 long H5Fopen(String name, int flags, long access_id) throws HDF5LibraryException, NullPointerException { long id = _H5Fopen(name, flags, access_id); if (id > 0) { log.trace("OPEN_IDS: H5Fopen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Fopen(String name, int flags, long 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 long H5Freopen(long file_id) throws HDF5LibraryException { long id = _H5Freopen(file_id); if (id > 0) { log.trace("OPEN_IDS: H5Freopen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Freopen(long 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: *
* 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(long ocpl_id, int[] attributes)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_attr_phase_change sets threshold values for attribute storage on an object. These
* thresholds determine the point at which attribute storage changes
* from compact storage (i.e., storage in the object header)
* to dense storage (i.e., storage in a heap and indexed with a B-tree).
*
* @param ocpl_id
* IN: : Object (dataset or group) creation property list identifier
* @param max_compact
* IN: Maximum number of attributes to be stored in compact storage (Default: 8)
* @param min_dense
* IN: Minimum number of attributes to be stored in dense storage (Default: 6)
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_attr_phase_change(long ocpl_id, int max_compact, int min_dense)
throws HDF5LibraryException;
/**
* 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(long 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(long ocpl_id, int crt_order_flags)
throws HDF5LibraryException;
/**
* 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(long 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
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_obj_track_times(long ocpl_id, boolean track_times)
throws HDF5LibraryException;
/**
* H5Pmodify_filter modifies the specified FILTER in the transient or permanent output filter pipeline
* depending on whether PLIST is a dataset creation or dataset
* transfer property list. The FLAGS argument specifies certain
* general properties of the filter and is documented below.
* The CD_VALUES is an array of CD_NELMTS integers which are
* auxiliary data for the filter. The integer vlues will be
* stored in the dataset object header as part of the filter
* information.
** The FLAGS argument is a bit vector of the following fields: *
* H5Z_FLAG_OPTIONAL(0x0001) * If this bit is set then the filter is optional. If the * filter fails during an H5Dwrite() operation then the filter * is just excluded from the pipeline for the chunk for which it * failed; the filter will not participate in the pipeline * during an H5Dread() of the chunk. If this bit is clear and * the filter fails then the entire I/O operation fails. * If this bit is set but encoding is disabled for a filter, * attempting to write will generate an error. *
* Note: This function currently supports only the permanent filter * pipeline. That is, PLIST_ID must be a dataset creation * property list. * * @param plist * IN: Property list identifier. * @param filter * IN: Filter to be modified 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. * @exception NullPointerException * - name or an array is null. * **/ public synchronized static native int H5Pmodify_filter(long plist, long filter, int flags, long cd_nelmts, int[] cd_values) throws 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(long plist, int filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException; /** * 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(long plist) throws HDF5LibraryException; /** * 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 HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name or an array is null. * **/ public static int H5Pget_filter(long 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(long plist, int filter_number, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, ArrayStoreException, 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 * N/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 HDF5LibraryException * - Error from the HDF-5 Library. * @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(long plist_id, long 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. * * @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 * N/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 HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name or an array is null. * **/ public synchronized static native int H5Pget_filter_by_id2(long plist_id, long filter_id, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws HDF5LibraryException, NullPointerException; /** * H5Pall_filters_avail query to verify that all the filters set * in the dataset creation property list are available currently. * * @param dcpl_id * IN: Property list identifier. * * @return * TRUE if all filters available * FALSE if one or more filters not currently available. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Pall_filters_avail(long dcpl_id) throws HDF5LibraryException, NullPointerException; /** * H5Premove_filter deletes a filter from the dataset creation property list; * deletes all filters if filter is H5Z_FILTER_NONE * * @param obj_id * IN: Property list identifier. * @param filter * IN: Filter identifier. * * @return a non-negative value and the size of the user block; if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Premove_filter(long obj_id, long 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(long plist, int level) throws HDF5LibraryException; /** * H5Pset_fletcher32 sets Fletcher32 checksum of EDC for a dataset creation * property list or group creation property list. * * @param plist * IN: Property list identifier. * * @return a non-negative value and the size of the user block; if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_fletcher32(long plist) throws HDF5LibraryException, NullPointerException; // /////// File creation property list (FCPL) routines /////// /** * 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(long 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(long plist, long size) 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(long 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(long plist, int sizeof_addr, int sizeof_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 1/2size.
*
*
* 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(long 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(long plist, int ik, int lk) throws HDF5LibraryException;
/**
* 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(long 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(long plist, int ik) throws HDF5LibraryException;
/**
* 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(long 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(long plist_id, int nindexes)
throws HDF5LibraryException, IllegalArgumentException;
/**
* 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(long 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(long fcpl_id, int index_num, int mesg_type_flags,
int min_mesg_size) 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(long 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(long fcpl_id, int max_list, int min_btree)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pset_file_space_strategy sets the file space management strategy for the file associated with fcpl_id to strategy.
* There are four strategies that applications can select and they are described in the Parameters section.
*
* @param fcpl_id
* IN: File creation property list identifier
* @param strategy
* IN: The strategy for file space management.
* H5F_FSPACE_STRATEGY_FSM_AGGR
* Mechanisms: free-space managers, aggregators, and virtual file drivers
* This is the library default when not set.
* H5F_FSPACE_STRATEGY_PAGE
* Mechanisms: free-space managers with embedded paged aggregation and virtual file drivers
* H5F_FSPACE_STRATEGY_AGGR
* Mechanisms: aggregators and virtual file drivers
* H5F_FSPACE_STRATEGY_NONE
* Mechanisms: virtual file drivers
* @param persist
* IN: True to persist free-space.
* @param threshold
* IN: The free-space section threshold. The library default is 1, which is to track all free-space sections.
* Passing a value of zero (0) indicates that the value of threshold is not to be modified.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - Invalid values of max_list and min_btree.
*
**/
public synchronized static native void H5Pset_file_space_strategy(long fcpl_id, int strategy, boolean persist, long threshold)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_file_space_strategy provides the means for applications to manage the HDF5 file's file space strategy for their specific needs.
*
* @param fcpl_id
* IN: File creation property list identifier
* @param persist
* IN/OUT: The current free-space persistence. NULL, persist not queried.
* @param threshold
* IN/OUT: The current free-space section threshold. NULL, threshold not queried.
*
* @return the current free-space strategy.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - Invalid values of max_list and min_btree.
*
**/
public synchronized static native int H5Pget_file_space_strategy(long fcpl_id, boolean[] persist, long[] threshold)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_file_space_strategy_persist provides the means for applications to manage the HDF5 file's file space strategy for their specific needs.
*
* @param fcpl_id
* IN: File creation property list identifier
*
* @return the current free-space persistence.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - Invalid values of max_list and min_btree.
*
**/
public synchronized static native boolean H5Pget_file_space_strategy_persist(long fcpl_id)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_file_space_strategy_threshold provides the means for applications to manage the HDF5 file's file space strategy for their specific needs.
*
* @param fcpl_id
* IN: File creation property list identifier
*
* @return the current free-space section threshold.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - Invalid values of max_list and min_btree.
*
**/
public synchronized static native long H5Pget_file_space_strategy_threshold(long fcpl_id)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pset_file_space_page_size retrieves the file space page size for aggregating small metadata or raw data.
*
* @param fcpl_id
* IN: File creation property list identifier
* @param page_size
* IN: the file space page size.
*
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - Invalid values of max_list and min_btree.
*
**/
public synchronized static native void H5Pset_file_space_page_size(long fcpl_id, long page_size)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_file_space_page_size Sets the file space page size for paged aggregation.
*
* @param fcpl_id
* IN: File creation property list identifier
*
* @return the current file space page size.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - Invalid values of max_list and min_btree.
*
**/
public synchronized static native long H5Pget_file_space_page_size(long fcpl_id)
throws HDF5LibraryException, IllegalArgumentException;
// /////// File access property list (FAPL) routines ///////
/**
* 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(long 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(long plist, long threshold, long alignment)
throws HDF5LibraryException;
/**
* 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
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*/
public synchronized static native long H5Pget_driver(long plid) throws HDF5LibraryException;
/**
* H5Pget_family_offset gets offset for family driver.
*
* @param fapl_id
* IN: File access property list identifier
*
* @return the offset.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native long H5Pget_family_offset(long fapl_id) throws HDF5LibraryException;
/**
* H5Pset_family_offset sets the offset for family driver.
*
* @param fapl_id
* IN: File access property list identifier
* @param offset
* IN: the offset value
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pset_family_offset(long fapl_id, long offset) throws HDF5LibraryException;
/**
* 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(long plist, int[] mdc_nelmts, long[] rdcc_nelmts,
long[] rdcc_nbytes, double[] rdcc_w0) throws HDF5LibraryException, NullPointerException;
/**
* 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(long plist, int mdc_nelmts, long rdcc_nelmts, long rdcc_nbytes,
double rdcc_w0) throws HDF5LibraryException;
/**
* H5Pget_mdc_config gets the initial metadata cache configuration contained in a file access property list.
* 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(long plist_id) throws HDF5LibraryException;
/**
* H5Pset_mdc_config sets 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.
* @param config_ptr
* IN: H5AC_cache_config_t, the initial metadata cache configuration.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Pset_mdc_config(long plist_id, H5AC_cache_config_t config_ptr)
throws HDF5LibraryException;
/**
* H5Pget_gc_references Returns the current setting for the garbage collection refernces property from a file access
* property list.
*
* @param fapl_id
* IN File access property list
*
* @return GC is on (true) or off (false)
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native boolean H5Pget_gc_references(long fapl_id) throws HDF5LibraryException;
/**
* 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(long fapl_id, boolean gc_ref)
throws HDF5LibraryException;
/**
* H5Pget_fclose_degree returns the degree for the file close behavior for a file access
* property list.
*
* @param fapl_id
* IN File access property list
*
* @return the degree for the file close behavior
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pget_fclose_degree(long fapl_id) throws HDF5LibraryException,
NullPointerException;
/**
* H5Pset_fclose_degree sets the degree for the file close behavior.
*
* @param fapl_id
* IN File access property list
* @param degree
* IN the degree for the file close behavior
*
* @return non-negative if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_fclose_degree(long fapl_id, int degree) throws HDF5LibraryException,
NullPointerException;
/**
* 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(long 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_meta_block_size(long fapl_id, long size) throws HDF5LibraryException;
/**
* H5Pget_sieve_buf_size retrieves the current settings for the data sieve buffer size
* property from a file access property list.
*
* @param fapl_id
* IN: Identifier for property list to query.
*
* @return a non-negative value and the size of the user block; if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native long H5Pget_sieve_buf_size(long fapl_id) throws HDF5LibraryException;
/**
* H5Pset_sieve_buf_size Sets the maximum size of the data seive buffer used for file
* drivers which are capable of using data sieving. The data sieve
* buffer is used when performing I/O on datasets in the file. Using a
* buffer which is large anough to hold several pieces of the dataset
* being read in for hyperslab selections boosts performance by quite a
* bit.
* * The default value is set to 64KB, indicating that file I/O for raw data * reads and writes will occur in at least 64KB blocks. Setting the value to 0 * with this function will turn off the data sieving * * @param fapl_id * IN: Identifier of property list to modify. * @param size * IN: maximum size of the data seive buffer. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Pset_sieve_buf_size(long fapl_id, long 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. * * @return a non-negative value and the size of the user block; if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Pget_small_data_block_size(long 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(long plist, long size) 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. * *
* 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(long 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(long fapl_id, int low, int high)
throws HDF5LibraryException, IllegalArgumentException;
/**
* 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(long 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_elink_file_cache_size(long fapl_id, int efc_size)
throws HDF5LibraryException;
/**
* H5Pset_mdc_log_options sets metadata cache logging options.
*
* @param fapl_id
* IN: File access property list identifier
* @param is_enabled
* IN: Whether logging is enabled.
* @param location
* IN: Location of log in UTF-8/ASCII (file path/name) (On Windows, this must be ASCII).
* @param start_on_access
* IN: Whether the logging begins as soon as the file is opened or created.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - location is null.
*
**/
public synchronized static native void H5Pset_mdc_log_options(long fapl_id, boolean is_enabled, String location, boolean start_on_access)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_mdc_log_options gets metadata cache logging options.
*
* @param fapl_id
* IN: File access property list identifier
* @param mdc_log_options
* the options
* mdc_logging_options[0] = is_enabled, whether logging is enabled
* mdc_logging_options[1] = start_on_access, whether the logging begins as soon as the file is opened or created
*
* @return the location of log in UTF-8/ASCII (file path/name) (On Windows, this must be ASCII).
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native String H5Pget_mdc_log_options(long fapl_id, boolean[] mdc_log_options)
throws HDF5LibraryException;
/**
* H5Pget_metadata_read_attempts retrieves the number of read attempts that is set in the file access property list plist_id.
*
* @param plist_id
* IN: File access property list identifier
*
* @return The number of read attempts.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native long H5Pget_metadata_read_attempts(long plist_id) throws HDF5LibraryException;
/**
* H5Pset_metadata_read_attempts sets the number of reads that the library will try when reading checksummed
* metadata in an HDF5 file opened with SWMR access. When reading such metadata, the library will compare the
* checksum computed for the metadata just read with the checksum stored within the piece of checksum. When
* performing SWMR operations on a file, the checksum check might fail when the library reads data on a system
* that is not atomic. To remedy such situations, the library will repeatedly read the piece of metadata until
* the check passes or finally fails the read when the allowed number of attempts is reached.
*
* @param plist_id
* IN: File access property list identifier
* @param attempts
* IN: The number of read attempts which is a value greater than 0.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_metadata_read_attempts(long plist_id, long attempts)
throws HDF5LibraryException;
/**
* H5Pget_evict_on_close retrieves the file access property list setting that determines whether an HDF5 object
* will be evicted from the library's metadata cache when it is closed.
*
* @param fapl_id
* IN: File access property list identifier
*
* @return indication if the object will be evicted on close.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native boolean H5Pget_evict_on_close(long fapl_id)
throws HDF5LibraryException;
/**
* H5Pset_evict_on_close controls the library's behavior of evicting metadata associated with a closed object.
*
* @param fapl_id
* IN: File access property list identifier
* @param evict_on_close
* IN: Whether the HDF5 object should be evicted on close.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close)
throws HDF5LibraryException;
/**
* H5Pget_use_file_locking retrieves whether we are using file locking.
*
* @param fapl_id
* IN: File access property list identifier
*
* @return indication if file locking is used.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native boolean H5Pget_use_file_locking(long fapl_id)
throws HDF5LibraryException;
/**
* H5Pget_use_file_locking retrieves whether we ignore file locks when they are disabled.
*
* @param fapl_id
* IN: File access property list identifier
*
* @return indication if file locking is ignored.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native boolean H5Pget_ignore_disabled_file_locking(long fapl_id)
throws HDF5LibraryException;
/**
* H5Pset_file_locking sets parameters related to file locking.
*
* @param fapl_id
* IN: File access property list identifier
*
* @param use_file_locking
* IN: Whether the library will use file locking when opening files (mainly for SWMR semantics).
*
* @param ignore_when_disabled
* IN: Whether file locking will be ignored when disabled on a file system (useful for Lustre).
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_file_locking(long fapl_id, boolean use_file_locking, boolean ignore_when_disabled)
throws HDF5LibraryException;
// ///// unimplemented /////
// herr_t H5Pset_vol(hid_t plist_id, hid_t new_vol_id, const void *new_vol_info);
// herr_t H5Pget_vol_id(hid_t plist_id, hid_t *vol_id);
// herr_t H5Pget_vol_info(hid_t plist_id, void **vol_info);
// Dataset creation property list (DCPL) routines //
/**
* 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(long 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(long plist, int layout) 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(long 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(long plist, int ndims, byte[] dim) 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 HDF5Exception
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - dims array is null.
* @exception IllegalArgumentException
* - dims <=0
**/
public synchronized static int H5Pset_chunk(long 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;
}
/**
* H5Pset_virtual maps elements of the virtual dataset (VDS) described by the
* virtual dataspace identifier vspace_id to the elements of the source dataset
* described by the source dataset dataspace identifier src_space_id. The source
* dataset is identified by the name of the file where it is located, src_file_name,
* and the name of the dataset, src_dset_name.
*
* @param dcpl_id
* IN: The identifier of the dataset creation property list that will be used when creating the virtual dataset.
* @param vspace_id
* IN: The dataspace identifier with the selection within the virtual dataset applied, possibly an unlimited selection.
* @param src_file_name
* IN: The name of the HDF5 file where the source dataset is located. The file might not exist yet. The name can be specified using a C-style printf statement.
* @param src_dset_name
* IN: The path to the HDF5 dataset in the file specified by src_file_name. The dataset might not exist yet. The dataset name can be specified using a C-style printf statement.
* @param src_space_id
* IN: The source dataset dataspace identifier with a selection applied, possibly an unlimited selection.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - an name string is null.
* @exception IllegalArgumentException
* - An id is <=0
**/
public synchronized static native void H5Pset_virtual(long dcpl_id, long vspace_id, String src_file_name, String src_dset_name, long src_space_id) throws HDF5LibraryException,
NullPointerException, IllegalArgumentException;
/**
* H5Pget_virtual_count gets the number of mappings for a virtual dataset that has the creation property list specified by dcpl_id.
*
* @param dcpl_id
* IN: The identifier of the virtual dataset creation property list.
*
* @return a non-negative number of mappings if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - An id is <=0
**/
public synchronized static native long H5Pget_virtual_count(long dcpl_id) throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_virtual_vspace takes the dataset creation property list for the virtual dataset, dcpl_id, and the mapping index, index,
* and returns a dataspace identifier for the selection within the virtual dataset used in the mapping.
*
* @param dcpl_id
* IN: The identifier of the virtual dataset creation property list.
* @param index
* IN: Mapping index.
*
* @return a valid dataspace identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - An id is <=0
**/
public synchronized static native long H5Pget_virtual_vspace(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_virtual_srcspace takes the dataset creation property list for the virtual dataset, dcpl_id, and the mapping index, index,
* and returns a dataspace identifier for the selection within the source dataset used in the mapping.
*
* @param dcpl_id
* IN: The identifier of the virtual dataset creation property list.
* @param index
* IN: Mapping index.
*
* @return a valid dataspace identifier if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - An id is <=0
**/
public synchronized static native long H5Pget_virtual_srcspace(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_virtual_filename takes the dataset creation property list for the virtual dataset, dcpl_id, the mapping index, index,
* the size of the filename for a source dataset, size, and retrieves the name of the file for a source dataset used in the mapping.
*
* @param dcpl_id
* IN: The identifier of the virtual dataset creation property list.
* @param index
* IN: Mapping index.
*
* @return the name of the file containing the source dataset if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - An id is <=0
**/
public synchronized static native String H5Pget_virtual_filename(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_virtual_dsetname takes the dataset creation property list for the virtual dataset, dcpl_id, the mapping index, index, the
* size of the dataset name for a source dataset, size, and retrieves the name of the source dataset used in the mapping.
*
* @param dcpl_id
* IN: The identifier of the virtual dataset creation property list.
* @param index
* IN: Mapping index.
*
* @return the name of the source dataset if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - An id is <=0
**/
public synchronized static native String H5Pget_virtual_dsetname(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException;
// ///// unimplemented /////
// /**
// * H5Pget_vds_file_cache_size retrieves the size of the vds link open file cache.
// *
// * @param fapl_id
// * IN: File access property list identifier
// *
// * @return VDS link open file cache size in number of files.
// *
// * @exception HDF5LibraryException
// * - Error from the HDF-5 Library.
// *
// **/
// public synchronized static native int H5Pget_vds_file_cache_size(long fapl_id) throws HDF5LibraryException;
//
// /**
// * H5Pset_vds_file_cache_size sets the number of files that can be held open in an vds link open file cache.
// *
// * @param fapl_id
// * IN: File access property list identifier
// * @param efc_size
// * IN: VDS link open file cache size in number of files.
// *
// * @exception HDF5LibraryException
// * - Error from the HDF-5 Library.
// *
// **/
// public synchronized static native void H5Pset_vds_file_cache_size(long fapl_id, int efc_size)
// throws HDF5LibraryException;
/**
* 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(long 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(long 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(long plist) throws HDF5LibraryException;
/**
* H5Pset_szip Sets up the use of the szip filter.
*
* @param plist
* IN: Dataset creation property list identifier.
* @param options_mask
* IN: Bit vector specifying certain general properties of the filter.
* @param pixels_per_block
* IN: Number of pixels in blocks
*
* @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_szip(long plist, int options_mask, int pixels_per_block)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_shuffle Sets up the use of the shuffle 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_shuffle(long plist_id) 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(long 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(long plist_id, int scale_type, int scale_factor)
throws HDF5LibraryException, IllegalArgumentException;
/**
* 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
*
* @exception HDF5Exception
* - Error converting data array.
**/
public synchronized static native int H5Pget_fill_value(long plist_id, long 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
*
* @exception HDF5Exception
* - Error converting data array.
**/
public synchronized static int H5Pget_fill_value(long plist_id, long 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(long plist_id, long 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(long plist_id, long 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;
}
/**
* H5Pset_fill_value checks if the fill value is defined for a dataset creation property list.
*
* @param plist_id
* IN: Property list identifier.
* @param status
* IN: The fill value setting:
* H5D_FILL_VALUE_UNDEFINED
* H5D_FILL_VALUE_DEFAULT
* H5D_FILL_VALUE_USER_DEFINED
* H5D_FILL_VALUE_ERROR
*
* @return a non-negative value if successful
*
* @exception HDF5Exception
* - Error converting data array
**/
public synchronized static native int H5Pfill_value_defined(long plist_id, int[] status)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_alloc_time Gets space allocation time for dataset during creation.
*
* @param plist_id
* IN: Dataset creation property list identifier.
* @param alloc_time
* OUT: allocation time.
*
* @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_alloc_time(long plist_id, int[] alloc_time)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_alloc_time Sets space allocation time for dataset during creation.
*
* @param plist_id
* IN: Dataset creation property list identifier.
* @param alloc_time
* IN: allocation time.
*
* @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_alloc_time(long plist_id, int alloc_time) throws HDF5LibraryException,
NullPointerException;
/**
* H5Pset_fill_time Gets fill value writing time.
*
* @param plist_id
* IN: Dataset creation property list identifier.
* @param fill_time
* OUT: fill time.
*
* @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_fill_time(long plist_id, int[] fill_time) throws HDF5LibraryException;
/**
* H5Pset_fill_time Sets the fill value writing time.
*
* @param plist_id
* IN: Dataset creation property list identifier.
* @param fill_time
* IN: fill time.
*
* @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_fill_time(long plist_id, int fill_time) throws HDF5LibraryException;
/**
* H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list.
*
* @param dcpl_id
* IN: Dataset creation property list identifier
* @param opts
* IN: Edge chunk option flag. Valid values are:
* H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS - filters are not applied to partial edge chunks.
* 0 - Disables option; partial edge chunks will be compressed.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library
**/
public synchronized static native void H5Pset_chunk_opts(long dcpl_id, int opts) throws HDF5LibraryException;
/**
* H5Pget_chunk_opts retrieves the edge chunk option setting stored in the dataset creation property list .
*
* @param dcpl_id
* IN: Dataset creation property list
* @return The edge chunk option setting.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library
**/
public synchronized static native int H5Pget_chunk_opts(long dcpl_id) throws HDF5LibraryException;
/**
* H5Pget_dset_no_attrs_hint accesses the flag for whether or not datasets created by the given dcpl
* will be created with a "minimized" object header.
*
* @param dcpl_id
* IN: Dataset creation property list
*
* @return true if the given dcpl is set to create minimized dataset object headers, false if not.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native boolean H5Pget_dset_no_attrs_hint(long dcpl_id)
throws HDF5LibraryException;
/**
* H5Pset_dset_no_attrs_hint sets the dcpl to minimize (or explicitly to not minimized) dataset object
* headers upon creation.
*
* @param dcpl_id
* IN: Dataset creation property list
*
* @param minimize
* the minimize hint setting
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Pset_dset_no_attrs_hint(long dcpl_id, boolean minimize)
throws HDF5LibraryException;
// /////// Dataset access property list (DAPL) routines ///////
/**
* 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - an array is null.
**/
public synchronized static native void H5Pget_chunk_cache(long 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Pset_chunk_cache(long dapl_id, long rdcc_nslots, long rdcc_nbytes,
double rdcc_w0) throws HDF5LibraryException;
/**
* H5Pset_virtual_view takes the access property list for the virtual dataset, dapl_id, and the flag,
* view, and sets the VDS view according to the flag value.
*
* @param dapl_id
* IN: Dataset access property list identifier for the virtual dataset
* @param view
* IN: Flag specifying the extent of the data to be included in the view.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library
**/
public synchronized static native void H5Pset_virtual_view(long dapl_id, int view) throws HDF5LibraryException;
/**
* H5Pget_virtual_view takes the virtual dataset access property list, dapl_id, and retrieves the flag,
* view, set by the H5Pset_virtual_view call.
*
* @param dapl_id
* IN: Dataset access property list identifier for the virtual dataset
* @return The flag specifying the view of the virtual dataset.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library
**/
public synchronized static native int H5Pget_virtual_view(long dapl_id) throws HDF5LibraryException;
/**
* H5Pset_virtual_printf_gap sets the access property list for the virtual dataset, dapl_id, to instruct the
* library to stop looking for the mapped data stored in the files and/or datasets with the printf-style names
* after not finding gap_size files and/or datasets. The found source files and datasets will determine the
* extent of the unlimited virtual dataset with the printf-style mappings.
*
* @param dapl_id
* IN: Dataset access property list identifier for the virtual dataset
* @param gap_size
* IN: Maximum number of files and/or datasets allowed to be missing for determining
* the extent of an unlimited virtual dataset with printf-style mappings.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library
**/
public synchronized static native void H5Pset_virtual_printf_gap(long dapl_id, long gap_size) throws HDF5LibraryException;
/**
* H5Pget_virtual_printf_gap returns the maximum number of missing printf-style files and/or datasets for
* determining the extent of an unlimited virtual dataaset, gap_size, using the access property list for
* the virtual dataset, dapl_id.
*
* @param dapl_id
* IN: Dataset access property list identifier for the virtual dataset
* @return Maximum number of files and/or datasets allowed to be missing for determining
* the extent of an unlimited virtual dataset with printf-style mappings.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library
**/
public synchronized static native long H5Pget_virtual_printf_gap(long dapl_id) throws HDF5LibraryException;
/**
* H5Pget_virtual_prefix Retrieves prefix applied to virtual file paths.
*
* @param dapl_id
* IN: Link access property list identifier
*
* @return the prefix to be applied to virtual file paths.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native String H5Pget_virtual_prefix(long dapl_id)
throws HDF5LibraryException;
/**
* H5Pset_virtual_prefix Sets prefix to be applied to virtual file paths.
*
* @param dapl_id
* IN: Dataset access property list identifier
* @param prefix
* IN: Prefix to be applied to virtual file paths
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - prefix is null.
*
**/
public synchronized static native void H5Pset_virtual_prefix(long dapl_id, String prefix)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_efile_prefix Retrieves prefix applied to external file paths.
*
* @param dapl_id
* IN: Link access property list identifier
*
* @return the prefix to be applied to external file paths.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native String H5Pget_efile_prefix(long dapl_id)
throws HDF5LibraryException;
/**
* H5Pset_efile_prefix Sets prefix to be applied to external file paths.
*
* @param dapl_id
* IN: Dataset access property list identifier
* @param prefix
* IN: Prefix to be applied to external file paths
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - prefix is null.
*
**/
public synchronized static native void H5Pset_efile_prefix(long dapl_id, String prefix)
throws HDF5LibraryException, NullPointerException;
// public synchronized static native void H5Pset_append_flush(long plist_id, int ndims, long[] boundary, H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException;
// public synchronized static native void H5Pget_append_flush(long plist_id, int dims, long[] boundary, H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException;
// /////// Dataset xfer property list (DXPL) routines ///////
/**
* 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(long 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(long plist_id, String expression)
throws HDF5LibraryException, NullPointerException;
/**
* 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(long plist, byte[] tconv, byte[] bkg)
throws HDF5LibraryException, IllegalArgumentException;
/**
* H5Pget_buffer_size gets type conversion and background buffer size, in bytes, if successful;
* otherwise 0 on failure.
*
* @param plist
* Identifier for the dataset transfer property list.
*
* @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 long H5Pget_buffer_size(long 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.
*
* @param plist
* Identifier for the dataset transfer property list.
* @param size
* Size, in bytes, of the type conversion and background buffers.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception IllegalArgumentException
* - plist is invalid.
**/
public synchronized static native void H5Pset_buffer_size(long plist, long size) throws HDF5LibraryException,
IllegalArgumentException;
/**
* H5Pget_edc_check gets the error-detecting algorithm in use.
*
* @param plist
* Identifier for the dataset transfer property list.
*
* @return the error-detecting algorithm
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pget_edc_check(long plist) throws HDF5LibraryException;
/**
* H5Pset_edc_check sets the error-detecting algorithm.
*
* @param plist
* Identifier for the dataset transfer property list.
* @param check
* the error-detecting algorithm to use.
*
* @return non-negative if succeed
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException;
/**
* 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(long 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(long plist_id, double left, double middle, double right)
throws HDF5LibraryException;
/**
* H5Pget_hyper_vector_size reads values previously set with H5Pset_hyper_vector_size.
*
* @param dxpl_id
* IN: Dataset transfer property list identifier.
* @param vector_size
* OUT: hyper vector 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_hyper_vector_size(long dxpl_id, long[] vector_size)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_hyper_vector_size sets the number of
* "I/O vectors" (offset and length pairs) which are to be
* accumulated in memory before being issued to the lower levels
* of the library for reading or writing the actual data.
* Increasing the number should give better performance, but use
* more memory during hyperslab I/O. The vector size must be
* greater than 1.
*,p.
* The default is to use 1024 vectors for I/O during hyperslab
* reading/writing.
*
* @param dxpl_id
* IN: Dataset transfer property list identifier.
* @param vector_size
* IN: hyper vestor 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_hyper_vector_size(long dxpl_id, long vector_size)
throws HDF5LibraryException, NullPointerException;
// /////// Link creation property list (LCPL) routines ///////
/**
* 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(long 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(long lcpl_id, boolean crt_intermed_group)
throws HDF5LibraryException;
// /////// Group creation property list (GCPL) routines ///////
/**
* 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(long 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(long gcpl_id, long size_hint)
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(long 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(long gcpl_id, int max_compact, int min_dense)
throws HDF5LibraryException, IllegalArgumentException;
/**
* 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(long 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(long gcpl_id, int est_num_entries, int est_name_len)
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(long 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(long gcpl_id, int crt_order_flags)
throws HDF5LibraryException;
// /////// String creation property list (STRCPL) routines ///////
/**
* H5Pget_char_encoding gets the character encoding of the string.
*
* @param plist_id
* IN: the property list identifier
*
* @return Returns the character encoding of the string.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native int H5Pget_char_encoding(long plist_id) throws HDF5LibraryException;
/**
* H5Pset_char_encoding sets the character encoding of the string.
*
* @param plist_id
* IN: the property list identifier
* @param encoding
* IN: the character encoding of the string
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_char_encoding(long plist_id, int encoding)
throws HDF5LibraryException;
// /////// Link access property list (LAPL) routines ///////
/**
* 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(long 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 lapl_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(long lapl_id, long nlinks) throws HDF5LibraryException,
IllegalArgumentException;
/**
* 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(long 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(long lapl_id, String prefix) throws HDF5LibraryException,
NullPointerException;
/**
* 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 long H5Pget_elink_fapl(long lapl_id) throws HDF5LibraryException {
long id = _H5Pget_elink_fapl(lapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Pget_elink_fapl add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Pget_elink_fapl(long 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(long lapl_id, long fapl_id) throws HDF5LibraryException;
/**
* 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(long 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(long lapl_id, int flags) throws HDF5LibraryException,
IllegalArgumentException;
// /////// Object copy property list (OCPYPL) routines ///////
/**
* 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(long 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
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_copy_object(long ocp_plist_id, int copy_options)
throws HDF5LibraryException;
// /////// file drivers property list routines ///////
/**
* H5Pget_fapl_core retrieve H5FD_CORE I/O settings.
*
* @param fapl_id
* IN: File access property list identifier
* @param increment
* OUT: how much to grow the memory each time
* @param backing_store
* OUT: write to file name on flush setting
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pget_fapl_core(long fapl_id, long[] increment, boolean[] backing_store)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_fapl_core modifies the file access property list to use the H5FD_CORE driver.
*
* @param fapl_id
* IN: File access property list identifier
* @param increment
* IN: how much to grow the memory each time
* @param backing_store
* IN: write to file name on flush setting
*
* @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_core(long fapl_id, long increment, boolean backing_store)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_fapl_direct queries properties set by the H5Pset_fapl_direct.
*
* @param fapl_id
* IN: File access property list identifier
* @param info
* OUT: Returned property list information
* info[0] = increment -how much to grow the memory each time
* info[1] = backing_store - write to file name on flush setting
*
* @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(long 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(long fapl_id, long alignment, long block_size,
long cbuf_size) throws HDF5LibraryException;
/**
* H5Pget_fapl_family Returns information about the family file access property list.
*
* @param fapl_id
* IN: File access property list identifier
* @param memb_size
* OUT: the size in bytes of each file member (used only when creating a new file)
* @param memb_fapl_id
* OUT: the file access property list to be used for each family member
*
* @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_family(long fapl_id, long[] memb_size, long[] memb_fapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_fapl_family Sets up use of the direct I/O driver.
*
* @param fapl_id
* IN: File access property list identifier
* @param memb_size
* IN: the size in bytes of each file member (used only when creating a new file)
* @param memb_fapl_id
* IN: the file access property list to be used for each family member
*
* @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_family(long fapl_id, long memb_size, long memb_fapl_id)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_fapl_hdfs Modify the file access property list to use the H5FD_HDFS driver.
*
* @param fapl_id
* IN: File access property list identifier
* @param fapl_conf
* IN: the properties of the hdfs driver
*
* @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_hdfs(long fapl_id, H5FD_hdfs_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_fapl_hdfs gets the properties hdfs I/O driver.
*
* @param fapl_id
* IN: File access property list identifier
*
* @return the properties of the hdfs driver.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native H5FD_hdfs_fapl_t H5Pget_fapl_hdfs(long fapl_id) throws HDF5LibraryException, NullPointerException;
/**
* 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(long fapl_id, int[] memb_map, long[] 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(long fapl_id, int[] memb_map, long[] memb_fapl,
String[] memb_name, long[] memb_addr, boolean relax) throws HDF5LibraryException, NullPointerException;
/**
* 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(long fapl_id, String logfile, long flags, long buf_size)
throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_fapl_sec2 Sets up use of the sec2 I/O driver.
*
* @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_fapl_sec2(long fapl_id) throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_fapl_split Sets up use of the split I/O driver. Makes the multi driver act like the
* old split driver which stored meta data in one file and raw
* data in another file
*
* @param fapl_id
* IN: File access property list identifier
* @param meta_ext
* IN: meta filename extension
* @param meta_plist_id
* IN: File access property list identifier for metadata
* @param raw_ext
* IN: raw data filename extension
* @param raw_plist_id
* IN: File access property list identifier raw data
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native void H5Pset_fapl_split(long fapl_id, String meta_ext, long meta_plist_id,
String raw_ext, long raw_plist_id) throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_fapl_stdio Sets up use of the stdio I/O driver.
*
* @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_fapl_stdio(long fapl_id) throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_fapl_windows Sets up use of the windows I/O driver.
*
* @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_fapl_windows(long fapl_id) throws HDF5LibraryException, NullPointerException;
/**
* H5Pset_fapl_ros3 Modify the file access property list to use the H5FD_ROS3 driver.
*
* @param fapl_id
* IN: File access property list identifier
* @param fapl_conf
* IN: the properties of the ros3 driver
*
* @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_ros3(long fapl_id, H5FD_ros3_fapl_t fapl_conf) throws HDF5LibraryException, NullPointerException;
/**
* H5Pget_fapl_ros3 gets the properties of the ros3 I/O driver.
*
* @param fapl_id
* IN: File access property list identifier
*
* @return the properties of the ros3 driver.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
*
**/
public synchronized static native H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id) throws HDF5LibraryException, NullPointerException;
// /////// unimplemented ////////
// Generic property list routines //
// herr_t H5Pencode(hid_t plist_id, void *buf, size_t *nalloc);
// hid_t H5Pdecode(const void *buf);
// Object creation property list (OCPL) routines //
// File creation property list (FCPL) routines //
// File access property list (FAPL) routines //
// herr_t H5Pset_driver(hid_t plist_id, hid_t new_driver_id, const void *new_driver_info)
// const void *H5Pget_driver_info(hid_t plist_id)
// 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)
// herr_t H5Pget_file_image(hid_t fapl_id, void **buf_ptr_ptr, size_t *buf_len_ptr);
// herr_t H5Pset_file_image(hid_t fapl_id, void *buf_ptr, size_t buf_len);
// herr_t H5Pget_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callbacks_ptr);
// herr_t H5Pset_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callbacks_ptr);
// herr_t H5Pset_core_write_tracking(hid_t fapl_id, hbool_t is_enabled, size_t page_size);
// herr_t H5Pget_core_write_tracking(hid_t fapl_id, hbool_t *is_enabled, size_t *page_size);
// #ifdef H5_HAVE_PARALLEL
// herr_t H5Pset_all_coll_metadata_ops(hid_t accpl_id, hbool_t is_collective);
// herr_t H5Pget_all_coll_metadata_ops(hid_t plist_id, hbool_t *is_collective);
// herr_t H5Pset_coll_metadata_write(hid_t fapl_id, hbool_t is_collective);
// herr_t H5Pget_coll_metadata_write(hid_t fapl_id, hbool_t *is_collective);
// #endif /* H5_HAVE_PARALLEL */
// herr_t H5Pset_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr);
// herr_t H5Pget_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr /*out*/);
// herr_t H5Pset_page_buffer_size(hid_t plist_id, size_t buf_size, unsigned min_meta_per, unsigned min_raw_per);
// herr_t H5Pget_page_buffer_size(hid_t fapl_id, size_t *buf_size, unsigned *min_meta_perc, unsigned *min_raw_perc);
// herr_t H5Pset_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t func, void *user_data);
// herr_t H5Pget_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t *func, void **user_data);
// Dataset creation property list (DCPL) routines //
// Dataset access property list (DAPL) routines //
// herr_t H5Pset_append_flush (hid_t dapl_id, int ndims, const hsize_t boundary[], H5D_append_cb_t func, void *user_data);
// herr_t H5Pget_append_flush(hid_t dapl_id, int ndims, hsize_t boundary[], H5D_append_cb_t *func, void **user_data)
// Dataset xfer property list (DXPL) routines //
// herr_t H5Pset_buffer(hid_t plist_id, size_t size, void *tconv, void *bkg);
// herr_t H5Pset_preserve(hid_t plist_id, hbool_t status);
// int H5Pget_preserve(hid_t plist_id);
// herr_t H5Pset_filter_callback(hid_t plist, H5Z_filter_func_t func, void *op_data)
// 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 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)
// #ifdef H5_HAVE_PARALLEL
// herr_t H5Pget_mpio_actual_chunk_opt_mode(hid_t plist_id, H5D_mpio_actual_chunk_opt_mode_t *actual_chunk_opt_mode);
// herr_t H5Pget_mpio_actual_io_mode(hid_t plist_id, H5D_mpio_actual_io_mode_t *actual_io_mode);
// herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_cause, uint32_t *global_no_collective_cause);
// #endif /* H5_HAVE_PARALLEL */
// Link creation property list (LCPL) routines //
// Group creation property list (GCPL) routines //
// String creation property list (STRCPL) routines //
// Link access property list (LAPL) routines //
// 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 )
// Object copy property list (OCPYPL) routines //
// herr_t H5Padd_merge_committed_dtype_path(hid_t plist_id, const char *path);
// herr_t H5Pfree_merge_committed_dtype_paths(hid_t plist_id);
// herr_t H5Pget_mcdt_search_cb(hid_t plist_id, H5O_mcdt_search_cb_t *func, void **op_data);
// herr_t H5Pset_mcdt_search_cb(hid_t plist_id, H5O_mcdt_search_cb_t func, void *op_data);
// ////////////////////////////////////////////////////////////
// //
// H5PL: HDF5 1.8 Plugin API Functions //
// //
// ////////////////////////////////////////////////////////////
/**
* H5PLset_loading_state uses one argument to enable or disable individual plugins.
* The plugin_flags parameter is an encoded integer in which each bit controls a specific
* plugin or class of plugins.
* A plugin bit set to 0 (zero) prevents the use of the dynamic plugin corresponding
* to that bit position. A plugin bit set to 1 (one) allows the use of that dynamic plugin.
* All dynamic plugins can be enabled by setting plugin_flags to a negative value.
* A value of 0 (zero) will disable all dynamic plugins.
*
* H5PLset_loading_state inspects the HDF5_PLUGIN_PRELOAD environment variable every
* time it is called. If the environment variable is set to the special :: string,
* all dynamic plugins will be disabled.
*
* @param plugin_flags
* IN: The list of dynamic plugin types to enable or disable.
* A plugin bit set to 0 (zero) prevents use of that dynamic plugin.
* A plugin bit set to 1 (one) enables use of that dynamic plugin.
* Setting plugin_flags to a negative value enables all dynamic plugins.
* Setting plugin_flags to 0 (zero) disables all dynamic plugins.
*
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5PLset_loading_state(int plugin_flags) throws HDF5LibraryException;
/**
* H5PLget_loading_state retrieves the state of the dynamic plugins flag, plugin_flags..
*
* @return the list of dynamic plugin types that are enabled or disabled.
* A plugin bit set to 0 (zero) indicates that that dynamic plugin is disabled.
* A plugin bit set to 1 (one) indicates that that dynamic plugin is enabled.
* If the value of plugin_flags is negative, all dynamic plugins are enabled.
* If the value of plugin_flags is 0 (zero), all dynamic plugins are disabled.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5PLget_loading_state() throws HDF5LibraryException;
/**
* H5PLappend inserts the plugin path at the end of the table.
*
* @param plugin_path
* IN: Path for location of filter plugin libraries.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5PLappend(String plugin_path) throws HDF5LibraryException;
/**
* H5PLprepend inserts the plugin path at the beginning of the table.
*
* @param plugin_path
* IN: Path for location of filter plugin libraries.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5PLprepend(String plugin_path) throws HDF5LibraryException;
/**
* H5PLreplace replaces the plugin path at the specified index.
*
* @param plugin_path
* IN: Path for location of filter plugin libraries.
* @param index
* IN: The table index (0-based).
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5PLreplace(String plugin_path, int index) throws HDF5LibraryException;
/**
* H5PLinsert inserts the plugin path at the specified index.
*
* @param plugin_path
* IN: Path for location of filter plugin libraries.
* @param index
* IN: The table index (0-based).
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5PLinsert(String plugin_path, int index) throws HDF5LibraryException;
/**
* H5PLremove removes the plugin path at the specified index.
*
* @param index
* IN: The table index (0-based).
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5PLremove(int index) throws HDF5LibraryException;
/**
* H5PLget retrieves the plugin path at the specified index.
*
* @param index
* IN: The table index (0-based).
*
* @return the current path at the index in plugin path table
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native String H5PLget(int index) throws HDF5LibraryException;
/**
* H5PLsize retrieves the size of the current list of plugin paths.
*
* @return the current number of paths in the plugin path table
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5PLsize() throws HDF5LibraryException;
// ////////////////////////////////////////////////////////////
// //
// H5R: HDF5 1.12 Reference API Functions //
// //
// ////////////////////////////////////////////////////////////
// Constructors //
/**
* H5Rcreate_object creates a reference pointing to the object named 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 access_id
* IN: Object access identifier to the object being pointed to.
*
* @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 native byte[] H5Rcreate_object(long loc_id, String name, long access_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Rcreate_region creates the reference, pointing to the region represented by
* space id within the object named 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 space_id
* IN: Identifies the dataset region that a dataset region reference points to.
* @param access_id
* IN: Object access identifier to the object being pointed to.
*
* @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 native byte[] H5Rcreate_region(long loc_id, String name, long space_id, long access_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Rcreate_attr creates the reference, pointing to the attribute named attr name
* and attached to the object named 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 attr_name
* IN: Name of the attribute within the object.
* @param access_id
* IN: Object access identifier to the object being pointed to.
*
* @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 native byte[] H5Rcreate_attr(long loc_id, String name, String attr_name, long access_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Rdestroy destroys a reference and releases resources.
*
* @param ref_ptr
* IN: Reference to an object, region or attribute attached to an object.
*
* @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 H5Rdestroy(byte[] ref_ptr)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
// Info //
/**
* H5Rget_type retrieves the type of a reference.
*
* @param ref_ptr
* IN: Reference to an object, region or attribute attached to an object.
*
* @return a valid reference type if successful; otherwise returns H5R UNKNOWN.
*
* @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 int H5Rget_type(byte[] ref_ptr)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Requal determines whether two references point to the same object, region or attribute.
*
* @param ref1_ptr
* IN: Reference to an object, region or attribute attached to an object.
* @param ref2_ptr
* IN: Reference to an object, region or attribute attached to an object.
*
* @return true if equal, else false
*
* @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 boolean H5Requal(byte[] ref1_ptr, byte[] ref2_ptr)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Rcopy creates a copy of an existing reference.
*
* @param src_ref_ptr
* IN: Reference to an object, region or attribute attached to an object.
*
* @return a valid copy of 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 native byte[] H5Rcopy(byte[] src_ref_ptr)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
// Dereference //
/**
* H5Ropen_object opens that object and returns an identifier.
* The object opened with this function should be closed when it is no longer needed
* so that resource leaks will not develop. Use the appropriate close function such
* as H5Oclose or H5Dclose for datasets.
*
* @param ref_ptr
* IN: Reference to an object, region or attribute attached to an object.
* @param rapl_id
* IN: A reference access property list identifier for the reference. The access property
* list can be used to access external files that the reference points
* to (through a file access property list).
* @param oapl_id
* IN: An object access property list identifier for the reference. The access property
* property list must be of the same type as the object being referenced,
* that is a group or dataset property list.
*
* @return a valid identifier 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 native long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Ropen region creates a copy of the dataspace of the dataset pointed to by a region reference,
* ref ptr, and defines a selection matching the selection pointed to by ref ptr within the dataspace copy.
* Use H5Sclose to release the dataspace identifier returned by this function when the identifier is no longer needed.
*
* @param ref_ptr
* IN: Reference to an object, region or attribute attached to an object.
* @param rapl_id
* IN: A reference access property list identifier for the reference. The access property
* list can be used to access external files that the reference points
* to (through a file access property list).
* @param oapl_id
* IN: An object access property list identifier for the reference. The access property
* property list must be of the same type as the object being referenced,
* that is a group or dataset property list.
*
* @return a valid dataspace identifier 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 native long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Ropen_attr opens the attribute attached to the object and returns an identifier.
* The attribute opened with this function should be closed with H5Aclose when it is no longer needed
* so that resource leaks will not develop.
*
* @param ref_ptr
* IN: Reference to an object, region or attribute attached to an object.
* @param rapl_id
* IN: A reference access property list identifier for the reference. The access property
* list can be used to access external files that the reference points
* to (through a file access property list).
* @param aapl_id
* IN: An attribute access property list identifier for the reference. The access property
* property list must be of the same type as the object being referenced,
* that is a group or dataset property list.
*
* @return a valid attribute identifier 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 native long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
// Get type //
/**
* H5Rget obj type3 retrieves the type of the referenced object pointed to.
*
* @param ref_ptr
* IN: Reference to an object, region or attribute attached to an object.
* @param rapl_id
* IN: A reference access property list identifier for the reference. The access property
* list can be used to access external files that the reference points
* to (through a file access property list).
*
* @return Returns the object type
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - array is null.
* @exception IllegalArgumentException
* - array is invalid.
**/
public synchronized static native int H5Rget_obj_type3(byte[] ref_ptr, long rapl_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
// Get name //
/**
* H5Rget_file_name retrieves the file name for the object, region or attribute reference pointed to.
*
* @param ref_ptr
* IN: Reference to an object, region or attribute attached to an object.
*
* @return Returns the file name of the reference
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - array is null.
* @exception IllegalArgumentException
* - array is invalid.
**/
public synchronized static native String H5Rget_file_name(byte[] ref_ptr)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Rget_obj_name retrieves the object name for the object, region or attribute reference pointed to.
*
* @param ref_ptr
* IN: Reference to an object, region or attribute attached to an object.
* @param rapl_id
* IN: A reference access property list identifier for the reference. The access property
* list can be used to access external files that the reference points
* to (through a file access property list).
*
* @return Returns the object name of the reference
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - array is null.
* @exception IllegalArgumentException
* - array is invalid.
**/
public synchronized static native String H5Rget_obj_name(byte[] ref_ptr, long rapl_id)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* H5Rget_attr_name retrieves the attribute name for the object, region or attribute reference pointed to.
*
* @param ref_ptr
* IN: Reference to an object, region or attribute attached to an object.
*
* @return Returns the attribute name of the reference
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - array is null.
* @exception IllegalArgumentException
* - array is invalid.
**/
public synchronized static native String H5Rget_attr_name(byte[] ref_ptr)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
// ////////////////////////////////////////////////////////////
// //
// H5R: HDF5 1.8 Reference API Functions //
// //
// ////////////////////////////////////////////////////////////
private synchronized static native int H5Rcreate(byte[] ref, long loc_id, String name, int ref_type, long 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(long loc_id, String name, int ref_type, long 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 access_list
* IN: Property list of the object being referenced.
* @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 long H5Rdereference(long dataset, long access_list, int ref_type, byte[] ref)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException {
long id = _H5Rdereference(dataset, access_list, ref_type, ref);
if (id > 0) {
log.trace("OPEN_IDS: H5Rdereference add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Rdereference(long dataset, long access_list, 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(long loc_id, int ref_type, byte[] ref, String[] name, long size)
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
*
* @return Returns the object type
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - array is null.
* @exception IllegalArgumentException
* - array is invalid.
**/
public synchronized static native int H5Rget_obj_type(long loc_id, int ref_type, byte ref[])
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
/**
* 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[])
**/
private synchronized static native int H5Rget_obj_type2(long 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 long H5Rget_region(long loc_id, int ref_type, byte[] ref) throws HDF5LibraryException,
NullPointerException, IllegalArgumentException {
long id = _H5Rget_region(loc_id, ref_type, ref);
if (id > 0) {
log.trace("OPEN_IDS: H5Rget_region add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Rget_region(long loc_id, int ref_type, byte[] ref)
throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
// ////////////////////////////////////////////////////////////
// //
// H5S: Dataspace Interface Functions //
// //
// ////////////////////////////////////////////////////////////
/**************** Operations on dataspaces ********************/
/**
* 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 long H5Screate(int type) throws HDF5LibraryException {
long id = _H5Screate(type);
if (id > 0) {
log.trace("OPEN_IDS: H5Screate add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _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 long H5Screate_simple(int rank, long[] dims, long[] maxdims) throws HDF5Exception,
NullPointerException {
long id = _H5Screate_simple(rank, dims, maxdims);
if (id > 0) {
log.trace("OPEN_IDS: H5Screate_simple add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Screate_simple(int rank, long[] dims, long[] maxdims)
throws HDF5Exception, NullPointerException;
/**
* 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 long H5Sset_extent_simple(long space_id, int rank, long[] current_size,
long[] maximum_size) throws HDF5LibraryException, NullPointerException;
/**
* 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 long H5Sset_extent_simple(long 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);
}
/**
* 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 long H5Scopy(long space_id) throws HDF5LibraryException {
long id = _H5Scopy(space_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Scopy add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException;
/**
* 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(long space_id) throws HDF5LibraryException {
if (space_id < 0)
return 0; // throw new HDF5LibraryException("Negative ID");;
log.trace("OPEN_IDS: H5Sclose remove {}", space_id);
OPEN_IDS.remove(space_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
return _H5Sclose(space_id);
}
private synchronized static native int _H5Sclose(long space_id) throws HDF5LibraryException;
/**
* 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(long obj_id) throws HDF5LibraryException, NullPointerException;
/**
* 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 long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException;
/**
* 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(long space_id) throws HDF5LibraryException;
/**
* 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(long 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(long space_id, long[] dims, long[] maxdims)
throws HDF5LibraryException, NullPointerException;
/**
* 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(long 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(long 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(long space_id) throws HDF5LibraryException;
/**
* 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(long dest_space_id, long 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(long first_space_id, long second_space_id)
throws HDF5LibraryException;
/***************** Operations on dataspace selections *****************/
/**
* 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(long space_id) 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(long space_id) throws HDF5LibraryException;
/**
* H5Sselect_copy copies all the selection information (including offset) from the source
* dataspace to the destination dataspace.
* @param dst_id ID of the destination dataspace
* @param src_id ID of the source dataspace
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Sselect_copy(long dst_id, long src_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(long space_id) throws HDF5LibraryException;
/**
* H5Sselect_adjust moves a selection by subtracting an offset from it.
*
* @param space_id
* ID of dataspace to adjust
* @param offset
* Offset to subtract
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - offset is null.
**/
public synchronized static native void H5Sselect_adjust(long space_id, long[][] offset)
throws HDF5LibraryException, NullPointerException;
/**
* H5Sget_select_bounds retrieves the coordinates of the bounding box containing the current selection and places
* them into user-supplied buffers.
* * The start and end buffers must be large enough to hold the dataspace rank number of coordinates. * * @param space_id * 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(long space_id, long[] start, long[] end) throws HDF5LibraryException, NullPointerException; /** * H5Sselect_shape_same checks to see if the current selection in the dataspaces are the same * dimensionality and shape. * This is primarily used for reading the entire selection in one swoop. * * @param space1_id ID of 1st Dataspace pointer to compare * @param space2_id ID of 2nd Dataspace pointer to compare * * @return true if the selection is the same dimensionality and shape; * false otherwise * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sselect_shape_same(long space1_id, long space2_id) throws HDF5LibraryException; /** * H5Sselect_intersect_block checks to see if the current selection in the * dataspace intersects with the block given. * * @param space_id * ID of dataspace pointer to compare * @param start * Starting coordinate of block * @param end * Opposite ("ending") coordinate of block * * @return a TRUE if the current selection in the dataspace intersects with the block given * FALSE otherwise * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - offset is null. **/ public synchronized static native boolean H5Sselect_intersect_block(long space_id, long[] start, long[] end) throws HDF5LibraryException, NullPointerException; /** * 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(long space_id, byte[] offset) throws HDF5LibraryException, NullPointerException; /** * 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 int H5Soffset_simple(long 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(long space_id) throws HDF5LibraryException; /** * 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(long 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(long 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(long 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; } /** * 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(long 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(long spaceid, long startpoint, long numpoints, long[] buf) 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 IllegalArgumentException * - an input array is invalid. **/ public synchronized static int H5Sselect_hyperslab(long 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); } /** * 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 IllegalArgumentException * - an input array is invalid. **/ public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Scombine_hyperslab combines a hyperslab selection with the current selection for a dataspace, * creating a new dataspace to return the generated selection. * If the current selection is not a hyperslab, it is freed and the hyperslab * parameters passed in are combined with the H5S_SEL_ALL hyperslab (ie. a * selection composing the entire current extent). If STRIDE or BLOCK is * NULL, they are assumed to be set to all '1'. * * @param space_id * IN: Dataspace ID of selection to use * @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 dataspace ID on success / H5I_INVALID_HID on failure * * @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 long H5Scombine_hyperslab(long space_id, int op, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Smodify_select refine an existing hyperslab selection with an operation, using a second * hyperslab. The first selection is modified to contain the result of * space1 operated on by space2. * * @param space1_id * ID of the destination dataspace * @param op * Operation to perform on current selection. * @param space2_id * ID of the source dataspace * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Smodify_select(long space1_id, int op, long space2_id) throws HDF5LibraryException; /** * H5Scombine_select combines two existing hyperslab selections with an operation, returning * a new dataspace with the resulting selection. The dataspace extent from * space1 is copied for the dataspace extent of the newly created dataspace. * * @param space1_id * ID of the first dataspace * @param op * Operation to perform on current selection. * @param space2_id * ID of the second dataspace * * @return a dataspace ID on success / H5I_INVALID_HID on failure * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Scombine_select(long space1_id, int op, long space2_id) throws HDF5LibraryException; /** * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified * by space_id. * * @param space_id * IN: Identifier of dataspace selection to query * * @return a TRUE/FALSE for hyperslab selection if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException; /** * H5Sget_regular_hyperslab determines if a hyperslab selection is regular 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 start * OUT: Offset of start of hyperslab * @param stride * OUT: Hyperslab stride. * @param count * OUT: Number of blocks included in hyperslab. * @param block * OUT: Size of block in hyperslab. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an output array is null. * @exception IllegalArgumentException * - an output array is invalid. **/ public synchronized static native void H5Sget_regular_hyperslab(long space_id, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * 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(long spaceid) throws HDF5LibraryException; /** * 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: * *
* <"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(long spaceid, long startblock, long numblocks,
long[] buf) throws HDF5LibraryException, NullPointerException;
/**
* H5Sselect_project_intersection projects the intersection of the selections of src_space_id and
* src_intersect_space_id within the selection of src_space_id as a
* selection within the selection of dst_space_id.
*
* @param src_space_id
* Selection that is mapped to dst_space_id, and intersected with src_intersect_space_id
* @param dst_space_id
* Selection that is mapped to src_space_id
* @param src_intersect_space_id
* Selection whose intersection with src_space_id is projected to dst_space_id to obtain the result
*
* @return a dataspace with a selection equal to the intersection of
* src_intersect_space_id and src_space_id projected from src_space to dst_space on success
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native long H5Sselect_project_intersection(long src_space_id, long dst_space_id,
long src_intersect_space_id) throws HDF5LibraryException;
// /////// unimplemented ////////
///// Operations on dataspace selections /////
//
///// Operations on dataspace selection iterators /////
//public synchronized static native H5Ssel_iter_create(hid_t spaceid, size_t elmt_size, unsigned flags);
//public synchronized static native H5Ssel_iter_get_seq_list(hid_t sel_iter_id, size_t maxseq, size_t maxbytes, size_t *nseq,
// size_t *nbytes, hsize_t *off, size_t *len);
//public synchronized static native H5Ssel_iter_reset(hid_t sel_iter_id, hid_t space_id);
//public synchronized static native H5Ssel_iter_close(hid_t sel_iter_id);
// ////////////////////////////////////////////////////////////
// //
// H5T: Datatype Interface Functions //
// //
// ////////////////////////////////////////////////////////////
/**
* 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 long H5Tarray_create(long base_id, int ndims, long[] dim) throws HDF5LibraryException,
NullPointerException {
long id = _H5Tarray_create2(base_id, ndims, dim);
if (id > 0) {
log.trace("OPEN_IDS: H5Tarray_create add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Tarray_create2(long 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(long type_id) throws HDF5LibraryException {
if (type_id < 0)
return 0; // throw new HDF5LibraryException("Negative ID");;
log.trace("OPEN_IDS: H5Tclose remove {}", type_id);
OPEN_IDS.remove(type_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
return _H5Tclose(type_id);
}
private synchronized static native int _H5Tclose(long type_id) throws HDF5LibraryException;
/**
* 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native void H5Tcommit(long loc_id, String name, long type_id, long lcpl_id,
long tcpl_id, long 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tcommit_anon(long loc_id, long type_id, long tcpl_id, long 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(long type_id) 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tcompiler_conv(long src_id, long 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - buf is null.
**/
public synchronized static native void H5Tconvert(long src_id, long dst_id, long nelmts, byte[] buf,
byte[] background, long 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 long H5Tcopy(long type_id) throws HDF5LibraryException {
long id = _H5Tcopy(type_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Tcopy add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Tcopy(long type_id) throws HDF5LibraryException;
/**
* H5Tcreate creates a new dataype of the specified class with the specified number of bytes.
*
* @param tclass
* 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 long H5Tcreate(int tclass, long size) throws HDF5LibraryException {
long id = _H5Tcreate(tclass, size);
if (id > 0) {
log.trace("OPEN_IDS: H5Tcreate add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _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 static long H5Tdecode(byte[] buf) throws HDF5LibraryException, NullPointerException {
long id = _H5Tdecode(buf);
if (id > 0) {
log.trace("OPEN_IDS: H5Tdecode add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _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(long 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(long 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 long H5Tenum_create(long base_id) throws HDF5LibraryException {
long id = _H5Tenum_create(base_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Tenum_create add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Tenum_create(long 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
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - name is null.
**/
public synchronized static native void H5Tenum_insert(long 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(long type, String name, int[] value) throws HDF5LibraryException,
NullPointerException {
return H5Tenum_insert_int(type, name, value);
}
/**
* 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(long 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(long 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(long 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(long 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(long 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
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tenum_valueof(long 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(long type, String name, int[] value) throws HDF5LibraryException,
NullPointerException {
return H5Tenum_valueof_int(type, name, value);
}
private synchronized static native int H5Tenum_valueof_int(long 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(long type_id1, long type_id2) throws HDF5LibraryException;
/**
* 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(long 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.
*
* @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 synchronized static native int H5Tget_array_dims2(long 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(long 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(long 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(long 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 static long H5Tget_create_plist(long type_id) throws HDF5LibraryException {
long id = _H5Tget_create_plist(type_id);
if (id > 0) {
log.trace("OPEN_IDS: _H5Tget_create_plist add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Tget_create_plist(long 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(long 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(long 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(long 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(long 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(long 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tset_ebias(long 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.
*
* 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(long type_id, int[] fields) throws HDF5LibraryException, NullPointerException,
IllegalArgumentException {
return H5Tget_fields_int(type_id, fields);
}
private synchronized static native int H5Tget_fields_int(long 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tset_fields(long 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(long 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(long 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(long type_id, int inpad) throws HDF5LibraryException;
/**
* H5Tget_member_class returns the class of datatype of the specified member.
*
* @param type_id
* IN: Datatype identifier of compound object.
* @param membno
* IN: Compound object member number.
*
* @return the class of the datatype of the field if successful;
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tget_member_class(long 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.
**/
public synchronized static native int H5Tget_member_index(long 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.
**/
public synchronized static native String H5Tget_member_name(long 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(long 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 long H5Tget_member_type(long type_id, int field_idx) throws HDF5LibraryException {
long id = _H5Tget_member_type(type_id, field_idx);
if (id > 0) {
log.trace("OPEN_IDS: H5Tget_member_type add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Tget_member_type(long 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
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
* @exception NullPointerException
* - value is null.
**/
public synchronized static native void H5Tget_member_value(long 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(long 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(long 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 long H5Tget_native_type(long type_id) throws HDF5LibraryException {
return H5Tget_native_type(type_id, 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 long H5Tget_native_type(long type_id, int direction) throws HDF5LibraryException {
long id = _H5Tget_native_type(type_id, direction);
if (id > 0) {
log.trace("OPEN_IDS: H5Tget_native_type add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Tget_native_type(long 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(long 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(long 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(long 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(long 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(long 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tset_offset(long 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(long 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(long 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(long 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(long 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(long 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(long 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(long 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.
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native void H5Tset_precision(long 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(long 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(long type_id, int sign) throws HDF5LibraryException;
/**
* 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 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 a non-negative value if successful
*
* @exception HDF5LibraryException
* - Error from the HDF-5 Library.
**/
public synchronized static native int H5Tset_size(long 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(long 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(long 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 long H5Tget_super(long type) throws HDF5LibraryException {
long id = _H5Tget_super(type);
if (id > 0) {
log.trace("OPEN_IDS: H5Tget_super add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Tget_super(long 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(long 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(long 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(long type_id, String name, long offset, long 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(long 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(long type_id) throws HDF5LibraryException;
/**
* 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 long H5Topen(long loc_id, String name, long tapl_id) throws HDF5LibraryException,
NullPointerException {
long id = _H5Topen2(loc_id, name, tapl_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Topen add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return id;
}
private synchronized static native long _H5Topen2(long loc_id, String name, long 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.
* * 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(long type_id) throws HDF5LibraryException; /** * H5Treclaim reclaims buffer used for VL data. * * @param type_id * Identifier of the datatype. * @param space_id * Identifier of the dataspace. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param buf * Buffer with data to be reclaimed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native void H5Treclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf) 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 long H5Tvlen_create(long base_id) throws HDF5LibraryException { long id = _H5Tvlen_create(base_id); if (id > 0) { log.trace("OPEN_IDS: H5Tvlen_create add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tvlen_create(long base_id) throws HDF5LibraryException; /** * H5Tflush causes all buffers associated with a committed datatype to be immediately flushed to disk * without removing the data from the cache. * * @param dtype_id * IN: Identifier of the committed datatype to be flushed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Tflush(long dtype_id) throws HDF5LibraryException; /** * H5Trefresh causes all buffers associated with a committed datatype to be cleared and immediately * re-loaded with updated contents from disk. This function essentially closes the datatype, evicts * all metadata associated with it from the cache, and then re-opens the datatype. The reopened datatype * is automatically re-registered with the same ID. * * @param dtype_id * IN: Identifier of the committed datatype to be refreshed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Trefresh(long dtype_id) throws HDF5LibraryException; // /////// unimplemented //////// // H5T_conv_t H5Tfind(int src_id, int dst_id, H5T_cdata_t *pcdata); // 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; // //////////////////////////////////////////////////////////// // // // H5VL: VOL Interface Functions // // // // //////////////////////////////////////////////////////////// /// VOL Connector Functionality /** * H5VLregister_connector_by_name registers a new VOL connector as a member of the virtual object layer class. * * @param connector_name * IN: name of the connector. * @param vipl_id * IN: VOL initialization property list which must be * created with H5Pcreate(H5P_VOL_INITIALIZE) (or H5P_DEFAULT). * * @return a VOL connector ID * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id); /** * H5VLregister_connector_by_value registers a new VOL connector as a member of the virtual object layer class. * * @param connector_value * IN: value of the connector. * @param vipl_id * IN: VOL initialization property list which must be * created with H5Pcreate(H5P_VOL_INITIALIZE) (or H5P_DEFAULT). * * @return a VOL connector ID * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id); /** * H5VLis_connector_registered_by_name tests whether a VOL class has been registered. * * @param name * IN: name of the connector. * * @return true if a VOL connector with that name has been registered * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5VLis_connector_registered_by_name(String name); /** * H5VLis_connector_registered_by_value tests whether a VOL class has been registered. * * @param connector_value * IN: value of the connector. * * @return true if a VOL connector with that value has been registered * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5VLis_connector_registered_by_value(int connector_value); /** * H5VLget_connector_id retrieves the ID for a registered VOL connector for a given object. * * @param object_id * IN: Identifier of the object. * * @return a VOL connector ID * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5VLget_connector_id(long object_id); /** * H5VLget_connector_id_by_name retrieves the ID for a registered VOL connector. * * @param name * IN: name of the connector. * * @return a VOL connector ID * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5VLget_connector_id_by_name(String name); /** * H5VLget_connector_id_by_value retrieves the ID for a registered VOL connector. * * @param connector_value * IN: value of the connector. * * @return a VOL connector ID * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5VLget_connector_id_by_value(int connector_value); /** * H5VLget_connector_name returns the connector name for the VOL associated with the * object or file ID. * * @param object_id * IN: Identifier of the object. * * @return the connector name * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5VLget_connector_name(long object_id); /** * H5VLclose closes a VOL connector ID. * * @param connector_id * IN: Identifier of the connector. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5VLclose(long connector_id); /** * H5VLunregister_connector removes a VOL connector ID from the library. * * @param connector_id * IN: Identifier of the connector. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5VLunregister_connector(long connector_id); // /////// unimplemented //////// // hid_t H5VLregister_connector(const H5VL_class_t *cls, hid_t vipl_id); // //////////////////////////////////////////////////////////// // // // H5Z: Filter Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Zfilter_avail checks if a filter is available. * * @param filter * IN: filter number. * * @return a non-negative(TRUE/FALSE) value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Zfilter_avail(int filter) throws HDF5LibraryException; /** * H5Zget_filter_info gets information about a pipeline data filter. * * @param filter * IN: filter number. * * @return the filter information flags * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Zget_filter_info(int filter) throws HDF5LibraryException; /** * H5Zunregister unregisters a filter. * * @param filter * IN: filter number. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException; // /////// unimplemented //////// // herr_t H5Zregister(const void *cls); }