* 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 @ref RM *
* Mapping of arguments for Java * *
* In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in * the @ref RM. * *
| HDF5 | *Java | *
| @ref H5T_NATIVE_INT | *int, Integer | *
| @ref H5T_NATIVE_SHORT | *short, Short | *
| @ref H5T_NATIVE_FLOAT | *float, Float | *
| @ref H5T_NATIVE_DOUBLE | *double, Double | *
| @ref H5T_NATIVE_CHAR | *byte, Byte | *
| @ref H5T_C_S1 | *java.lang.String | *
| void * * (i.e., pointer to Any) |
* Special -- see @ref 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 Java functions will raise an exception upon failure in the Java version, * rather than just return int as in the C. Functions that return a value are declared * equivalent to the C function. * However, in most cases the Java method will raise an exception instead of returning an error code. * @see @ref ERRORS. *
* Java does not support pass by reference of arguments, so arguments that are returned through OUT * parameters must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in * arrays. Where possible the Java function may return the OUT parameter as an object or basic type. *
* For instance, a function that returns two integers declared as: * *
* h_err_t HDF5dummy( int *a1, int *a2) ** * For the Java interface, this would be declared: * *
* public static int HDF5dummy(int args[]); ** OR *
* public static int[] HDF5dummy(); ** * where a1 is args[0] and a2 is args[1], and would be invoked: * *
* H5.HDF5dummy(a); ** OR *
* a = H5.HDF5dummy(); ** *
* All the routines where this convention is used will have specific documentation of the details, given * below. *
* @ref HDFARRAY *
* 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, * * @code * herr_t H5Dread(long fid, long filetype, long memtype, long memspace, void *data); * @endcode * *
* where "void *" means that the data may be any valid numeric type, and is a contiguous block of bytes that * is the data for a multi-dimensional array. The other parameters describe the dimensions, rank, and datatype * of the array ondisk (source) and in memory (destination). *
* For Java, this "ANY" is a problem, as the type of data must always be declared. Furthermore, * multidimensional arrays are definitely not laid out contiguously in memory. It would be infeasible * to declare a separate routine for every combination of number type and dimensionality. For that reason, the * @ref HDFARRAY 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 * static 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: * * @code * public 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 {} * @endcode * * and the parameter data can be any multi-dimensional array of numbers, such as float[][], or * int[][][], or Double[][]. *
* @ref HDF5CONST *
* The HDF5 API defines a set of constants and enumerated values. Most of these values are available to Java * programs via the class @ref HDF5CONST HDF5Constants. For example, * the parameters for the h5open() call include two numeric values, HDFConstants.H5F_ACC_RDWR * and HDF5Constants.H5P_DEFAULT. * As would be expected, these numbers correspond to the C constants * #H5F_ACC_RDWR and #H5P_DEFAULT. *
* The HDF5 API defines a set of values that describe number types and sizes, such as "H5T_NATIVE_INT" and * "hsize_t". These values are determined at run time by the HDF5 C library. To support these parameters, * the Java HDFConstants class looks up the values * when initiated. The values can be accessed as public variables of the Java class, such as: * * @code * long data_type = HDFConstants.H5T_NATIVE_INT; * @endcode * * The Java application uses both types of constants the same way, the only difference is that the * HDFConstants may have different values on different platforms. *
* @ref ERRORS *
* The HDF5 error API (@ref H5E) manages the behavior of the error stack in the HDF5 library. This API is * omitted from the JHI5. Errors are converted into Java exceptions. This is totally different from the C * interface, but is very natural for Java programming.
The exceptions of the JHI5 are organized as * sub-classes of the class * @ref ERRORS HDF5Exception. There are two subclasses of * HDF5Exception, @ref ERRORSLIB HDF5LibraryException * and @ref ERRORSJAVA HDF5JavaException. The * sub-classes of the former represent errors from the HDF5 C library, while sub-classes of the latter * represent errors in the JHI5 wrapper and support code. *
* The super-class HDF5LibraryException implements the method 'printStackTrace()', * which prints out the HDF5 error stack, as described in the HDF5 C API @ref H5Eprint(). This * may be used by Java exception handlers to print out the HDF5 error stack.
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 HDF5 Library. **/ private static int H5dont_atexit() throws HDF5LibraryException { int retVal = -1; if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5dont_atexit()) < 0) h5libraryError(); return retVal; } /** * @ingroup JH5 * * Turn off error handling. By default, the C library prints the error stack of the HDF5 C library on * stdout. This behavior may be disabled by calling H5error_off(). * * @return a non-negative value if successful */ public static int H5error_off() { // TODO: Implement error handling callbacks // if (org.hdfgroup.javahdf5.hdf5_h.H5Eget_auto2(H5E_DEFAULT(), errorFunc, errorData) < 0) // return -1; // // if (org.hdfgroup.javahdf5.hdf5_h.H5Eset_auto2(H5E_DEFAULT(), MemorySegment.NULL, // MemorySegment.NULL) < 0) // return -1; return 0; } /** * @ingroup JH5 * * Turn on error handling. By default, the C library prints the error stack of the HDF5 C library on * stdout. This behavior may be re-enabled by calling H5error_on(). */ public static void H5error_on() { org.hdfgroup.javahdf5.hdf5_h.H5Eset_auto2(H5E_DEFAULT(), errorFunc, errorData); } /** * @ingroup JH5 * * H5garbage_collect collects on all free-lists of all types. * * @return a non-negative value if successful * * @exception HDF5LibraryException * Error from the HDF5 Library. **/ public static int H5garbage_collect() throws HDF5LibraryException { int retVal = -1; if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5garbage_collect()) < 0) h5libraryError(); return retVal; } /** * @ingroup JH5 * * 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 HDF5 Library.
* @exception NullPointerException
* If the libversion array is null or has less than 3 elements.
**/
public static int H5get_libversion(int[] libversion) throws HDF5LibraryException, NullPointerException
{
if (libversion == null || libversion.length < 3) {
throw new NullPointerException("libversion array must be non-null and have at least 3 elements");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the array bytes
MemorySegment majnum_segment = arena.allocateFrom(ValueLayout.JAVA_INT, libversion[0]);
MemorySegment minnum_segment = arena.allocateFrom(ValueLayout.JAVA_INT, libversion[1]);
MemorySegment relnum_segment = arena.allocateFrom(ValueLayout.JAVA_INT, libversion[2]);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5get_libversion(majnum_segment, minnum_segment,
relnum_segment)) < 0)
h5libraryError();
// Set the version numbers
libversion[0] = majnum_segment.get(ValueLayout.JAVA_INT, 0);
libversion[1] = minnum_segment.get(ValueLayout.JAVA_INT, 0);
libversion[2] = relnum_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5
*
* 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 HDF5 Library.
*/
public static 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
{
int retVal = -1;
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5set_free_list_limits(reg_global_lim, reg_list_lim,
arr_global_lim, arr_list_lim,
blk_global_lim, blk_list_lim)) < 0)
h5libraryError();
return retVal;
}
/**
* @ingroup JH5
*
* 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_id
* The identifier 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 HDF5 Library.
**/
public static void H5export_dataset(String file_export_name, long file_id, String object_path,
int binary_order) throws HDF5LibraryException
{
throw new HDF5LibraryException("H5export_dataset not implemented yet");
}
/**
* @ingroup JH5
*
* H5export_attribute is a utility function to save data in a file.
*
* @param file_export_name
* The file name to export data into.
* @param dataset_id
* The identifier of the dataset containing the attribute.
* @param attribute_name
* The attribute 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 HDF5 Library.
**/
public static void H5export_attribute(String file_export_name, long dataset_id, String attribute_name,
int binary_order) throws HDF5LibraryException
{
throw new HDF5LibraryException("H5export_attribute not implemented yet");
}
/**
* @ingroup JH5
*
* H5is_library_threadsafe Checks to see if the library was built with thread-safety enabled.
*
* @return true if hdf5 library implements threadsafe
*
**/
private static boolean H5is_library_threadsafe()
{
boolean is_ts = false;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the boolean value
MemorySegment is_ts_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN);
// Call the native function to check if the library is thread-safe
if (org.hdfgroup.javahdf5.hdf5_h.H5is_library_threadsafe(is_ts_segment) < 0)
h5libraryError();
// Read the boolean value from the segment
is_ts = is_ts_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
}
return is_ts;
}
/**
* Helper method to copy a Java String into a fixed-size char array in a MemorySegment.
* The string is null-terminated and truncated if it exceeds maxLen-1 characters.
*
* @param arena
* Arena for temporary allocations
* @param str
* Java String to copy (null is treated as empty string)
* @param dest
* Destination MemorySegment (fixed-size char array)
* @param maxLen
* Maximum length of the char array (including null terminator)
*/
private static void copyStringToCharArray(Arena arena, String str, MemorySegment dest, int maxLen)
{
// Handle null or empty strings
if (str == null || str.isEmpty()) {
// Write null terminator at position 0
dest.set(ValueLayout.JAVA_BYTE, 0, (byte)0);
return;
}
// Convert string to null-terminated C string
MemorySegment srcSegment = arena.allocateFrom(str, StandardCharsets.UTF_8);
long srcLen = srcSegment.byteSize();
// Calculate copy length (leave room for null terminator)
long copyLen = Math.min(srcLen, maxLen - 1);
// Copy string bytes
MemorySegment.copy(srcSegment, 0, dest, 0, copyLen);
// Ensure null terminator
if (copyLen < maxLen) {
dest.set(ValueLayout.JAVA_BYTE, copyLen, (byte)0);
}
}
/**
* Helper method to extract a Java String from a fixed-size null-terminated char array in a
* MemorySegment.
*
* @param charArray
* Source MemorySegment containing null-terminated char array
* @return Java String extracted from the char array
*/
private static String extractStringFromCharArray(MemorySegment charArray)
{
// Find null terminator
long length = 0;
long maxLen = charArray.byteSize();
while (length < maxLen && charArray.get(ValueLayout.JAVA_BYTE, length) != 0) {
length++;
}
if (length == 0) {
return "";
}
// Extract bytes up to null terminator
byte[] bytes = new byte[(int)length];
MemorySegment.copy(charArray, ValueLayout.JAVA_BYTE, 0, bytes, 0, (int)length);
// Convert to Java String
return new String(bytes, StandardCharsets.UTF_8);
}
// /////// unimplemented ////////
// herr_t H5free_memory(void *mem);
// SEE int org.hdfgroup.javahdf5.hdf5_h.H5free_memory(MemorySegment mem)
// void *H5allocate_memory(size_t size, hbool_t clear);
// SEE MemorySegment org.hdfgroup.javahdf5.hdf5_h.H5allocate_memory(long size, boolean clear)
// void *H5resize_memory(void *mem, size_t size);
// SEE MemorySegment org.hdfgroup.javahdf5.hdf5_h.H5resize_memory(MemorySegment mem, long size)
// ////////////////////////////////////////////////////////////
// //
// H5A: HDF5 Attribute Interface API Functions //
// //
// ////////////////////////////////////////////////////////////
/**
* @defgroup JH5A Java Attribute (H5A) Interface
*
* An HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary
*data object. A primary data object may be a dataset, group, or committed datatype.
*
* @see H5A, C-API
*
* @see @ref H5A_UG, User Guide
**/
/**
* @ingroup JH5A
*
* 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
**/
public static int H5Aclose(long attr_id)
{
log.trace("OPEN_IDS: H5Aclose remove {}", attr_id);
OPEN_IDS.remove(attr_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Aclose(attr_id);
return retVal;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
*/
public static int H5Acopy(long src_aid, long dst_aid) throws HDF5LibraryException
{
int retVal = -1;
if (src_aid < 0 || dst_aid < 0) {
throw new HDF5FunctionArgumentException("Source or destination attribute ID is negative");
}
throw new HDF5LibraryException("H5Acopy not implemented yet");
// This is a stub implementation, as the actual implementation is not provided in the original code.
// int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Acopy(src_aid, dst_aid);
// if (retVal < 0) {
// h5libraryError();
//}
// return retVal;
}
/**
* @ingroup JH5A
*
* 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 HDF5 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
{
if (attr_name == null)
throw new NullPointerException("attr_name cannot be null");
long attr_id = H5I_INVALID_HID();
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment name_segment = arena.allocateFrom(attr_name);
if ((attr_id = H5Acreate2(loc_id, name_segment, type_id, space_id, acpl_id, aapl_id)) < 0) {
h5libraryError();
}
}
if (attr_id > 0) {
log.trace("OPEN_IDS: H5A create add {}", attr_id);
OPEN_IDS.add(attr_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return attr_id;
}
/**
* @ingroup JH5A
*
* 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 HDF5 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
{
if (attr_name == null)
throw new NullPointerException("attr_name cannot be null");
if (obj_name == null)
throw new NullPointerException("obj_name cannot be null");
long attr_id = H5I_INVALID_HID();
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment obj_name_segment = arena.allocateFrom(obj_name);
MemorySegment attr_name_segment = arena.allocateFrom(attr_name);
attr_id = org.hdfgroup.javahdf5.hdf5_h.H5Acreate_by_name(
loc_id, obj_name_segment, attr_name_segment, type_id, space_id, acpl_id, aapl_id, lapl_id);
}
if (attr_id > 0) {
log.trace("OPEN_IDS: H5Acreate_by_name add {}", attr_id);
OPEN_IDS.add(attr_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return attr_id;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static int H5Adelete(long loc_id, String name) throws HDF5LibraryException, NullPointerException
{
if (name == null) {
throw new NullPointerException("Attribute name cannot be null");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment name_segment = arena.allocateFrom(name);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Adelete(loc_id, name_segment);
}
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* obj_name is null.
**/
public static void H5Adelete_by_idx(long loc_id, String obj_name, int idx_type, int order, long n,
long lapl_id) throws HDF5LibraryException, NullPointerException
{
if (obj_name == null) {
throw new NullPointerException("Object name cannot be null");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment obj_name_segment = arena.allocateFrom(obj_name);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Adelete_by_idx(loc_id, obj_name_segment, idx_type, order,
n, lapl_id);
}
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static int H5Adelete_by_name(long loc_id, String obj_name, String attr_name, long lapl_id)
throws HDF5LibraryException, NullPointerException
{
if (obj_name == null || attr_name == null) {
throw new NullPointerException("Object name or attribute name cannot be null");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate MemorySegments to hold the string bytes
MemorySegment obj_name_segment = arena.allocateFrom(obj_name);
MemorySegment attr_name_segment = arena.allocateFrom(attr_name);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Adelete_by_name(loc_id, obj_name_segment,
attr_name_segment, lapl_id);
}
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* attr_name is null.
**/
public static boolean H5Aexists(long obj_id, String attr_name)
throws HDF5LibraryException, NullPointerException
{
if (attr_name == null) {
throw new NullPointerException("Attribute name cannot be null");
}
boolean exists = false;
try (Arena arena = Arena.ofConfined()) {
int retVal = -1;
// Allocate a MemorySegment to hold the string bytes
MemorySegment attr_name_segment = arena.allocateFrom(attr_name);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Aexists(obj_id, attr_name_segment)) < 0)
h5libraryError();
if (retVal > 0)
exists = true;
else
exists = false;
}
return exists;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static boolean H5Aexists_by_name(long loc_id, String obj_name, String attr_name, long lapl_id)
throws HDF5LibraryException, NullPointerException
{
int retVal = -1;
if (obj_name == null || attr_name == null) {
throw new NullPointerException("Object name or attribute name cannot be null");
}
boolean exists = false;
try (Arena arena = Arena.ofConfined()) {
// Allocate MemorySegments to hold the string bytes
MemorySegment obj_name_segment = arena.allocateFrom(obj_name);
MemorySegment attr_name_segment = arena.allocateFrom(attr_name);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Aexists_by_name(loc_id, obj_name_segment,
attr_name_segment, lapl_id);
}
if (retVal < 0) {
h5libraryError();
}
else if (retVal > 0) {
exists = true;
}
else {
exists = false;
}
return exists;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
**/
public static hdf.hdf5lib.structs.H5A_info_t H5Aget_info(long attr_id) throws HDF5LibraryException
{
hdf.hdf5lib.structs.H5A_info_t info = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ainfo_segment = arena.allocate(org.hdfgroup.javahdf5.H5A_info_t.sizeof());
if (org.hdfgroup.javahdf5.hdf5_h.H5Aget_info(attr_id, ainfo_segment) < 0)
h5libraryError();
// Unpack the H5A_info_t from the MemorySegment
info = new hdf.hdf5lib.structs.H5A_info_t(
org.hdfgroup.javahdf5.H5A_info_t.corder_valid(ainfo_segment),
org.hdfgroup.javahdf5.H5A_info_t.corder(ainfo_segment),
org.hdfgroup.javahdf5.H5A_info_t.cset(ainfo_segment),
org.hdfgroup.javahdf5.H5A_info_t.data_size(ainfo_segment));
}
return info;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* obj_name is null.
**/
public static hdf.hdf5lib.structs.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
{
if (obj_name == null) {
throw new NullPointerException("Object name cannot be null");
}
hdf.hdf5lib.structs.H5A_info_t info = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ainfo_segment = arena.allocate(org.hdfgroup.javahdf5.H5A_info_t.sizeof());
// Allocate MemorySegments to hold the string bytes
MemorySegment obj_name_segment = arena.allocateFrom(obj_name);
if (org.hdfgroup.javahdf5.hdf5_h.H5Aget_info_by_idx(loc_id, obj_name_segment, idx_type, order, n,
ainfo_segment, lapl_id) < 0)
h5libraryError();
// Unpack the H5A_info_t from the MemorySegment
info = new hdf.hdf5lib.structs.H5A_info_t(
org.hdfgroup.javahdf5.H5A_info_t.corder_valid(ainfo_segment),
org.hdfgroup.javahdf5.H5A_info_t.corder(ainfo_segment),
org.hdfgroup.javahdf5.H5A_info_t.cset(ainfo_segment),
org.hdfgroup.javahdf5.H5A_info_t.data_size(ainfo_segment));
}
return info;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* obj_name is null.
**/
public static hdf.hdf5lib.structs.H5A_info_t H5Aget_info_by_name(long loc_id, String obj_name,
String attr_name, long lapl_id)
throws HDF5LibraryException, NullPointerException
{
if (obj_name == null || attr_name == null) {
throw new NullPointerException("Object name or attribute name cannot be null");
}
hdf.hdf5lib.structs.H5A_info_t info = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ainfo_segment = arena.allocate(org.hdfgroup.javahdf5.H5A_info_t.sizeof());
// Allocate MemorySegments to hold the string bytes
MemorySegment obj_name_segment = arena.allocateFrom(obj_name);
MemorySegment attr_name_segment = arena.allocateFrom(attr_name);
if (org.hdfgroup.javahdf5.hdf5_h.H5Aget_info_by_name(loc_id, obj_name_segment, attr_name_segment,
ainfo_segment, lapl_id) < 0)
h5libraryError();
// Unpack the H5A_info_t from the MemorySegment
info = new hdf.hdf5lib.structs.H5A_info_t(
org.hdfgroup.javahdf5.H5A_info_t.corder_valid(ainfo_segment),
org.hdfgroup.javahdf5.H5A_info_t.corder(ainfo_segment),
org.hdfgroup.javahdf5.H5A_info_t.cset(ainfo_segment),
org.hdfgroup.javahdf5.H5A_info_t.data_size(ainfo_segment));
}
return info;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
**/
public static String H5Aget_name(long attr_id) throws HDF5LibraryException
{
long buf_size = -1;
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Aget_name(attr_id, 0, MemorySegment.NULL)) < 0)
h5libraryError();
String ret_name = null;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment name_segment = arena.allocate(buf_size + 1);
/* Get the attribute name */
if (org.hdfgroup.javahdf5.hdf5_h.H5Aget_name(attr_id, buf_size + 1, name_segment) < 0)
h5libraryError();
ret_name = name_segment.getString(0, StandardCharsets.UTF_8);
}
return ret_name;
}
/**
* @ingroup JH5A
*
* 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 static String H5Aget_name_by_idx(long attr_id, String obj_name, int idx_type, int order, long n,
long lapl_id) throws HDF5LibraryException, NullPointerException
{
long status_size = -1;
if (obj_name == null) {
throw new NullPointerException("Object name cannot be null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment obj_name_segment = arena.allocateFrom(obj_name);
if ((status_size = org.hdfgroup.javahdf5.hdf5_h.H5Aget_name_by_idx(
attr_id, obj_name_segment, idx_type, order, n, MemorySegment.NULL, 0, lapl_id)) < 0)
h5libraryError();
}
String ret_name = null;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment obj_name_segment = arena.allocateFrom(obj_name);
// Allocate a MemorySegment to hold the string bytes
MemorySegment name_segment = arena.allocate(status_size + 1);
/* Get the attribute name */
if (org.hdfgroup.javahdf5.hdf5_h.H5Aget_name_by_idx(attr_id, obj_name_segment, idx_type, order, n,
name_segment, status_size + 1, lapl_id) < 0)
h5libraryError();
ret_name = name_segment.getString(0, StandardCharsets.UTF_8);
}
return ret_name;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
**/
public static long H5Aget_space(long attr_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
**/
public static long H5Aget_storage_size(long attr_id) throws HDF5LibraryException
{
long size = org.hdfgroup.javahdf5.hdf5_h.H5Aget_storage_size(attr_id);
if (size == 0) {
h5libraryError();
}
return size;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
**/
public static long H5Aget_type(long attr_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* Name is null.
**/
public static long H5Aopen(long obj_id, String attr_name, long aapl_id)
throws HDF5LibraryException, NullPointerException
{
long id = H5I_INVALID_HID();
if (attr_name == null) {
throw new NullPointerException("Attribute name cannot be null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment name_segment = arena.allocateFrom(attr_name);
id = org.hdfgroup.javahdf5.hdf5_h.H5Aopen(obj_id, name_segment, aapl_id);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Aopen add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5A
*
* 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 HDF5 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 = H5I_INVALID_HID();
if (obj_name == null) {
throw new NullPointerException("Object name cannot be null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment name_segment = arena.allocateFrom(obj_name);
id = org.hdfgroup.javahdf5.hdf5_h.H5Aopen_by_idx(loc_id, name_segment, 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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5A
*
* 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 HDF5 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 = H5I_INVALID_HID();
if (obj_name == null || attr_name == null) {
throw new NullPointerException("Object name or attribute name cannot be null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment obj_name_segment = arena.allocateFrom(obj_name);
MemorySegment attr_name_segment = arena.allocateFrom(attr_name);
id = org.hdfgroup.javahdf5.hdf5_h.H5Aopen_by_name(loc_id, obj_name_segment, attr_name_segment,
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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static int H5Aread(long attr_id, long mem_type_id, byte[] obj, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (obj == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the byte array
MemorySegment obj_segment = arena.allocate(ValueLayout.JAVA_BYTE, obj.length);
if (isCriticalPinning) {
obj_segment.copyFrom(MemorySegment.ofArray(obj));
}
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Aread(attr_id, mem_type_id, obj_segment)) < 0)
h5libraryError();
MemorySegment.copy(obj_segment, ValueLayout.JAVA_BYTE, 0L, obj, 0, obj.length);
}
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static int H5Aread(long attr_id, long mem_type_id, byte[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Aread(attr_id, mem_type_id, buf, true);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null. See public static int H5Aread( )
**/
public 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("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(attr_id, mem_type_id, (String[])obj);
}
else if (is1D && (dataClass.getComponentType() == String.class)) {
log.trace("H5Aread_string type");
status = H5Aread(attr_id, mem_type_id, (String[])obj);
}
else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
log.trace("H5AreadVL type - using H5AreadVL directly");
status = H5AreadVL(attr_id, mem_type_id, (Object[])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;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static int H5Aread_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the double array
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_DOUBLE, buf.length);
if (isCriticalPinning) {
buf_segment.copyFrom(MemorySegment.ofArray(buf));
}
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Aread(attr_id, mem_type_id, buf_segment)) < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_DOUBLE, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static int H5Aread_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the float array
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_FLOAT, buf.length);
if (isCriticalPinning) {
buf_segment.copyFrom(MemorySegment.ofArray(buf));
}
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Aread(attr_id, mem_type_id, buf_segment)) < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_FLOAT, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static int H5Aread_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the int array
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_INT, buf.length);
if (isCriticalPinning) {
buf_segment.copyFrom(MemorySegment.ofArray(buf));
}
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Aread(attr_id, mem_type_id, buf_segment)) < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_INT, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static int H5Aread_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the long array
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_LONG, buf.length);
if (isCriticalPinning) {
buf_segment.copyFrom(MemorySegment.ofArray(buf));
}
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Aread(attr_id, mem_type_id, buf_segment)) < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_LONG, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static int H5Aread_reg_ref(long attr_id, long mem_type_id, String[] buf)
throws HDF5LibraryException, NullPointerException
{
throw new HDF5LibraryException("H5Aread_reg_ref not implemented yet");
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static int H5Aread_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the short array
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_SHORT, buf.length);
if (isCriticalPinning) {
buf_segment.copyFrom(MemorySegment.ofArray(buf));
}
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Aread(attr_id, mem_type_id, buf_segment)) < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_SHORT, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static int H5AreadVL(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
boolean vl_data_class = false;
// CRITICAL FIX: Use global Arena to prevent automatic cleanup conflicts with HDF5 VL memory
Arena arena = Arena.global();
try {
// Detect VL data to determine if H5Treclaim is needed (JNI pattern)
vl_data_class = detectVLData(mem_type_id);
// Check the datatype class to determine reading strategy
int typeClass = H5Tget_class(mem_type_id);
if (typeClass == HDF5Constants.H5T_COMPOUND) {
// For compound datatypes, read heterogeneous field structures
ArrayList[] result = VLDataConverter.readCompoundDatatype(attr_id, mem_type_id, buf.length,
arena, false, -1, -1, -1);
System.arraycopy(result, 0, buf, 0, buf.length);
status = 0; // Success
}
else if (typeClass == HDF5Constants.H5T_ARRAY) {
// For array datatypes, read directly into array buffer (not hvl_t)
ArrayList[] result =
VLDataConverter.readArrayDatatype(attr_id, mem_type_id, buf.length, arena);
System.arraycopy(result, 0, buf, 0, buf.length);
status = 0; // Success
}
else if (typeClass == HDF5Constants.H5T_STRING && H5Tis_variable_str(mem_type_id)) {
// CRITICAL FIX: For variable-length string datatypes, use string pointer array
// to match the write path format - this fixes the off-by-one indexing issue
MemorySegment stringArray = arena.allocate(ValueLayout.ADDRESS, buf.length);
// Call native H5Aread to read string pointers
status = org.hdfgroup.javahdf5.hdf5_h.H5Aread(attr_id, mem_type_id, stringArray);
if (status >= 0) {
// Convert string pointer array back to ArrayList array
for (int i = 0; i < buf.length; i++) {
ArrayList
* // Create variable-length string type
* long strType = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
* H5.H5Tset_size(strType, HDF5Constants.H5T_VARIABLE);
*
* // Determine buffer size from attribute dataspace
* long space_id = H5.H5Aget_space(attr_id);
* long[] dims = new long[1];
* H5.H5Sget_simple_extent_dims(space_id, dims, null);
*
* // Read VL strings
* String[] buffer = new String[(int)dims[0]];
* H5.H5Aread_VLStrings(attr_id, strType, buffer);
*
* // Clean up
* H5.H5Sclose(space_id);
* H5.H5Tclose(strType);
*
**/
public static int H5Aread_VLStrings(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException
{
// Input validation
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
// Type validation - ensure it's a variable-length string type
if (!H5.H5Tis_variable_str(mem_type_id)) {
throw new HDF5LibraryException("Type is not a variable-length string");
}
if (log.isTraceEnabled()) {
log.trace("H5Aread_VLStrings: attr_id={}, mem_type_id={}, buffer size={}", attr_id, mem_type_id,
buf.length);
}
// Get attribute dataspace to determine size
long space_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = new long[1];
int status = -1;
try {
space_id = H5.H5Aget_space(attr_id);
if (space_id < 0) {
throw new HDF5LibraryException("Failed to get attribute dataspace");
}
int rank = H5.H5Sget_simple_extent_ndims(space_id);
if (rank > 0) {
long[] fullDims = new long[rank];
H5.H5Sget_simple_extent_dims(space_id, fullDims, null);
// Calculate total size
long totalSize = 1;
for (long dim : fullDims) {
totalSize *= dim;
}
// Buffer size validation
if (buf.length < totalSize) {
throw new IllegalArgumentException("Buffer too small: " + buf.length + " < " + totalSize);
}
dims[0] = totalSize;
}
else {
// Scalar attribute
dims[0] = 1;
}
if (log.isTraceEnabled()) {
log.trace("H5Aread_VLStrings: reading {} elements", dims[0]);
}
// Use global Arena to prevent automatic cleanup conflicts with HDF5 VL memory
Arena arena = Arena.global();
// Allocate hvl_t array for reading
MemorySegment hvlArray = org.hdfgroup.javahdf5.hvl_t.allocateArray((int)dims[0], arena);
// Read from HDF5
status = org.hdfgroup.javahdf5.hdf5_h.H5Aread(attr_id, mem_type_id, hvlArray);
if (status < 0) {
h5libraryError();
}
// Convert from hvl_t to Java ArrayList[]
ArrayList[] vlResult = VLDataConverter.convertFromHVL(hvlArray, (int)dims[0], mem_type_id);
// Extract strings from ArrayList[] to String[]
for (int i = 0; i < dims[0] && i < buf.length; i++) {
if (vlResult[i] != null && !vlResult[i].isEmpty()) {
buf[i] = (String)vlResult[i].get(0);
}
else {
buf[i] = "";
}
}
if (log.isTraceEnabled()) {
log.trace("H5Aread_VLStrings: successfully read {} strings, status={}", dims[0], status);
}
// CRITICAL: Reclaim VL memory managed by HDF5
// This must be called to prevent memory leaks
int reclaim_status = org.hdfgroup.javahdf5.hdf5_h.H5Treclaim(
mem_type_id, space_id, org.hdfgroup.javahdf5.hdf5_h.H5P_DEFAULT(), hvlArray);
if (reclaim_status < 0 && log.isTraceEnabled()) {
log.trace("H5Aread_VLStrings: H5Treclaim returned {}", reclaim_status);
}
}
catch (HDF5JavaException ex) {
throw new HDF5LibraryException("VL string read failed: " + ex.getMessage());
}
finally {
// Clean up dataspace
if (space_id >= 0) {
try {
H5.H5Sclose(space_id);
}
catch (Exception ex) {
if (log.isTraceEnabled()) {
log.trace("H5Aread_VLStrings: H5Sclose failed: {}", ex.getMessage());
}
}
}
}
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static int H5AreadComplex(long attr_id, long mem_type_id, String[] buf)
throws HDF5LibraryException, NullPointerException
{
throw new HDF5LibraryException("H5AreadComplex not implemented yet");
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* Name is null.
**/
public static int H5Arename(long loc_id, String old_attr_name, String new_attr_name)
throws HDF5LibraryException, NullPointerException
{
int status = -1;
if (old_attr_name == null || new_attr_name == null) {
throw new NullPointerException("old_attr_name or new_attr_name is null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate MemorySegments for the old and new attribute names
MemorySegment old_attr_name_segment = arena.allocateFrom(old_attr_name);
MemorySegment new_attr_name_segment = arena.allocateFrom(new_attr_name);
status =
org.hdfgroup.javahdf5.hdf5_h.H5Arename(loc_id, old_attr_name_segment, new_attr_name_segment);
}
if (status < 0) {
h5libraryError();
}
log.trace("H5Arename: {} renamed to {}", old_attr_name, new_attr_name);
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* Name is null.
**/
public static int H5Arename_by_name(long loc_id, String obj_name, String old_attr_name,
String new_attr_name, long lapl_id)
throws HDF5LibraryException, NullPointerException
{
int status = -1;
if (obj_name == null || old_attr_name == null || new_attr_name == null) {
throw new NullPointerException(
"H5Arename_by_name: obj_name, old_attr_name or new_attr_name is null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate MemorySegments for the object name and attribute names
MemorySegment obj_name_segment = arena.allocateFrom(obj_name);
MemorySegment old_attr_name_segment = arena.allocateFrom(old_attr_name);
MemorySegment new_attr_name_segment = arena.allocateFrom(new_attr_name);
status = org.hdfgroup.javahdf5.hdf5_h.H5Arename_by_name(
loc_id, obj_name_segment, old_attr_name_segment, new_attr_name_segment, lapl_id);
}
if (status < 0) {
h5libraryError();
}
log.trace("H5Arename_by_name: {} renamed to {}", old_attr_name, new_attr_name);
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public static int H5Awrite(long attr_id, long mem_type_id, byte[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment for the data buffer
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_BYTE, buf.length);
buf_segment.copyFrom(MemorySegment.ofArray(buf));
status = org.hdfgroup.javahdf5.hdf5_h.H5Awrite(attr_id, mem_type_id, buf_segment);
if (status < 0) {
h5libraryError();
}
}
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public static int H5Awrite(long attr_id, long mem_type_id, byte[] buf)
throws HDF5LibraryException, NullPointerException
{
return H5Awrite(attr_id, mem_type_id, buf, true);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data object is null
**/
public 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("data is not an array");
}
String cname = dataClass.getName();
is1D = (cname.lastIndexOf('[') == cname.indexOf('['));
char dname = cname.charAt(cname.lastIndexOf("[") + 1);
if (is1D && (dataClass.getComponentType() == String.class)) {
log.trace("H5Awrite_string type - routing to H5Awrite_VLStrings");
status = H5Awrite_VLStrings(attr_id, mem_type_id, (String[])obj);
}
else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
log.trace("H5AwriteVL type - using H5AwriteVL directly");
status = H5AwriteVL(attr_id, mem_type_id, (Object[])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;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public static int H5Awrite_double(long attr_id, long mem_type_id, double[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
throw new HDF5LibraryException("H5Awrite_double not implemented yet");
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public static int H5Awrite_float(long attr_id, long mem_type_id, float[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
throw new HDF5LibraryException("H5Awrite_float not implemented yet");
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public static int H5Awrite_int(long attr_id, long mem_type_id, int[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
throw new HDF5LibraryException("H5Awrite_int not implemented yet");
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public static int H5Awrite_long(long attr_id, long mem_type_id, long[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
throw new HDF5LibraryException("H5Awrite_long not implemented yet");
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public static int H5Awrite_short(long attr_id, long mem_type_id, short[] buf, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
throw new HDF5LibraryException("H5Awrite_short not implemented yet");
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public 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);
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public static int H5Awrite_string(long attr_id, long mem_type_id, String[] buf)
throws HDF5LibraryException, NullPointerException
{
throw new HDF5LibraryException("H5Awrite_string not implemented yet");
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
* @exception NullPointerException
* data is null.
**/
public static int H5AwriteVL(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
boolean vl_data_class = false;
// CRITICAL FIX: Use global Arena to prevent automatic cleanup conflicts with HDF5 VL memory
Arena arena = Arena.global();
MemorySegment hvlArray = null;
MemorySegment arrayBuffer = null;
MemorySegment stringArray = null;
long space_id = HDF5Constants.H5I_INVALID_HID;
try {
// Detect VL data to determine if H5Treclaim is needed (JNI pattern)
vl_data_class = detectVLData(mem_type_id);
ArrayList[] arrayData = (ArrayList[])buf;
// Check the datatype class to determine conversion strategy
int typeClass = H5Tget_class(mem_type_id);
if (typeClass == HDF5Constants.H5T_COMPOUND) {
// For compound datatypes, convert ArrayList array to packed compound structures
arrayBuffer = VLDataConverter.convertCompoundDatatype(arrayData, mem_type_id, arena);
status = org.hdfgroup.javahdf5.hdf5_h.H5Awrite(attr_id, mem_type_id, arrayBuffer);
}
else if (typeClass == HDF5Constants.H5T_ARRAY) {
// For array datatypes, convert to packed array elements (not hvl_t)
arrayBuffer = VLDataConverter.convertArrayDatatype(arrayData, mem_type_id, arena);
status = org.hdfgroup.javahdf5.hdf5_h.H5Awrite(attr_id, mem_type_id, arrayBuffer);
}
else if (typeClass == HDF5Constants.H5T_STRING && H5Tis_variable_str(mem_type_id)) {
// For variable-length string datatypes, convert to string pointers
stringArray = VLDataConverter.convertVLStrings(arrayData, arena);
status = org.hdfgroup.javahdf5.hdf5_h.H5Awrite(attr_id, mem_type_id, stringArray);
}
else {
// For VL datatypes, convert to hvl_t structures
hvlArray = VLDataConverter.convertToHVL(arrayData, arena);
status = org.hdfgroup.javahdf5.hdf5_h.H5Awrite(attr_id, mem_type_id, hvlArray);
}
if (status < 0) {
h5libraryError();
}
}
catch (HDF5JavaException ex) {
throw new HDF5LibraryException("VL data conversion failed: " + ex.getMessage());
}
catch (ClassCastException ex) {
throw new HDF5LibraryException("Input data must be ArrayList array: " + ex.getMessage());
}
finally {
// CRITICAL: Reclaim VL memory after write (JNI pattern)
// This allows HDF5 to properly free any VL memory it allocated during the write
if ((status >= 0) && vl_data_class && hvlArray != null) {
try {
// Get dataspace for H5Treclaim
space_id = org.hdfgroup.javahdf5.hdf5_h.H5Aget_space(attr_id);
org.hdfgroup.javahdf5.hdf5_h.H5Treclaim(
mem_type_id, space_id, org.hdfgroup.javahdf5.hdf5_h.H5P_DEFAULT(), hvlArray);
}
catch (Exception reclaimEx) {
// Log but don't fail if reclaim has issues
System.err.println("Warning: H5Treclaim failed in H5AwriteVL: " + reclaimEx.getMessage());
}
finally {
if (space_id >= 0) {
try {
org.hdfgroup.javahdf5.hdf5_h.H5Sclose(space_id);
}
catch (Exception ex) {
// Ignore close errors
}
}
}
}
}
return status;
}
/**
* @ingroup JH5A
*
* H5Awrite_VLStrings writes a variable length String attribute, specified by its identifier attr_id, from
* the application memory buffer buffer of variable-length strings into the file.
*
* ---- contributed by Rosetta Biosoftware
*
* @param attr_id
* Identifier of the attribute to write to.
* @param mem_type_id
* Identifier of the memory datatype (must be variable-length string type).
* @param buf
* Buffer of variable-length strings with data to be written to the file.
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
* @exception NullPointerException
* buf is null.
* @exception IllegalArgumentException
* buf is empty or type is not variable-length string.
*
* @note Uses Arena.global() for memory management
* @note Null strings in input are converted to empty strings
* @note Memory is automatically reclaimed by HDF5
*
**/
public static int H5Awrite_VLStrings(long attr_id, long mem_type_id, Object[] buf)
throws HDF5LibraryException, NullPointerException
{
// Input validation
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
if (buf.length == 0) {
throw new IllegalArgumentException("Buffer cannot be empty");
}
// Type validation - ensure it's a variable-length string type
if (!H5.H5Tis_variable_str(mem_type_id)) {
throw new HDF5LibraryException("Type is not a variable-length string");
}
// Validate buffer elements are Strings
for (int i = 0; i < buf.length; i++) {
if (buf[i] != null && !(buf[i] instanceof String)) {
throw new IllegalArgumentException("Buffer element " + i +
" is not a String: " + buf[i].getClass().getName());
}
}
if (log.isTraceEnabled()) {
log.trace("H5Awrite_VLStrings: attr_id={}, mem_type_id={}, writing {} strings", attr_id,
mem_type_id, buf.length);
}
int status = -1;
// Use global Arena to prevent automatic cleanup conflicts with HDF5 VL memory
Arena arena = Arena.global();
try {
// Convert String array to VL format for HDF5
String[] stringArray = (String[])buf;
// Handle null strings - convert to empty strings
for (int i = 0; i < stringArray.length; i++) {
if (stringArray[i] == null) {
if (log.isTraceEnabled()) {
log.trace("H5Awrite_VLStrings: converting null at index {} to empty string", i);
}
stringArray[i] = "";
}
}
// For VL strings, we need to manually create hvl_t structures
// VLDataConverter is for array types, not VL string types
MemorySegment hvlArray = org.hdfgroup.javahdf5.hvl_t.allocateArray(stringArray.length, arena);
for (int i = 0; i < stringArray.length; i++) {
MemorySegment hvlElement = org.hdfgroup.javahdf5.hvl_t.asSlice(hvlArray, i);
String str = stringArray[i];
if (str == null || str.isEmpty()) {
// Empty string: set length to 1 (for null terminator) and allocate single byte
org.hdfgroup.javahdf5.hvl_t.len(hvlElement, 1);
MemorySegment emptyStr = arena.allocate(1);
emptyStr.set(ValueLayout.JAVA_BYTE, 0, (byte)0);
org.hdfgroup.javahdf5.hvl_t.p(hvlElement, emptyStr);
}
else {
// Convert string to null-terminated C string
MemorySegment stringSegment = arena.allocateFrom(str, StandardCharsets.UTF_8);
// Set length to string length + 1 for null terminator
org.hdfgroup.javahdf5.hvl_t.len(hvlElement, str.length() + 1);
org.hdfgroup.javahdf5.hvl_t.p(hvlElement, stringSegment);
}
}
// Call H5Awrite (not H5Dwrite) - attributes don't use space parameters
status = org.hdfgroup.javahdf5.hdf5_h.H5Awrite(attr_id, mem_type_id, hvlArray);
if (status < 0) {
h5libraryError();
}
if (log.isTraceEnabled()) {
log.trace("H5Awrite_VLStrings: successfully wrote {} strings, status={}", buf.length, status);
}
}
catch (HDF5JavaException ex) {
throw new HDF5LibraryException("VL string write failed: " + ex.getMessage());
}
return status;
}
/**
* @ingroup JH5A
*
* 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 HDF5 Library.
**/
public static long H5Aget_create_plist(long attr_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5A
*
* H5Aiterate 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 alphanumeric 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 HDF5 Library.
* @exception NullPointerException
* buf is null.
**/
public static int H5Aiterate(long loc_id, int idx_type, int order, long idx,
hdf.hdf5lib.callbacks.H5A_iterate_cb op,
hdf.hdf5lib.callbacks.H5A_iterate_t op_data)
throws HDF5LibraryException, NullPointerException
{
if (op == null) {
throw new NullPointerException("op is null");
}
int status = -1;
long start_idx = idx;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment start_idx_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
start_idx_segment.set(ValueLayout.JAVA_LONG, 0, start_idx);
MemorySegment op_segment = H5A_operator2_t.allocate(op, arena);
MemorySegment op_data_segment =
Linker.nativeLinker().upcallStub(H5Aiterate2$handle(), H5Aiterate2$descriptor(), arena);
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Aiterate2(loc_id, idx_type, order, start_idx_segment,
op_segment, op_data_segment)) < 0)
h5libraryError();
}
return status;
}
/**
* @ingroup JH5A
*
* 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 alphanumeric 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 HDF5 Library.
* @exception NullPointerException
* buf is null.
**/
public static int H5Aiterate_by_name(long loc_id, String obj_name, int idx_type, int order, long idx,
hdf.hdf5lib.callbacks.H5A_iterate_cb op,
hdf.hdf5lib.callbacks.H5A_iterate_t op_data, long lapl_id)
throws HDF5LibraryException, NullPointerException
{
if (null == obj_name)
throw new HDF5FunctionArgumentException("object name is NULL");
if (op == null) {
throw new NullPointerException("op is null");
}
int status = -1;
long start_idx = idx;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment name_segment = arena.allocateFrom(obj_name);
MemorySegment start_idx_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
start_idx_segment.set(ValueLayout.JAVA_LONG, 0, start_idx);
MemorySegment op_segment = H5A_operator2_t.allocate(op, arena);
MemorySegment op_data_segment = Linker.nativeLinker().upcallStub(
H5Aiterate_by_name$handle(), H5Aiterate_by_name$descriptor(), arena);
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Aiterate_by_name(
loc_id, name_segment, idx_type, order, start_idx_segment, op_segment, op_data_segment,
lapl_id)) < 0)
h5libraryError();
}
return status;
}
// ////////////////////////////////////////////////////////////
// //
// 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 //
// //
// ////////////////////////////////////////////////////////////
/**
* @defgroup JH5D Java Datasets (H5D) Interface
*
* @see H5D, C-API
*
* @see @ref H5D_UG, User Guide
**/
/**
* @ingroup JH5D
*
* 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 destination dataset
*
* @return a non-negative value if successful
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
*/
public static int H5Dcopy(long src_did, long dst_did) throws HDF5LibraryException
{
if (src_did < 0 || dst_did < 0) {
throw new HDF5FunctionArgumentException("Negative dataset identifier");
}
throw new HDF5LibraryException("H5Dcopy not implemented yet");
}
/**
* @ingroup JH5D
*
* 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
**/
public static int H5Dclose(long dataset_id)
{
log.trace("OPEN_IDS: H5Dclose remove {}", dataset_id);
OPEN_IDS.remove(dataset_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Dclose(dataset_id);
if (retVal < 0)
h5libraryError();
return retVal;
}
/**
* @ingroup JH5D
*
* 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 HDF5 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 dset_id = H5I_INVALID_HID();
if (name == null) {
throw new NullPointerException("name is null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment name_segment = arena.allocateFrom(name);
if ((dset_id = H5Dcreate2(loc_id, name_segment, type_id, space_id, lcpl_id, dcpl_id, dapl_id)) <
0) {
h5libraryError();
}
}
if (dset_id > 0) {
log.trace("OPEN_IDS: H5Dcreate add {}", dset_id);
OPEN_IDS.add(dset_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
return dset_id;
}
/**
* @ingroup JH5D
*
* 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 HDF5 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 = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* buf is null.
**/
public static void H5Dfill(byte[] fill, long fill_type, byte[] buf, long buf_type, long space_id)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("buf is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment fill_segment = MemorySegment.NULL;
if (fill != null) {
fill_segment = arena.allocate(ValueLayout.JAVA_BYTE, fill.length);
for (int i = 0; i < fill.length; i++) {
fill_segment.set(ValueLayout.JAVA_BYTE, i, fill[i]);
}
}
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_BYTE, buf.length);
for (int i = 0; i < buf.length; i++) {
buf_segment.set(ValueLayout.JAVA_BYTE, i, buf[i]);
}
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Dfill(fill_segment, fill_type, buf_segment, buf_type,
space_id)) < 0)
h5libraryError();
for (int i = 0; i < buf.length; i++) {
buf[i] = buf_segment.get(ValueLayout.JAVA_BYTE, i);
}
}
}
/**
* @ingroup JH5D
*
* H5Dget_access_plist returns an identifier for a copy of the dataset access property list for a dataset.
*
* @param dataset_id
* IN: Identifier of the dataset to query.
*
* @return a dataset access property list identifier
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static long H5Dget_access_plist(long dataset_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.H5Dget_access_plist(dataset_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Dget_access_plist add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
**/
public static long H5Dget_create_plist(long dataset_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5D
*
* H5Dget_offset returns the address in the file of the dataset dset_id.
*
* @param dataset_id
* IN: Identifier of the dataset in question
*
* @return the offset in bytes.
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static long H5Dget_offset(long dataset_id) throws HDF5LibraryException
{
long offset = org.hdfgroup.javahdf5.hdf5_h.H5Dget_offset(dataset_id);
if (offset < 0) {
h5libraryError();
}
return offset;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
**/
public static long H5Dget_space(long dataset_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5D
*
* H5Dget_space_status determines whether space has been allocated for the dataset dset_id.
*
* @param dataset_id
* IN: Identifier of the dataset to query.
*
* @return the space allocation status
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static int H5Dget_space_status(long dataset_id) throws HDF5LibraryException
{
int space_status = HDF5Constants.H5D_SPACE_STATUS_ERROR;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment int_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
int status = org.hdfgroup.javahdf5.hdf5_h.H5Dget_space_status(dataset_id, int_segment);
if (status < 0)
h5libraryError();
space_status = int_segment.get(ValueLayout.JAVA_INT, 0);
}
return space_status;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
**/
public static long H5Dget_storage_size(long dataset_id) throws HDF5LibraryException
{
long size = org.hdfgroup.javahdf5.hdf5_h.H5Dget_storage_size(dataset_id);
if (size == 0)
h5libraryError();
return size;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
**/
public static long H5Dget_type(long dataset_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* buf is null.
**/
public static int H5Diterate(byte[] buf, long buf_type, long space_id,
hdf.hdf5lib.callbacks.H5D_iterate_cb op,
hdf.hdf5lib.callbacks.H5D_iterate_t op_data)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("buf is null");
}
if (op == null) {
throw new NullPointerException("op is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, buf);
MemorySegment op_segment = H5D_operator_t.allocate(op, arena);
MemorySegment op_data_segment =
Linker.nativeLinker().upcallStub(H5Diterate$handle(), H5Diterate$descriptor(), arena);
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Diterate(buf_segment, buf_type, space_id, op_segment,
op_data_segment)) < 0)
h5libraryError();
}
return status;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static long H5Dopen(long loc_id, String name, long dapl_id)
throws HDF5LibraryException, NullPointerException
{
long id = H5I_INVALID_HID();
if (name == null) {
throw new NullPointerException("Dataset name cannot be null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment name_segment = arena.allocateFrom(name);
id = H5Dopen2(loc_id, name_segment, dapl_id);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Dopen add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static 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
{
if (obj == null) {
throw new NullPointerException("data buffer is null");
}
boolean vl_data_class = false;
// if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
// H5_LIBRARY_ERROR(ENVONLY);
if (vl_data_class) {
long typeSize = -1;
if ((typeSize = H5Tget_size(mem_type_id)) < 0)
h5libraryError();
System.out.println("typeSize = " + typeSize);
int rank = -1;
if ((rank = H5Sget_simple_extent_ndims(mem_space_id)) < 0)
h5libraryError();
System.out.println("rank = " + rank);
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment obj_segment = arena.allocate(ValueLayout.JAVA_BYTE, obj.length);
status = org.hdfgroup.javahdf5.hdf5_h.H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, obj_segment);
if (status < 0)
h5libraryError();
MemorySegment.copy(obj_segment, ValueLayout.JAVA_BYTE, 0L, obj, 0, obj.length);
}
return status;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
boolean vl_data_class = false;
// if ((vl_data_class = h5str_detect_vlen(mem_type_id)) < 0)
// H5_LIBRARY_ERROR(ENVONLY);
if (vl_data_class) {
long typeSize = -1;
if ((typeSize = H5Tget_size(mem_type_id)) < 0)
h5libraryError();
System.out.println("typeSize = " + typeSize);
int rank = -1;
if ((rank = H5Sget_simple_extent_ndims(mem_space_id)) < 0)
h5libraryError();
System.out.println("rank = " + rank);
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment obj_segment = arena.allocate(ValueLayout.JAVA_BYTE, buf.length);
status = org.hdfgroup.javahdf5.hdf5_h.H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, obj_segment);
if (status < 0)
h5libraryError();
MemorySegment.copy(obj_segment, ValueLayout.JAVA_BYTE, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data object is null.
**/
public 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("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')) {
System.err.println("H5Dread_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 - routing to H5DreadVL");
status =
H5DreadVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[])obj);
}
else if (is1D && (dataClass.getComponentType() == String.class)) {
log.trace("H5Dread_string type - routing to H5DreadVL");
status =
H5DreadVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[])obj);
}
else if (H5.H5Tget_class(mem_type_id) == HDF5Constants.H5T_VLEN) {
log.trace("H5DreadVL type - using H5DreadVL directly");
status =
H5DreadVL(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[])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;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_DOUBLE, buf.length);
status = org.hdfgroup.javahdf5.hdf5_h.H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf_segment);
if (status < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_DOUBLE, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_FLOAT, buf.length);
status = org.hdfgroup.javahdf5.hdf5_h.H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf_segment);
if (status < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_FLOAT, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_INT, buf.length);
status = org.hdfgroup.javahdf5.hdf5_h.H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf_segment);
if (status < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_INT, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_LONG, buf.length);
status = org.hdfgroup.javahdf5.hdf5_h.H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf_segment);
if (status < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_LONG, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static 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
{
throw new HDF5LibraryException("H5Dread_reg_ref not implemented yet");
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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, boolean isCriticalPinning)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_SHORT, buf.length);
status = org.hdfgroup.javahdf5.hdf5_h.H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf_segment);
if (status < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_SHORT, 0L, buf, 0, buf.length);
}
return status;
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public 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);
}
/**
* @ingroup JH5D
*
* 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 HDF5 Library.
* @exception NullPointerException
* data buffer is null.
**/
public static 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
{
if (buf == null) {
throw new NullPointerException("data buffer is null");
}
int status = -1;
boolean vl_data_class = false;
// CRITICAL FIX: Use global Arena to prevent automatic cleanup conflicts with HDF5 VL memory
Arena arena = Arena.global();
try {
// Detect VL data to determine if H5Treclaim is needed (JNI pattern)
vl_data_class = detectVLData(mem_type_id);
// Check the datatype class to determine reading strategy
int typeClass = H5Tget_class(mem_type_id);
if (typeClass == HDF5Constants.H5T_COMPOUND) {
// For compound datatypes, read heterogeneous field structures
ArrayList[] result =
VLDataConverter.readCompoundDatatype(dataset_id, mem_type_id, buf.length, arena, true,
mem_space_id, file_space_id, xfer_plist_id);
System.arraycopy(result, 0, buf, 0, buf.length);
status = 0; // Success
}
else if (typeClass == HDF5Constants.H5T_ARRAY) {
// For array datatypes, read directly into array buffer (not hvl_t)
ArrayList[] result = VLDataConverter.readArrayDatatypeFromDataset(
dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf.length, arena);
System.arraycopy(result, 0, buf, 0, buf.length);
status = 0; // Success
}
else if (typeClass == HDF5Constants.H5T_STRING && H5Tis_variable_str(mem_type_id)) {
// CRITICAL FIX: For variable-length string datatypes, use string pointer array
// to match the write path format - this fixes the off-by-one indexing issue
MemorySegment stringArray = arena.allocate(ValueLayout.ADDRESS, buf.length);
// Call native H5Dread to read string pointers
status = org.hdfgroup.javahdf5.hdf5_h.H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, stringArray);
if (status >= 0) {
// Convert string pointer array back to ArrayList array
for (int i = 0; i < buf.length; i++) {
ArrayListThis may be used by exception handlers to assure that the error condition * in the HDF5 library has been reset. * * @return Returns a non-negative value if successful * * @exception HDF5LibraryException * Error from the HDF5 Library. **/ public static int H5Eclear() throws HDF5LibraryException { H5Eclear2(HDF5Constants.H5E_DEFAULT); return 0; } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static void H5Eclear(long stack_id) throws HDF5LibraryException { H5Eclear2(stack_id); } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static void H5Eclear2(long stack_id) throws HDF5LibraryException { if (org.hdfgroup.javahdf5.hdf5_h.H5Eclear2(stack_id) < 0) { h5libraryError(); } } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static void H5Eclose_msg(long err_id) throws HDF5LibraryException { if (org.hdfgroup.javahdf5.hdf5_h.H5Eclose_msg(err_id) < 0) { h5libraryError(); } } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static void H5Eclose_stack(long stack_id) throws HDF5LibraryException { if (org.hdfgroup.javahdf5.hdf5_h.H5Eclose_stack(stack_id) < 0) { h5libraryError(); } } /** * @ingroup JH5E * * 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 HDF5 Library. * @exception NullPointerException * msg is null. **/ public static long H5Ecreate_msg(long cls_id, int msg_type, String msg) throws HDF5LibraryException, NullPointerException { if (msg == null) { throw new NullPointerException("msg must not be null"); } long msg_id = -1; try (Arena arena = Arena.ofConfined()) { // Allocate MemorySegment for the msg MemorySegment msg_segment = arena.allocateFrom(msg); msg_id = org.hdfgroup.javahdf5.hdf5_h.H5Ecreate_msg(cls_id, msg_type, msg_segment); if (msg_id < 0) h5libraryError(); } return msg_id; } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static long H5Ecreate_stack() throws HDF5LibraryException { long stack_id = org.hdfgroup.javahdf5.hdf5_h.H5Ecreate_stack(); if (stack_id < 0) { h5libraryError(); } return stack_id; } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static String H5Eget_class_name(long class_id) throws HDF5LibraryException { String className = null; long buf_size = -1; if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Eget_class_name(class_id, MemorySegment.NULL, 0)) < 0) h5libraryError(); try (Arena arena = Arena.ofConfined()) { // Allocate a MemorySegment to hold the string bytes MemorySegment name_segment = arena.allocate(buf_size + 1); // Call the native method to get the error class name if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Eget_class_name(class_id, name_segment, buf_size + 1)) < 0) h5libraryError(); className = name_segment.getString(0, StandardCharsets.UTF_8); } return className; } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static long H5Eget_current_stack() throws HDF5LibraryException { long stack_id = org.hdfgroup.javahdf5.hdf5_h.H5Eget_current_stack(); if (stack_id < 0) { h5libraryError(); } return stack_id; } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static void H5Eset_current_stack(long stack_id) throws HDF5LibraryException { if (org.hdfgroup.javahdf5.hdf5_h.H5Eset_current_stack(stack_id) < 0) h5libraryError(); } /** * @ingroup JH5E * * 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 HDF5 Library. * @exception NullPointerException * type_list is null or not of length 1. **/ public static String H5Eget_msg(long msg_id, int[] type_list) throws HDF5LibraryException, NullPointerException { if (type_list == null || type_list.length != 1) { throw new NullPointerException("type_list must be a non-null array of length 1"); } String msg = null; long buf_size = -1; if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Eget_msg(msg_id, MemorySegment.NULL, MemorySegment.NULL, 0L)) < 0) { h5libraryError(); } else if (buf_size > 0) { try (Arena arena = Arena.ofConfined()) { // Allocate a MemorySegment to hold the string bytes MemorySegment msg_segment = arena.allocate(buf_size + 1); MemorySegment type_list_segment = arena.allocate(ValueLayout.JAVA_INT, 1); // Call the native method to get the error message if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Eget_msg(msg_id, type_list_segment, msg_segment, buf_size + 1)) < 0) h5libraryError(); msg = msg_segment.getString(0); type_list[0] = type_list_segment.get(ValueLayout.JAVA_INT, 0); } } return msg; } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static long H5Eget_num(long stack_id) throws HDF5LibraryException, NullPointerException { long num = org.hdfgroup.javahdf5.hdf5_h.H5Eget_num(stack_id); if (num < 0) { h5libraryError(); } return num; } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static void H5Eprint2(long stack_id, Object stream) throws HDF5LibraryException { if (stream != null) { throw new HDF5FunctionArgumentException("Print error stack to file not implemented"); } if (stack_id < 0) throw new HDF5FunctionArgumentException("Invalid error stack identifier: " + stack_id); // TODO need to add FILE* stream parameter handling org.hdfgroup.javahdf5.hdf5_h.H5Eprint2(stack_id, MemorySegment.NULL); } /** * @ingroup JH5E * * 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 HDF5 Library. **/ public static void H5Epop(long stack_id, long count) throws HDF5LibraryException { if (org.hdfgroup.javahdf5.hdf5_h.H5Epop(stack_id, count) < 0) { h5libraryError(); } } /** * @ingroup JH5E * * 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 HDF5 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); } /** * @ingroup JH5E * * 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 HDF5 Library. * @exception NullPointerException * file, func, or msg is null. **/ public static 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 { if (file == null || func == null || msg == null) { throw new NullPointerException("file, func, or msg is null"); } if (stack_id < 0) throw new HDF5FunctionArgumentException("Invalid error stack identifier: " + stack_id); if (cls_id < 0) throw new HDF5FunctionArgumentException("Invalid error class identifier: " + cls_id); if (maj_id < 0) throw new HDF5FunctionArgumentException("Invalid major error identifier: " + maj_id); if (min_id < 0) throw new HDF5FunctionArgumentException("Invalid minor error identifier: " + min_id); int retVal = -1; try (Arena arena = Arena.ofConfined()) { // Allocate MemorySegments to hold the string bytes MemorySegment file_segment = arena.allocateFrom(file); MemorySegment func_segment = arena.allocateFrom(func); MemorySegment msg_segment = arena.allocateFrom(msg); // Create a variadic invoker with no additional arguments // The message string is treated as a format string with no format arguments var invoker = org.hdfgroup.javahdf5.hdf5_h.H5Epush2.makeInvoker(); // Call the native method with empty variadic args if ((retVal = invoker.apply(stack_id, file_segment, func_segment, line, cls_id, maj_id, min_id, msg_segment)) < 0) h5libraryError(); } } /** * @ingroup JH5E * * 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 HDF5 Library. * @exception NullPointerException * name is null. **/ public static long H5Eregister_class(String cls_name, String lib_name, String version) throws HDF5LibraryException, NullPointerException { if (cls_name == null || lib_name == null || version == null) { throw new NullPointerException("cls_name, lib_name, or version is null"); } long class_id = H5I_INVALID_HID(); try (Arena arena = Arena.ofConfined()) { // Allocate a MemorySegment to hold the string bytes MemorySegment name_segment = arena.allocateFrom(cls_name); MemorySegment lib_segment = arena.allocateFrom(lib_name); MemorySegment version_segment = arena.allocateFrom(version); // Call the native method to register the error class class_id = org.hdfgroup.javahdf5.hdf5_h.H5Eregister_class(name_segment, lib_segment, version_segment); if (class_id < 0) { h5libraryError(); } } return class_id; } /** * @ingroup JH5E * * H5Eunregister_class removes the error class specified by class_id. * * @param class_id * IN: Error class identifier. * * @exception HDF5LibraryException * Error from the HDF5 Library. **/ public static void H5Eunregister_class(long class_id) throws HDF5LibraryException { if (org.hdfgroup.javahdf5.hdf5_h.H5Eunregister_class(class_id) < 0) { h5libraryError(); } } /** * @ingroup JH5E * * 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 HDF5 Library. * @exception NullPointerException * func is null. **/ public static void H5Ewalk(long stack_id, long direction, hdf.hdf5lib.callbacks.H5E_walk_cb func, hdf.hdf5lib.callbacks.H5E_walk_t client_data) throws HDF5LibraryException, NullPointerException { H5Ewalk2(stack_id, direction, func, client_data); } /** * @ingroup JH5E * * 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 HDF5 Library. * @exception NullPointerException * func is null. **/ public static void H5Ewalk2(long stack_id, long direction, hdf.hdf5lib.callbacks.H5E_walk_cb func, hdf.hdf5lib.callbacks.H5E_walk_t client_data) throws HDF5LibraryException, NullPointerException { if (func == null) { throw new NullPointerException("func must not be null"); } try (Arena arena = Arena.ofConfined()) { MemorySegment func_segment = H5E_walk2_t.allocate(func, arena); MemorySegment client_data_segment = Linker.nativeLinker().upcallStub(H5Ewalk2$handle(), H5Ewalk2$descriptor(), arena); if (org.hdfgroup.javahdf5.hdf5_h.H5Ewalk2(stack_id, (int)direction, func_segment, client_data_segment) < 0) h5libraryError(); } } // /////// 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 static void H5Epush2(long err_stack, String file, String func, int line, // long cls_id, long maj_id, long min_id, String msg, ...); // //////////////////////////////////////////////////////////// // // // H5ES: Event Set Interface Functions // // // // //////////////////////////////////////////////////////////// /** * * @defgroup JH5ES Java Event Set (H5ES) Interface * * @see H5ES, C-API * * @see @ref H5ES_UG, User Guide */ // /////// unimplemented //////// // H5_DLL hid_t H5EScreate(void); // H5_DLL herr_t H5ESwait(hid_t es_id, uint64_t timeout, size_t *num_in_progress, hbool_t *err_occurred); // H5_DLL herr_t H5EScancel(hid_t es_id, size_t *num_not_canceled, hbool_t *err_occurred); // H5_DLL herr_t H5ESget_count(hid_t es_id, size_t *count); // H5_DLL herr_t H5ESget_op_counter(hid_t es_id, uint64_t *counter); // H5_DLL herr_t H5ESget_err_status(hid_t es_id, hbool_t *err_occurred); // H5_DLL herr_t H5ESget_err_count(hid_t es_id, size_t *num_errs); // H5_DLL herr_t H5ESget_err_info(hid_t es_id, size_t num_err_info, H5ES_err_info_t err_info[], // size_t *err_cleared); // H5_DLL herr_t H5ESfree_err_info(size_t num_err_info, H5ES_err_info_t err_info[]); // H5_DLL herr_t H5ESregister_insert_func(hid_t es_id, H5ES_event_insert_func_t func, void *ctx); // H5_DLL herr_t H5ESregister_complete_func(hid_t es_id, H5ES_event_complete_func_t func, void *ctx); // H5_DLL herr_t H5ESclose(hid_t es_id); // // //////////////////////////////////////////////////////////// // // // H5F: File Interface Functions // // // // //////////////////////////////////////////////////////////// /** * * @defgroup JH5F Java File (H5F) Interface * * @see H5F, C-API * * @see @ref H5F_UG, User Guide */ /** * @ingroup JH5F * * 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 **/ public static int H5Fclose(long file_id) { log.trace("OPEN_IDS: H5Fclose remove {}", file_id); OPEN_IDS.remove(file_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Fclose(file_id); if (retVal < 0) h5libraryError(); return retVal; } /** * @ingroup JH5F * * 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 HDF5 Library. * @exception NullPointerException * name is null. **/ public static long H5Fopen(String name, int flags, long access_id) throws HDF5LibraryException, NullPointerException { if (name == null) { throw new NullPointerException("name is null"); } long id = H5I_INVALID_HID(); try (Arena arena = Arena.ofConfined()) { // Allocate a MemorySegment to hold the string bytes MemorySegment name_segment = arena.allocateFrom(name); id = org.hdfgroup.javahdf5.hdf5_h.H5Fopen(name_segment, flags, access_id); } if (id > 0) { log.trace("OPEN_IDS: H5Fopen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } else h5libraryError(); return id; } /** * @ingroup JH5F * * H5Freopen reopens an HDF5 file. * * @param file_id * Identifier of a file to terminate and reopen access to. * * @return a new file identifier if successful * * @exception HDF5LibraryException * Error from the HDF5 Library. **/ public static long H5Freopen(long file_id) throws HDF5LibraryException { long id = org.hdfgroup.javahdf5.hdf5_h.H5Freopen(file_id); if (id > 0) { log.trace("OPEN_IDS: H5Freopen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } else h5libraryError(); return id; } /** * @ingroup JH5F * * 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 HDF5 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 HDF5 Library.
* @exception NullPointerException
* size is null.
*
**/
public static int H5Pget_attr_phase_change(long ocpl_id, int[] attributes)
throws HDF5LibraryException, NullPointerException
{
int retVal = -1;
if (attributes == null || attributes.length < 2) {
throw new NullPointerException("attributes is null or has less than 2 elements");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment max_compact_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment min_dense_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_attr_phase_change(ocpl_id, max_compact_segment,
min_dense_segment)) < 0)
h5libraryError();
attributes[0] = max_compact_segment.get(ValueLayout.JAVA_INT, 0);
attributes[1] = min_dense_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static void H5Pset_attr_phase_change(long ocpl_id, int max_compact, int min_dense)
throws HDF5LibraryException
{
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_attr_phase_change(ocpl_id, max_compact, min_dense) < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pget_attr_creation_order(long ocpl_id) throws HDF5LibraryException
{
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment int_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_attr_creation_order(ocpl_id, int_segment)) < 0)
h5libraryError();
retVal = int_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_attr_creation_order(long ocpl_id, int crt_order_flags)
throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_attr_creation_order(ocpl_id, crt_order_flags);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static boolean H5Pget_obj_track_times(long ocpl_id) throws HDF5LibraryException
{
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment int_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_obj_track_times(ocpl_id, int_segment)) < 0)
h5libraryError();
retVal = int_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal == 1;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static void H5Pset_obj_track_times(long ocpl_id, boolean track_times) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_obj_track_times(ocpl_id, track_times);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 values 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 HDF5 Library. * @exception NullPointerException * name or an array is null. * **/ public static int H5Pmodify_filter(long plist, int filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException, NullPointerException { if (cd_values == null) { throw new NullPointerException("cd_values is null"); } if (plist < 0) { throw new HDF5FunctionArgumentException("Negative property list identifier"); } int retVal = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment cd_values_segment = arena.allocateFrom(ValueLayout.JAVA_INT, cd_values); if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pmodify_filter(plist, filter, flags, cd_nelmts, cd_values_segment)) < 0) { h5libraryError(); } } return retVal; } /** * @ingroup JH5P * * 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 HDF5 Library. * @exception NullPointerException * cd_values array is null. **/ public static int H5Pset_filter(long plist, int filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException, NullPointerException { if (cd_values == null) { throw new NullPointerException("cd_values is null"); } if (plist < 0) { throw new HDF5FunctionArgumentException("Negative property list identifier"); } int retVal = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment cd_values_segment = arena.allocateFrom(ValueLayout.JAVA_INT, cd_values); if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_filter(plist, filter, flags, cd_nelmts, cd_values_segment)) < 0) { h5libraryError(); } } return retVal; } /** * @ingroup JH5P * * 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 HDF5 Library. **/ public static int H5Pget_nfilters(long plist) throws HDF5LibraryException { if (plist < 0) { throw new HDF5FunctionArgumentException("Negative property list identifier"); } int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_nfilters(plist); if (retVal < 0) { h5libraryError(); } return retVal; } /** * @ingroup JH5P * * 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 HDF5 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 hdf.hdf5lib.H5.H5Pget_filter2(plist, filter_number, flags, cd_nelmts, cd_values, namelen, name, filter_config); } /** * @ingroup JH5P * * 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 static 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 { if (flags == null || cd_nelmts == null || cd_values == null || name == null || filter_config == null) { throw new NullPointerException("One or more arrays are null"); } if (plist < 0) { throw new HDF5FunctionArgumentException("Negative property list identifier"); } int retVal = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment flags_segment = arena.allocateFrom(ValueLayout.JAVA_INT, flags); MemorySegment cd_nelmts_segment = arena.allocate(ValueLayout.JAVA_INT, 1); MemorySegment cd_values_segment = arena.allocateFrom(ValueLayout.JAVA_INT, cd_values); MemorySegment name_segment = arena.allocate(namelen + 1); MemorySegment filter_config_segment = arena.allocate(ValueLayout.JAVA_INT, 1); if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_filter2( plist, filter_number, flags_segment, cd_nelmts_segment, cd_values_segment, namelen, name_segment, filter_config_segment)) < 0) { h5libraryError(); } cd_nelmts[0] = cd_values_segment.get(ValueLayout.JAVA_INT, 0); filter_config[0] = filter_config_segment.get(ValueLayout.JAVA_INT, 0); name[0] = name_segment.getString(0, StandardCharsets.UTF_8); } return retVal; } /** * @ingroup JH5P * * 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 HDF5 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, int filter_id, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException { return hdf.hdf5lib.H5.H5Pget_filter_by_id2(plist_id, filter_id, flags, cd_nelmts, cd_values, namelen, name, filter_config); } /** * @ingroup JH5P * * 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 HDF5 Library. * @exception NullPointerException * name or an array is null. * **/ public static int H5Pget_filter_by_id2(long plist_id, int filter_id, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws HDF5LibraryException, NullPointerException { if (flags == null || cd_nelmts == null || cd_values == null || name == null || filter_config == null) { throw new NullPointerException("One or more arrays are null"); } int retVal = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment flags_segment = arena.allocateFrom(ValueLayout.JAVA_INT, flags); MemorySegment cd_nelmts_segment = arena.allocate(ValueLayout.JAVA_INT, 1); MemorySegment cd_values_segment = arena.allocateFrom(ValueLayout.JAVA_INT, cd_values); MemorySegment name_segment = arena.allocate(namelen + 1); MemorySegment filter_config_segment = arena.allocate(ValueLayout.JAVA_INT, 1); if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_filter_by_id2( plist_id, filter_id, flags_segment, cd_nelmts_segment, cd_values_segment, namelen, name_segment, filter_config_segment)) < 0) { h5libraryError(); } cd_nelmts[0] = cd_nelmts_segment.get(ValueLayout.JAVA_INT, 0); filter_config[0] = filter_config_segment.get(ValueLayout.JAVA_INT, 0); name[0] = name_segment.getString(0, StandardCharsets.UTF_8); } return retVal; } /** * @ingroup JH5P * * 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 HDF5 Library. **/ public static boolean H5Pall_filters_avail(long dcpl_id) throws HDF5LibraryException { int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pall_filters_avail(dcpl_id); if (retVal < 0) { h5libraryError(); } return retVal == 1; } /** * @ingroup JH5P * * H5Premove_filter deletes a filter from the dataset creation property list; * deletes all filters if filter is H5Z_FILTER_ALL * * @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 HDF5 Library. **/ public static int H5Premove_filter(long obj_id, int filter) throws HDF5LibraryException { if (filter < 0) { throw new HDF5FunctionArgumentException("Negative filter identifier"); } int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Premove_filter(obj_id, filter); if (retVal < 0) { h5libraryError(); } return retVal; } /** * @ingroup JH5P * * 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 HDF5 Library. **/ public static int H5Pset_deflate(long plist, int level) throws HDF5LibraryException { if (plist < 0) { throw new HDF5FunctionArgumentException("Negative property list identifier"); } if (level < 0 || level > 9) { throw new HDF5FunctionArgumentException("Compression level must be between 0 and 9"); } int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_deflate(plist, level); if (retVal < 0) { h5libraryError(); } return retVal; } /** * @ingroup JH5P * * 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 HDF5 Library. **/ public static int H5Pset_fletcher32(long plist) throws HDF5LibraryException { if (plist < 0) { throw new HDF5FunctionArgumentException("Negative property list identifier"); } int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_fletcher32(plist); if (retVal < 0) { h5libraryError(); } return retVal; } // /////// File creation property list (FCPL) routines /////// /** * @ingroup JH5P * * 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 HDF5 Library. * @exception NullPointerException * size is null. **/ public static int H5Pget_userblock(long plist, long[] size) throws HDF5LibraryException, NullPointerException { if (size == null || size.length < 1) { throw new NullPointerException("size is null or has less than 1 element"); } if (plist < 0) { throw new HDF5FunctionArgumentException("Negative property list identifier"); } int retVal = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1); if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_userblock(plist, size_segment)) < 0) h5libraryError(); size[0] = size_segment.get(ValueLayout.JAVA_LONG, 0); } return retVal; } /** * @ingroup JH5P * * 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 HDF5 Library. **/ public static int H5Pset_userblock(long plist, long size) throws HDF5LibraryException { if (plist < 0) { throw new HDF5FunctionArgumentException("Negative property list identifier"); } if (size < 0) { throw new HDF5FunctionArgumentException("User block size must be non-negative"); } int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_userblock(plist, size); if (retVal < 0) { h5libraryError(); } return retVal; } /** * @ingroup JH5P * * 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 HDF5 Library.
* @exception NullPointerException
* size is null.
* @exception HDF5FunctionArgumentException
* size is invalid.
**/
public static int H5Pget_sizes(long plist, long[] size)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (size == null || size.length < 2) {
throw new NullPointerException("size is null or has less than 2 elements");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment addr_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_sizes(plist, addr_segment, size_segment)) < 0)
h5libraryError();
size[0] = addr_segment.get(ValueLayout.JAVA_LONG, 0);
size[1] = size_segment.get(ValueLayout.JAVA_LONG, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pset_sizes(long plist, int sizeof_addr, int sizeof_size) throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (sizeof_addr <= 0 || sizeof_size <= 0) {
throw new HDF5FunctionArgumentException("Sizes must be positive integers");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_sizes(plist, sizeof_addr, sizeof_size);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* size is null.
* @exception HDF5FunctionArgumentException
* size is invalid.
**/
public static int H5Pget_sym_k(long plist, int[] size)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (size == null || size.length < 2) {
throw new NullPointerException("size is null or has less than 2 elements");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ik_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment lk_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_sym_k(plist, ik_segment, lk_segment)) < 0)
h5libraryError();
size[0] = ik_segment.get(ValueLayout.JAVA_INT, 0);
size[1] = lk_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pset_sym_k(long plist, int ik, int lk) throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (ik <= 0 || lk <= 0) {
throw new HDF5FunctionArgumentException("ik and lk must be positive integers");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_sym_k(plist, ik, lk);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* ik array is null.
**/
public static int H5Pget_istore_k(long plist, int[] ik) throws HDF5LibraryException, NullPointerException
{
if (ik == null || ik.length < 1) {
throw new NullPointerException("ik is null or has less than 1 element");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ik_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_istore_k(plist, ik_segment)) < 0)
h5libraryError();
ik[0] = ik_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pset_istore_k(long plist, int ik) throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (ik <= 0) {
throw new HDF5FunctionArgumentException("ik must be a positive integer");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_istore_k(plist, ik);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pget_shared_mesg_nindexes(long fcpl_id) throws HDF5LibraryException
{
int retVal = -1;
int nindexes = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment nindexes_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal =
org.hdfgroup.javahdf5.hdf5_h.H5Pget_shared_mesg_nindexes(fcpl_id, nindexes_segment)) < 0)
h5libraryError();
nindexes = nindexes_segment.get(ValueLayout.JAVA_INT, 0);
}
return nindexes;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid value of nindexes
*
**/
public static int H5Pset_shared_mesg_nindexes(long plist_id, int nindexes)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (nindexes < 0 || nindexes > 64) {
throw new HDF5FunctionArgumentException("nindexes must be between 0 and 64");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_shared_mesg_nindexes(plist_id, nindexes);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* mesg_info is null.
* @exception HDF5FunctionArgumentException
* Invalid value of nindexes
*
**/
public static int H5Pget_shared_mesg_index(long fcpl_id, int index_num, int[] mesg_info)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (mesg_info == null || mesg_info.length < 2) {
throw new NullPointerException("mesg_info is null or has less than 2 elements");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment mesg_type_flags_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment min_mesg_size_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_shared_mesg_index(
fcpl_id, index_num, mesg_type_flags_segment, min_mesg_size_segment)) < 0) {
h5libraryError();
}
mesg_info[0] = mesg_type_flags_segment.get(ValueLayout.JAVA_INT, 0);
mesg_info[1] = min_mesg_size_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid value of nindexes
*
**/
public static int H5Pset_shared_mesg_index(long fcpl_id, int index_num, int mesg_type_flags,
int min_mesg_size)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (index_num < 0 || index_num > 63) {
throw new HDF5FunctionArgumentException("index_num must be between 0 and 63");
}
if (mesg_type_flags < 0) {
throw new HDF5FunctionArgumentException("mesg_type_flags must be non-negative");
}
if (min_mesg_size < 0) {
throw new HDF5FunctionArgumentException("min_mesg_size must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_shared_mesg_index(fcpl_id, index_num,
mesg_type_flags, min_mesg_size);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* size is null.
*
**/
public static int H5Pget_shared_mesg_phase_change(long fcpl_id, int[] size)
throws HDF5LibraryException, NullPointerException
{
if (size == null || size.length < 2) {
throw new NullPointerException("size is null or has less than 2 elements");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment max_list_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment min_btree_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_shared_mesg_phase_change(
fcpl_id, max_list_segment, min_btree_segment)) < 0) {
h5libraryError();
}
size[0] = max_list_segment.get(ValueLayout.JAVA_INT, 0);
size[1] = min_btree_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid values of max_list and min_btree.
*
**/
public static int H5Pset_shared_mesg_phase_change(long fcpl_id, int max_list, int min_btree)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (max_list < 0 || min_btree < 0) {
throw new HDF5FunctionArgumentException("max_list and min_btree must be non-negative");
}
if (max_list < min_btree) {
throw new HDF5FunctionArgumentException("max_list must be greater than or equal to min_btree");
}
int retVal =
org.hdfgroup.javahdf5.hdf5_h.H5Pset_shared_mesg_phase_change(fcpl_id, max_list, min_btree);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid values of max_list and min_btree.
*
**/
public static void H5Pset_file_space_strategy(long fcpl_id, int strategy, boolean persist, long threshold)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (strategy < 0 || strategy > 3) {
throw new HDF5FunctionArgumentException("Invalid strategy value");
}
int retVal =
org.hdfgroup.javahdf5.hdf5_h.H5Pset_file_space_strategy(fcpl_id, strategy, persist, threshold);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid values of max_list and min_btree.
*
**/
public static int H5Pget_file_space_strategy(long fcpl_id, boolean[] persist, long[] threshold)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment strategy_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment persist_segment = MemorySegment.NULL;
if (persist != null && persist.length > 0)
persist_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
MemorySegment threshold_segment = MemorySegment.NULL;
if (threshold != null && threshold.length > 0)
threshold_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_file_space_strategy(
fcpl_id, strategy_segment, persist_segment, threshold_segment)) < 0) {
h5libraryError();
}
retVal = strategy_segment.get(ValueLayout.JAVA_INT, 0);
if (persist != null && persist.length > 0)
persist[0] = persist_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
if (threshold != null && threshold.length > 0)
threshold[0] = threshold_segment.get(ValueLayout.JAVA_LONG, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid values of max_list and min_btree.
*
**/
public static boolean H5Pget_file_space_strategy_persist(long fcpl_id)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
boolean persist[] = {false};
if (hdf.hdf5lib.H5.H5Pget_file_space_strategy(fcpl_id, persist, null) < 0) {
h5libraryError();
}
return persist[0];
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid values of max_list and min_btree.
*
**/
public static long H5Pget_file_space_strategy_threshold(long fcpl_id)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
long threshold[] = {-1};
if (hdf.hdf5lib.H5.H5Pget_file_space_strategy(fcpl_id, null, threshold) < 0) {
h5libraryError();
}
return threshold[0];
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid values of max_list and min_btree.
*
**/
public static void H5Pset_file_space_page_size(long fcpl_id, long page_size)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_file_space_page_size(fcpl_id, page_size);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid values of max_list and min_btree.
*
**/
public static long H5Pget_file_space_page_size(long fcpl_id)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
long page_size = -1;
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment page_size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_file_space_page_size(fcpl_id, page_size_segment) < 0)
h5libraryError();
page_size = page_size_segment.get(ValueLayout.JAVA_LONG, 0);
}
return page_size;
}
// /////// File access property list (FAPL) routines ///////
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* alignment array is null.
* @exception HDF5FunctionArgumentException
* alignment array is invalid.
**/
public static int H5Pget_alignment(long plist, long[] alignment)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (alignment == null || alignment.length < 2) {
throw new NullPointerException("alignment is null or has less than 2 elements");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment threshold_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment alignment_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_alignment(plist, threshold_segment,
alignment_segment)) < 0)
h5libraryError();
alignment[0] = threshold_segment.get(ValueLayout.JAVA_LONG, 0);
alignment[1] = alignment_segment.get(ValueLayout.JAVA_LONG, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pset_alignment(long plist, long threshold, long alignment) throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (threshold < 0 || alignment <= 0)
throw new HDF5FunctionArgumentException(
"threshold must be non-negative and alignment must be positive");
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_alignment(plist, threshold, alignment);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*/
public static long H5Pget_driver(long plid) throws HDF5LibraryException
{
long driver_id = org.hdfgroup.javahdf5.hdf5_h.H5Pget_driver(plid);
if (driver_id < 0) {
h5libraryError();
}
return driver_id;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static long H5Pget_family_offset(long fapl_id) throws HDF5LibraryException
{
long offset = -1;
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment offset_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_family_offset(fapl_id, offset_segment)) < 0)
h5libraryError();
offset = offset_segment.get(ValueLayout.JAVA_LONG, 0);
}
return offset;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_family_offset(long fapl_id, long offset) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_family_offset(fapl_id, offset);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* an array is null.
**/
public static int H5Pget_cache(long plist, int[] mdc_nelmts, long[] rdcc_nelmts, long[] rdcc_nbytes,
double[] rdcc_w0) throws HDF5LibraryException, NullPointerException
{
if (rdcc_nelmts == null || rdcc_nbytes == null || rdcc_w0 == null || rdcc_nelmts.length < 1 ||
rdcc_nbytes.length < 1 || rdcc_w0.length < 1) {
throw new NullPointerException("One or more arrays are null or have insufficient length");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment mdc_nelmts_segment = MemorySegment.NULL;
MemorySegment rdcc_nelmts_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment rdcc_nbytes_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment rdcc_w0_segment = arena.allocate(ValueLayout.JAVA_DOUBLE, 1);
if ((retVal =
org.hdfgroup.javahdf5.hdf5_h.H5Pget_cache(plist, mdc_nelmts_segment, rdcc_nelmts_segment,
rdcc_nbytes_segment, rdcc_w0_segment)) < 0) {
h5libraryError();
}
rdcc_nelmts[0] = rdcc_nelmts_segment.get(ValueLayout.JAVA_LONG, 0);
rdcc_nbytes[0] = rdcc_nbytes_segment.get(ValueLayout.JAVA_LONG, 0);
rdcc_w0[0] = rdcc_w0_segment.get(ValueLayout.JAVA_DOUBLE, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pset_cache(long plist, int mdc_nelmts, long rdcc_nelmts, long rdcc_nbytes,
double rdcc_w0) throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (rdcc_nelmts < 0 || rdcc_nbytes < 0 || rdcc_w0 < 0.0) {
throw new HDF5FunctionArgumentException(
"rdcc_nelmts, rdcc_nbytes must be non-negative and rdcc_w0 must be non-negative");
}
int retVal =
org.hdfgroup.javahdf5.hdf5_h.H5Pset_cache(plist, mdc_nelmts, rdcc_nelmts, rdcc_nbytes, rdcc_w0);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static hdf.hdf5lib.structs.H5AC_cache_config_t H5Pget_mdc_config(long plist_id)
throws HDF5LibraryException
{
hdf.hdf5lib.structs.H5AC_cache_config_t config = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment config_segment = arena.allocate(org.hdfgroup.javahdf5.H5AC_cache_config_t.sizeof());
org.hdfgroup.javahdf5.H5AC_cache_config_t.version(config_segment,
HDF5Constants.H5AC_CURR_CACHE_CONFIG_VERSION);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_mdc_config(plist_id, config_segment) < 0)
h5libraryError();
// Unpack the H5AC_cache_config_t from the MemorySegment
config = new hdf.hdf5lib.structs.H5AC_cache_config_t(
org.hdfgroup.javahdf5.H5AC_cache_config_t.version(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.rpt_fcn_enabled(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.open_trace_file(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.close_trace_file(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.trace_file_name(config_segment)
.getString(0, StandardCharsets.UTF_8),
org.hdfgroup.javahdf5.H5AC_cache_config_t.evictions_enabled(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.set_initial_size(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.initial_size(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.min_clean_fraction(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.max_size(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.min_size(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.epoch_length(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.incr_mode(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.lower_hr_threshold(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.increment(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.apply_max_increment(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.max_increment(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.flash_incr_mode(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.flash_multiple(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.flash_threshold(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.decr_mode(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.upper_hr_threshold(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.decrement(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.apply_max_decrement(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.max_decrement(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.epochs_before_eviction(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.apply_empty_reserve(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.empty_reserve(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.dirty_bytes_threshold(config_segment),
org.hdfgroup.javahdf5.H5AC_cache_config_t.metadata_write_strategy(config_segment));
}
return config;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* config_ptr is null.
**/
public static void H5Pset_mdc_config(long plist_id, hdf.hdf5lib.structs.H5AC_cache_config_t config_ptr)
throws HDF5LibraryException, NullPointerException
{
if (config_ptr == null) {
throw new NullPointerException("config_ptr is null");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment config_segment = arena.allocate(org.hdfgroup.javahdf5.H5AC_cache_config_t.sizeof());
org.hdfgroup.javahdf5.H5AC_cache_config_t.version(config_segment, config_ptr.version);
org.hdfgroup.javahdf5.H5AC_cache_config_t.rpt_fcn_enabled(config_segment,
config_ptr.rpt_fcn_enabled);
org.hdfgroup.javahdf5.H5AC_cache_config_t.open_trace_file(config_segment,
config_ptr.open_trace_file);
org.hdfgroup.javahdf5.H5AC_cache_config_t.close_trace_file(config_segment,
config_ptr.close_trace_file);
MemorySegment trace_file_name_segment = arena.allocate(1025);
trace_file_name_segment.fill((byte)0);
MemorySegment.copy(config_ptr.trace_file_name.getBytes(), 0, trace_file_name_segment,
ValueLayout.JAVA_BYTE, 0L, config_ptr.trace_file_name.length());
org.hdfgroup.javahdf5.H5AC_cache_config_t.trace_file_name(config_segment,
trace_file_name_segment);
org.hdfgroup.javahdf5.H5AC_cache_config_t.evictions_enabled(config_segment,
config_ptr.evictions_enabled);
org.hdfgroup.javahdf5.H5AC_cache_config_t.set_initial_size(config_segment,
config_ptr.set_initial_size);
org.hdfgroup.javahdf5.H5AC_cache_config_t.initial_size(config_segment, config_ptr.initial_size);
org.hdfgroup.javahdf5.H5AC_cache_config_t.min_clean_fraction(config_segment,
config_ptr.min_clean_fraction);
org.hdfgroup.javahdf5.H5AC_cache_config_t.max_size(config_segment, config_ptr.max_size);
org.hdfgroup.javahdf5.H5AC_cache_config_t.min_size(config_segment, config_ptr.min_size);
org.hdfgroup.javahdf5.H5AC_cache_config_t.epoch_length(config_segment,
(int)config_ptr.epoch_length);
org.hdfgroup.javahdf5.H5AC_cache_config_t.incr_mode(config_segment, config_ptr.incr_mode);
org.hdfgroup.javahdf5.H5AC_cache_config_t.lower_hr_threshold(config_segment,
config_ptr.lower_hr_threshold);
org.hdfgroup.javahdf5.H5AC_cache_config_t.increment(config_segment, config_ptr.increment);
org.hdfgroup.javahdf5.H5AC_cache_config_t.apply_max_increment(config_segment,
config_ptr.apply_max_increment);
org.hdfgroup.javahdf5.H5AC_cache_config_t.max_increment(config_segment, config_ptr.max_increment);
org.hdfgroup.javahdf5.H5AC_cache_config_t.flash_incr_mode(config_segment,
config_ptr.flash_incr_mode);
org.hdfgroup.javahdf5.H5AC_cache_config_t.flash_multiple(config_segment,
config_ptr.flash_multiple);
org.hdfgroup.javahdf5.H5AC_cache_config_t.flash_threshold(config_segment,
config_ptr.flash_threshold);
org.hdfgroup.javahdf5.H5AC_cache_config_t.decr_mode(config_segment, config_ptr.decr_mode);
org.hdfgroup.javahdf5.H5AC_cache_config_t.upper_hr_threshold(config_segment,
config_ptr.upper_hr_threshold);
org.hdfgroup.javahdf5.H5AC_cache_config_t.decrement(config_segment, config_ptr.decrement);
org.hdfgroup.javahdf5.H5AC_cache_config_t.apply_max_decrement(config_segment,
config_ptr.apply_max_decrement);
org.hdfgroup.javahdf5.H5AC_cache_config_t.max_decrement(config_segment, config_ptr.max_decrement);
org.hdfgroup.javahdf5.H5AC_cache_config_t.epochs_before_eviction(
config_segment, config_ptr.epochs_before_eviction);
org.hdfgroup.javahdf5.H5AC_cache_config_t.apply_empty_reserve(config_segment,
config_ptr.apply_empty_reserve);
org.hdfgroup.javahdf5.H5AC_cache_config_t.empty_reserve(config_segment, config_ptr.empty_reserve);
org.hdfgroup.javahdf5.H5AC_cache_config_t.dirty_bytes_threshold(config_segment,
config_ptr.dirty_bytes_threshold);
org.hdfgroup.javahdf5.H5AC_cache_config_t.metadata_write_strategy(
config_segment, config_ptr.metadata_write_strategy);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_mdc_config(plist_id, config_segment) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* H5Pget_gc_references Returns the current setting for the garbage collection references 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 HDF5 Library.
**/
public static boolean H5Pget_gc_references(long fapl_id) throws HDF5LibraryException
{
boolean gc_ref = false;
try (Arena arena = Arena.ofConfined()) {
MemorySegment gc_ref_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_gc_references(fapl_id, gc_ref_segment) < 0)
h5libraryError();
gc_ref = gc_ref_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
}
return gc_ref;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pset_gc_references(long fapl_id, boolean gc_ref) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_gc_references(fapl_id, gc_ref ? 1 : 0);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pget_fclose_degree(long fapl_id) throws HDF5LibraryException
{
int degree = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment degree_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_fclose_degree(fapl_id, degree_segment) < 0)
h5libraryError();
degree = degree_segment.get(ValueLayout.JAVA_INT, 0);
}
return degree;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pset_fclose_degree(long fapl_id, int degree) throws HDF5LibraryException
{
if (degree < 0 || degree > HDF5Constants.H5F_CLOSE_STRONG) {
throw new HDF5FunctionArgumentException(
"degree must be from H5F_CLOSE_DEFAULT to H5F_CLOSE_STRONG");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_fclose_degree(fapl_id, degree);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static long H5Pget_meta_block_size(long fapl_id) throws HDF5LibraryException
{
long size = -1;
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_meta_block_size(fapl_id, size_segment)) < 0)
h5libraryError();
size = size_segment.get(ValueLayout.JAVA_LONG, 0);
}
return size;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static void H5Pset_meta_block_size(long fapl_id, long size) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_meta_block_size(fapl_id, size);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static long H5Pget_sieve_buf_size(long fapl_id) throws HDF5LibraryException
{
long size = -1;
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_sieve_buf_size(fapl_id, size_segment)) < 0)
h5libraryError();
size = size_segment.get(ValueLayout.JAVA_LONG, 0);
}
return size;
}
/**
* @ingroup JH5P
*
* H5Pset_sieve_buf_size Sets the maximum size of the data sieve 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 enough 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 sieve buffer. * * @exception HDF5LibraryException * Error from the HDF5 Library. **/ public static void H5Pset_sieve_buf_size(long fapl_id, long size) throws HDF5LibraryException { int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_sieve_buf_size(fapl_id, size); if (retVal < 0) { h5libraryError(); } } /** * @ingroup JH5P * * 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 HDF5 Library. **/ public static long H5Pget_small_data_block_size(long plist) throws HDF5LibraryException { if (plist < 0) { throw new HDF5FunctionArgumentException("Negative property list identifier"); } long size = -1; int retVal = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1); if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_small_data_block_size(plist, size_segment)) < 0) h5libraryError(); size = size_segment.get(ValueLayout.JAVA_LONG, 0); } return size; } /** * @ingroup JH5P * * 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 HDF5 Library. **/ public static int H5Pset_small_data_block_size(long plist, long size) throws HDF5LibraryException { if (plist < 0) { throw new HDF5FunctionArgumentException("Negative property list identifier"); } if (size < 0) { throw new HDF5FunctionArgumentException("size must be non-negative"); } int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_small_data_block_size(plist, size); if (retVal < 0) { h5libraryError(); } return retVal; } /** * @ingroup JH5P * * 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 HDF5 Library.
* @exception NullPointerException
* size is null.
*
**/
public static int H5Pget_libver_bounds(long fapl_id, int[] libver)
throws HDF5LibraryException, NullPointerException
{
if (libver == null || libver.length < 2) {
throw new NullPointerException("libver is null or has insufficient length");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment low_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment high_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_libver_bounds(fapl_id, low_segment,
high_segment)) < 0)
h5libraryError();
libver[0] = low_segment.get(ValueLayout.JAVA_INT, 0);
libver[1] = high_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Argument is Illegal
*
**/
public static int H5Pset_libver_bounds(long fapl_id, int low, int high)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (low < 0 || high < 0 || low > high) {
throw new HDF5FunctionArgumentException("low and high must be non-negative and low <= high");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_libver_bounds(fapl_id, low, high);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pget_elink_file_cache_size(long fapl_id) throws HDF5LibraryException
{
int efc_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment efc_size_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_elink_file_cache_size(fapl_id, efc_size_segment) < 0)
h5libraryError();
efc_size = efc_size_segment.get(ValueLayout.JAVA_INT, 0);
}
return efc_size;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static void H5Pset_elink_file_cache_size(long fapl_id, int efc_size) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_elink_file_cache_size(fapl_id, efc_size);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* location is null.
*
**/
public static void H5Pset_mdc_log_options(long fapl_id, boolean is_enabled, String location,
boolean start_on_access)
throws HDF5LibraryException, NullPointerException
{
if (location == null) {
throw new NullPointerException("location is null");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment location_segment = arena.allocateFrom(location);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_mdc_log_options(fapl_id, is_enabled, location_segment,
start_on_access) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static String H5Pget_mdc_log_options(long fapl_id, boolean[] mdc_log_options)
throws HDF5LibraryException
{
long buf_size = -1;
if (mdc_log_options == null || mdc_log_options.length < 2) {
throw new NullPointerException("mdc_log_options is null or has insufficient length");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment is_enabled_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
MemorySegment start_on_access_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_mdc_log_options(fapl_id, is_enabled_segment,
MemorySegment.NULL, buf_size_segment,
start_on_access_segment) < 0)
h5libraryError();
buf_size = buf_size_segment.get(ValueLayout.JAVA_LONG, 0) + 1; // +1 for null terminator;
}
String location = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_size_segment = arena.allocate(ValueLayout.JAVA_LONG, buf_size);
MemorySegment location_segment = arena.allocate(buf_size);
MemorySegment is_enabled_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
MemorySegment start_on_access_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_mdc_log_options(fapl_id, is_enabled_segment,
location_segment, buf_size_segment,
start_on_access_segment) < 0)
h5libraryError();
mdc_log_options[0] = is_enabled_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
mdc_log_options[1] = start_on_access_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
location = location_segment.getString(0, StandardCharsets.UTF_8);
}
return location;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pget_metadata_read_attempts(long plist_id) throws HDF5LibraryException
{
int attempts = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment attempts_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_metadata_read_attempts(plist_id, attempts_segment) < 0)
h5libraryError();
attempts = attempts_segment.get(ValueLayout.JAVA_INT, 0);
}
return attempts;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static void H5Pset_metadata_read_attempts(long plist_id, int attempts) throws HDF5LibraryException
{
if (attempts <= 0) {
throw new HDF5FunctionArgumentException("attempts must be greater than 0");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_metadata_read_attempts(plist_id, attempts);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static boolean H5Pget_evict_on_close(long fapl_id) throws HDF5LibraryException
{
boolean evict_on_close = false;
try (Arena arena = Arena.ofConfined()) {
MemorySegment evict_on_close_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_evict_on_close(fapl_id, evict_on_close_segment) < 0)
h5libraryError();
evict_on_close = evict_on_close_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
}
return evict_on_close;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_evict_on_close(fapl_id, evict_on_close);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static boolean H5Pget_use_file_locking(long fapl_id) throws HDF5LibraryException
{
boolean use_file_locking = false;
try (Arena arena = Arena.ofConfined()) {
MemorySegment use_file_locking_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
MemorySegment unused_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_file_locking(fapl_id, use_file_locking_segment,
unused_segment) < 0)
h5libraryError();
use_file_locking = use_file_locking_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
}
return use_file_locking;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static boolean H5Pget_ignore_disabled_file_locking(long fapl_id) throws HDF5LibraryException
{
boolean ignore_when_disabled = false;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ignore_when_disabled_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
MemorySegment unused_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_file_locking(fapl_id, unused_segment,
ignore_when_disabled_segment) < 0)
h5libraryError();
ignore_when_disabled = ignore_when_disabled_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
}
return ignore_when_disabled;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static void H5Pset_file_locking(long fapl_id, boolean use_file_locking,
boolean ignore_when_disabled) throws HDF5LibraryException
{
int retVal =
org.hdfgroup.javahdf5.hdf5_h.H5Pset_file_locking(fapl_id, use_file_locking, ignore_when_disabled);
if (retVal < 0) {
h5libraryError();
}
}
// ///// 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 //
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pget_layout(long plist) throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
int layout = org.hdfgroup.javahdf5.hdf5_h.H5Pget_layout(plist);
if (layout < 0) {
h5libraryError();
}
return layout;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pset_layout(long plist, int layout) throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (layout < 0) {
throw new HDF5FunctionArgumentException("Invalid layout type specified");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_layout(plist, layout);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* dims array is null.
* @exception HDF5FunctionArgumentException
* max_ndims <=0
**/
public static int H5Pget_chunk(long plist, int max_ndims, long[] dims)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (dims == null || dims.length < max_ndims) {
throw new NullPointerException("dims is null or has insufficient length");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (max_ndims <= 0) {
throw new HDF5FunctionArgumentException("max_ndims must be greater than 0");
}
int ndims = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment dims_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, dims);
ndims = org.hdfgroup.javahdf5.hdf5_h.H5Pget_chunk(plist, max_ndims, dims_segment);
if (ndims < 0) {
h5libraryError();
}
for (int i = 0; i < ndims; i++) {
dims[i] = dims_segment.get(ValueLayout.JAVA_LONG, i * Long.BYTES);
}
}
return ndims;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* dims array is null.
* @exception HDF5FunctionArgumentException
* dims <=0
**/
public static int H5Pset_chunk(long plist, int ndims, byte[] dim)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (dim == null || dim.length < ndims * Long.BYTES) {
throw new NullPointerException("dim is null or has insufficient length");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (ndims <= 0) {
throw new HDF5FunctionArgumentException("ndims must be greater than 0");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment dim_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, dim);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_chunk(plist, ndims, dim_segment)) < 0)
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* dims array is null.
* @exception HDF5FunctionArgumentException
* dims <=0
**/
public static int H5Pset_chunk(long plist, int ndims, long[] dim)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (dim == null) {
throw new NullPointerException("dim is null");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment dim_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, dim);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_chunk(plist, ndims, dim_segment)) < 0)
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* an name string is null.
* @exception HDF5FunctionArgumentException
* an id is <=0
**/
public static void H5Pset_virtual(long dcpl_id, long vspace_id, String src_file_name,
String src_dset_name, long src_space_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (src_file_name == null || src_dset_name == null) {
throw new NullPointerException("src_file_name or src_dset_name is null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment src_file_name_segment = arena.allocateFrom(src_file_name);
MemorySegment src_dset_name_segment = arena.allocateFrom(src_dset_name);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_virtual(dcpl_id, vspace_id, src_file_name_segment,
src_dset_name_segment, src_space_id) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* An id is <=0
**/
public static long H5Pget_virtual_count(long dcpl_id)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
long count = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment count_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_count(dcpl_id, count_segment) < 0)
h5libraryError();
count = count_segment.get(ValueLayout.JAVA_LONG, 0);
}
return count;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* An id is <=0
**/
public static long H5Pget_virtual_vspace(long dcpl_id, long index)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (index < 0) {
throw new HDF5FunctionArgumentException("index must be non-negative");
}
long vspace_id = org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_vspace(dcpl_id, index);
if (vspace_id < 0)
h5libraryError();
return vspace_id;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* An id is <=0
**/
public static long H5Pget_virtual_srcspace(long dcpl_id, long index)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (index < 0) {
throw new HDF5FunctionArgumentException("index must be non-negative");
}
long src_space_id = org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_srcspace(dcpl_id, index);
if (src_space_id < 0)
h5libraryError();
return src_space_id;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* An id is <=0
**/
public static String H5Pget_virtual_filename(long dcpl_id, long index)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (index < 0) {
throw new HDF5FunctionArgumentException("index must be non-negative");
}
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_filename(dcpl_id, index,
MemorySegment.NULL, 0)) < 0)
h5libraryError();
}
String filename = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment filename_segment = arena.allocate(buf_size + 1); // +1 for null terminator
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_filename(dcpl_id, index, filename_segment,
buf_size + 1) < 0)
h5libraryError();
filename = filename_segment.getString(0, StandardCharsets.UTF_8);
}
return filename;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* An id is <=0
**/
public static String H5Pget_virtual_dsetname(long dcpl_id, long index)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (index < 0) {
throw new HDF5FunctionArgumentException("index must be non-negative");
}
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_dsetname(dcpl_id, index,
MemorySegment.NULL, 0)) < 0)
h5libraryError();
}
String dset_name = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment dset_name_segment = arena.allocate(buf_size + 1); // +1 for null terminator
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_dsetname(dcpl_id, index, dset_name_segment,
buf_size + 1) < 0)
h5libraryError();
dset_name = dset_name_segment.getString(0, StandardCharsets.UTF_8);
}
return dset_name;
}
// ///// 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 HDF5 Library.
// *
// **/
// public static 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 HDF5 Library.
// *
// **/
// public static void H5Pset_vds_file_cache_size(long fapl_id, int efc_size)
// throws HDF5LibraryException {}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* name or size is null.
* @exception HDF5FunctionArgumentException
* name_size <= 0 .
*
**/
public static int H5Pget_external(long plist, int idx, long name_size, String[] name, long[] size)
throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException,
NullPointerException, HDF5FunctionArgumentException
{
if (size == null || size.length < 2) {
throw new NullPointerException("name or size is null or has insufficient length");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (idx < 0) {
throw new HDF5FunctionArgumentException("idx must be non-negative");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment;
if (name == null || name.length < 1 || name_size <= 0) {
name_segment = null;
}
else
name_segment = arena.allocate(ValueLayout.JAVA_CHAR, name_size);
MemorySegment offset_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_external(plist, idx, name_size, name_segment,
offset_segment, size_segment);
if (retVal < 0) {
h5libraryError();
}
// Copy the external file name to the provided array
if (name != null && name.length > 0 && name_size > 0)
name[0] = name_segment.getString(0, StandardCharsets.UTF_8);
// Copy the offset and size values to the provided array
size[0] = offset_segment.get(ValueLayout.JAVA_LONG, 0);
size[1] = size_segment.get(ValueLayout.JAVA_LONG, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static int H5Pset_external(long plist, String name, long offset, long size)
throws HDF5LibraryException, NullPointerException
{
if (name == null) {
throw new NullPointerException("name is null");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment = arena.allocateFrom(name);
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_external(plist, name_segment, offset, size);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pget_external_count(long plist) throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
int count = org.hdfgroup.javahdf5.hdf5_h.H5Pget_external_count(plist);
if (count < 0) {
h5libraryError();
}
return count;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_szip(long plist, int options_mask, int pixels_per_block)
throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (options_mask < 0 || pixels_per_block < 0) {
throw new HDF5FunctionArgumentException("options_mask or pixels_per_block must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_szip(plist, options_mask, pixels_per_block);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_shuffle(long plist_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_shuffle(plist_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_nbit(long plist_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_nbit(plist_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid arguments
*
**/
public static int H5Pset_scaleoffset(long plist_id, int scale_type, int scale_factor)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (scale_type < 0 || scale_factor < 0) {
throw new HDF5FunctionArgumentException("scale_type or scale_factor must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_scaleoffset(plist_id, scale_type, scale_factor);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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.
* @exception NullPointerException
* value is null.
**/
public static int H5Pget_fill_value(long plist_id, long type_id, byte[] value)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (value == null) {
throw new NullPointerException("value is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment value_segment = arena.allocate(ValueLayout.JAVA_BYTE, value.length);
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Pget_fill_value(plist_id, type_id, value_segment)) <
0)
h5libraryError();
MemorySegment.copy(value_segment, ValueLayout.JAVA_BYTE, 0L, value, 0, value.length);
}
return status;
}
/**
* @ingroup JH5P
*
* 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 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 = hdf.hdf5lib.H5.H5Pget_fill_value(plist_id, type_id, buf);
if (status >= 0)
obj = theArray.arrayify(buf);
return status;
}
/**
* @ingroup JH5P
*
* 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 HDF5LibraryException
* Error converting data array
* @exception NullPointerException
* value is null.
**/
public static int H5Pset_fill_value(long plist_id, long type_id, byte[] value)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (value == null) {
throw new NullPointerException("value is null");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment value_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, value);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_fill_value(plist_id, type_id, value_segment)) <
0)
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 static int H5Pset_fill_value(long plist_id, long type_id, Object obj) throws HDF5Exception
{
HDFArray theArray = new HDFArray(obj);
byte[] buf = theArray.byteify();
// TODO: Add Arena support for buf
int retVal = hdf.hdf5lib.H5.H5Pset_fill_value(plist_id, type_id, buf);
buf = null;
theArray = null;
return retVal;
}
/**
* @ingroup JH5P
*
* 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
* @exception NullPointerException
* status is null.
**/
public static int H5Pfill_value_defined(long plist_id, int[] status)
throws HDF5LibraryException, NullPointerException
{
if (status == null || status.length < 1) {
throw new NullPointerException("status is null or has insufficient length");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment status_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pfill_value_defined(plist_id, status_segment)) < 0)
h5libraryError();
status[0] = status_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* alloc_time is null.
*
**/
public static int H5Pget_alloc_time(long plist_id, int[] alloc_time)
throws HDF5LibraryException, NullPointerException
{
if (alloc_time == null || alloc_time.length < 1) {
throw new NullPointerException("alloc_time is null or has insufficient length");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment alloc_time_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_alloc_time(plist_id, alloc_time_segment)) < 0)
h5libraryError();
alloc_time[0] = alloc_time_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_alloc_time(long plist_id, int alloc_time) throws HDF5LibraryException
{
if (alloc_time < 0) {
throw new HDF5FunctionArgumentException("alloc_time must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_alloc_time(plist_id, alloc_time);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* fill_time is null.
*
**/
public static int H5Pget_fill_time(long plist_id, int[] fill_time)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (fill_time == null || fill_time.length < 1) {
throw new NullPointerException("fill_time is null or has insufficient length");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment fill_time_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_fill_time(plist_id, fill_time_segment)) < 0)
h5libraryError();
fill_time[0] = fill_time_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException
{
if (fill_time < 0) {
throw new HDF5FunctionArgumentException("fill_time must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_fill_time(plist_id, fill_time);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library
**/
public static void H5Pset_chunk_opts(long dcpl_id, int opts) throws HDF5LibraryException
{
if (opts < 0) {
throw new HDF5FunctionArgumentException("opts must be non-negative");
}
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_chunk_opts(dcpl_id, opts) < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library
*
*/
public static int H5Pget_chunk_opts(long dcpl_id) throws HDF5LibraryException
{
int opts = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment opts_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_chunk_opts(dcpl_id, opts_segment) < 0)
h5libraryError();
opts = opts_segment.get(ValueLayout.JAVA_INT, 0);
}
return opts;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static boolean H5Pget_dset_no_attrs_hint(long dcpl_id) throws HDF5LibraryException
{
boolean minimize = false;
try (Arena arena = Arena.ofConfined()) {
MemorySegment minimize_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_dset_no_attrs_hint(dcpl_id, minimize_segment) < 0)
h5libraryError();
minimize = minimize_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
}
return minimize;
}
/**
* @ingroup JH5P
*
* 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
* IN: the minimize hint setting
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static void H5Pset_dset_no_attrs_hint(long dcpl_id, boolean minimize) throws HDF5LibraryException
{
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_dset_no_attrs_hint(dcpl_id, minimize) < 0) {
h5libraryError();
}
}
// /////// Dataset access property list (DAPL) routines ///////
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* an array is null.
**/
public static void H5Pget_chunk_cache(long dapl_id, long[] rdcc_nslots, long[] rdcc_nbytes,
double[] rdcc_w0) throws HDF5LibraryException, NullPointerException
{
if (rdcc_nslots == null || rdcc_nbytes == null || rdcc_w0 == null || rdcc_nslots.length < 1 ||
rdcc_nbytes.length < 1 || rdcc_w0.length < 1) {
throw new NullPointerException("one or more arrays are null or have insufficient length");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment nslots_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment nbytes_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment w0_segment = arena.allocate(ValueLayout.JAVA_DOUBLE, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_chunk_cache(dapl_id, nslots_segment, nbytes_segment,
w0_segment) < 0)
h5libraryError();
rdcc_nslots[0] = nslots_segment.get(ValueLayout.JAVA_LONG, 0);
rdcc_nbytes[0] = nbytes_segment.get(ValueLayout.JAVA_LONG, 0);
rdcc_w0[0] = w0_segment.get(ValueLayout.JAVA_DOUBLE, 0);
}
}
/**
* @ingroup JH5P
*
* 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 dataset 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 HDF5 Library.
**/
public static void H5Pset_chunk_cache(long dapl_id, long rdcc_nslots, long rdcc_nbytes, double rdcc_w0)
throws HDF5LibraryException
{
if (rdcc_nslots < 0 || rdcc_nbytes < 0 || rdcc_w0 < 0.0) {
throw new HDF5FunctionArgumentException(
"rdcc_nslots, rdcc_nbytes or rdcc_w0 must be non-negative");
}
int retVal =
org.hdfgroup.javahdf5.hdf5_h.H5Pset_chunk_cache(dapl_id, rdcc_nslots, rdcc_nbytes, rdcc_w0);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library
**/
public static void H5Pset_virtual_view(long dapl_id, int view) throws HDF5LibraryException
{
if (view < 0) {
throw new HDF5FunctionArgumentException("view must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_virtual_view(dapl_id, view);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library
*
*/
public static int H5Pget_virtual_view(long dapl_id) throws HDF5LibraryException
{
int view = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment view_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_view(dapl_id, view_segment) < 0)
h5libraryError();
view = view_segment.get(ValueLayout.JAVA_INT, 0);
}
return view;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library
**/
public static void H5Pset_virtual_printf_gap(long dapl_id, long gap_size) throws HDF5LibraryException
{
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_virtual_printf_gap(dapl_id, gap_size) < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library
*
*/
public static long H5Pget_virtual_printf_gap(long dapl_id) throws HDF5LibraryException
{
long gap_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment gap_size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_printf_gap(dapl_id, gap_size_segment) < 0)
h5libraryError();
gap_size = gap_size_segment.get(ValueLayout.JAVA_LONG, 0);
}
return gap_size;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static String H5Pget_virtual_prefix(long dapl_id) throws HDF5LibraryException
{
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((buf_size =
org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_prefix(dapl_id, MemorySegment.NULL, 0)) < 0)
h5libraryError();
}
String prefix = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment prefix_segment = arena.allocate(buf_size + 1); // +1 for null terminator
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_prefix(dapl_id, prefix_segment, buf_size + 1) < 0)
h5libraryError();
prefix = prefix_segment.getString(0, StandardCharsets.UTF_8);
}
return prefix;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* prefix is null.
*
**/
public static void H5Pset_virtual_prefix(long dapl_id, String prefix)
throws HDF5LibraryException, NullPointerException
{
if (prefix == null) {
throw new NullPointerException("prefix is null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment prefix_segment = arena.allocateFrom(prefix);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_virtual_prefix(dapl_id, prefix_segment) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static String H5Pget_efile_prefix(long dapl_id) throws HDF5LibraryException
{
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((buf_size =
org.hdfgroup.javahdf5.hdf5_h.H5Pget_efile_prefix(dapl_id, MemorySegment.NULL, 0)) < 0)
h5libraryError();
}
String prefix = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment prefix_segment = arena.allocate(buf_size + 1); // +1 for null terminator
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_efile_prefix(dapl_id, prefix_segment, buf_size + 1) < 0)
h5libraryError();
prefix = prefix_segment.getString(0, StandardCharsets.UTF_8);
}
return prefix;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* prefix is null.
*
**/
public static void H5Pset_efile_prefix(long dapl_id, String prefix)
throws HDF5LibraryException, NullPointerException
{
if (prefix == null) {
throw new NullPointerException("prefix is null");
}
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment prefix_segment = arena.allocateFrom(prefix);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_efile_prefix(dapl_id, prefix_segment) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* H5Pget_virtual_spatial_tree accesses the flag for whether to use/not use a spatial tree
* during mapping operations on a Virtual Dataset. The default value is true.
*
* Use of a spatial tree will accelerate the process of searching through mappings
* to determine which contain intersections with the user's selection region.
* With the tree disabled, all mappings will simply be iterated through and
* checked directly.
*
* Certain workflows may find that tree creation overhead outweighs the time saved
* on reads. In this case, disabling this property will lead to a performance improvement,
* though it is expected that almost all cases will benefit from the tree on net.
*
* @param dapl_id
* IN: Dataset access property list
*
* @return true if the given dapl is set to use a spatial tree, false if not.
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static boolean H5Pget_virtual_spatial_tree(long dapl_id) throws HDF5LibraryException
{
boolean use_tree = false;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the boolean value
MemorySegment use_tree_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_virtual_spatial_tree(dapl_id, use_tree_segment) < 0)
h5libraryError();
// Read the boolean value from the segment
use_tree = use_tree_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
}
return use_tree;
}
/**
* @ingroup JH5P
*
* H5Pset_virtual_spatial_tree sets the dapl to use/not use a spatial tree
* during mapping operations on a Virtual Dataset. The default value is true.
*
* Use of a spatial tree will accelerate the process of searching through mappings
* to determine which contain intersections with the user's selection region.
* With the tree disabled, all mappings will simply be iterated through and
* checked directly.
*
* Certain workflows may find that tree creation overhead outweighs the time saved
* on reads. In this case, disabling this property will lead to a performance improvement,
* though it is expected that almost all cases will benefit from the tree on net.
*
* @param dapl_id
* IN: Dataset access property list
*
* @param use_tree
* IN: the use_tree flag setting
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static void H5Pset_virtual_spatial_tree(long dapl_id, boolean use_tree) throws HDF5LibraryException
{
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_virtual_spatial_tree(dapl_id, use_tree) < 0) {
h5libraryError();
}
}
// public static void H5Pset_append_flush(long plist_id, int ndims, long[] boundary,
// H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException {}
// public static 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 ///////
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Size is <= 0.
* @exception NullPointerException
* expression is null.
*
**/
public static long H5Pget_data_transform(long plist_id, String[] expression, long size)
throws HDF5LibraryException, HDF5FunctionArgumentException, NullPointerException
{
if (expression == null || expression.length < 1) {
throw new NullPointerException("expression is null or has insufficient length");
}
if (size <= 0) {
throw new HDF5FunctionArgumentException("Size is <= 0");
}
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Pget_data_transform(plist_id, MemorySegment.NULL,
size)) < 0)
h5libraryError();
}
String xpression = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment xpression_segment = arena.allocate(buf_size + 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_data_transform(plist_id, xpression_segment,
buf_size + 1) < 0)
h5libraryError();
xpression = xpression_segment.getString(0, StandardCharsets.UTF_8);
}
if (xpression == null) {
throw new HDF5LibraryException("Failed to retrieve data transform expression");
}
expression[0] = xpression;
return buf_size;
}
/**
* @ingroup JH5P
*
* 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 value if successful; otherwise returns a negative value.
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
* @exception NullPointerException
* expression is null.
*
**/
public static int H5Pset_data_transform(long plist_id, String expression)
throws HDF5LibraryException, NullPointerException
{
if (expression == null) {
throw new NullPointerException("expression is null");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment expression_segment = arena.allocateFrom(expression);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_data_transform(plist_id, expression_segment);
if (retVal < 0) {
h5libraryError();
}
}
return retVal;
}
/**
* @ingroup JH5P
*
* H5Pget_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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* plist is invalid.
* @exception NullPointerException
* tconv or bkg is null.
**/
public static int H5Pget_buffer(long plist, byte[] tconv, byte[] bkg)
throws HDF5LibraryException, HDF5FunctionArgumentException, NullPointerException
{
if (tconv == null || bkg == null || tconv.length < 1 || bkg.length < 1) {
throw new NullPointerException("tconv or bkg is null or has insufficient length");
}
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment tconv_segment = arena.allocate(tconv.length);
MemorySegment bkg_segment = arena.allocate(bkg.length);
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Pget_buffer(plist, tconv_segment, bkg_segment)) <
0)
h5libraryError();
tconv = tconv_segment.toArray(ValueLayout.JAVA_BYTE);
bkg = bkg_segment.toArray(ValueLayout.JAVA_BYTE);
}
return (int)buf_size;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* plist is invalid.
**/
public static long H5Pget_buffer_size(long plist)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
long buf_size = -1;
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Pget_buffer(plist, MemorySegment.NULL,
MemorySegment.NULL)) < 0)
h5libraryError();
return buf_size;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* plist is invalid.
**/
public static void H5Pset_buffer_size(long plist, long size)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (size < 0) {
throw new HDF5FunctionArgumentException("size must be non-negative");
}
int retVal =
org.hdfgroup.javahdf5.hdf5_h.H5Pset_buffer(plist, size, MemorySegment.NULL, MemorySegment.NULL);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pget_edc_check(long plist) throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
int check = org.hdfgroup.javahdf5.hdf5_h.H5Pget_edc_check(plist);
if (check < 0)
h5libraryError();
return check;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException
{
if (plist < 0) {
throw new HDF5FunctionArgumentException("Negative property list identifier");
}
if (check < 0) {
throw new HDF5FunctionArgumentException("check must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_edc_check(plist, check);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
**/
public static int H5Pget_btree_ratios(long plist_id, double[] left, double[] middle, double[] right)
throws HDF5LibraryException, NullPointerException
{
int retVal = -1;
if (left == null || middle == null || right == null || left.length < 1 || middle.length < 1 ||
right.length < 1) {
throw new NullPointerException("one or more arrays are null or have insufficient length");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment left_segment = arena.allocate(ValueLayout.JAVA_DOUBLE, 1);
MemorySegment middle_segment = arena.allocate(ValueLayout.JAVA_DOUBLE, 1);
MemorySegment right_segment = arena.allocate(ValueLayout.JAVA_DOUBLE, 1);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_btree_ratios(plist_id, left_segment, middle_segment,
right_segment);
if (retVal < 0)
h5libraryError();
left[0] = left_segment.get(ValueLayout.JAVA_DOUBLE, 0);
middle[0] = middle_segment.get(ValueLayout.JAVA_DOUBLE, 0);
right[0] = right_segment.get(ValueLayout.JAVA_DOUBLE, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
**/
public static int H5Pset_btree_ratios(long plist_id, double left, double middle, double right)
throws HDF5LibraryException
{
if (left < 0.0 || middle < 0.0 || right < 0.0) {
throw new HDF5FunctionArgumentException("left, middle or right must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_btree_ratios(plist_id, left, middle, right);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* vector_size is null.
*
**/
public static int H5Pget_hyper_vector_size(long dxpl_id, long[] vector_size)
throws HDF5LibraryException, NullPointerException
{
int retVal = -1;
if (vector_size == null || vector_size.length < 1) {
throw new NullPointerException("vector_size is null or has insufficient length");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment vector_size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_hyper_vector_size(dxpl_id, vector_size_segment);
if (retVal < 0)
h5libraryError();
vector_size[0] = vector_size_segment.get(ValueLayout.JAVA_LONG, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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.
** 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 HDF5 Library. * **/ public static int H5Pset_hyper_vector_size(long dxpl_id, long vector_size) throws HDF5LibraryException { if (vector_size <= 1) { throw new HDF5FunctionArgumentException("vector_size must be greater than 1"); } int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_hyper_vector_size(dxpl_id, vector_size); if (retVal < 0) { h5libraryError(); } return retVal; } // /////// Link creation property list (LCPL) routines /////// /** * @ingroup JH5P * * 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 HDF5 Library. * **/ public static boolean H5Pget_create_intermediate_group(long lcpl_id) throws HDF5LibraryException { boolean crt_intermed_group = false; try (Arena arena = Arena.ofConfined()) { MemorySegment crt_intermed_group_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1); if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_create_intermediate_group(lcpl_id, crt_intermed_group_segment) < 0) h5libraryError(); crt_intermed_group = crt_intermed_group_segment.get(ValueLayout.JAVA_BOOLEAN, 0); } return crt_intermed_group; } /** * @ingroup JH5P * * 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 value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * Error from the HDF5 Library. * **/ public static int H5Pset_create_intermediate_group(long lcpl_id, boolean crt_intermed_group) throws HDF5LibraryException { int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_create_intermediate_group( lcpl_id, crt_intermed_group ? 1 : 0); if (retVal < 0) { h5libraryError(); } return retVal; } // /////// Group creation property list (GCPL) routines /////// /** * @ingroup JH5P * * 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 HDF5 Library. * **/ public static long H5Pget_local_heap_size_hint(long gcpl_id) throws HDF5LibraryException { long size_hint = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment size_hint_segment = arena.allocate(ValueLayout.JAVA_LONG, 1); if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_local_heap_size_hint(gcpl_id, size_hint_segment) < 0) h5libraryError(); size_hint = size_hint_segment.get(ValueLayout.JAVA_LONG, 0); } return size_hint; } /** * @ingroup JH5P * * 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 HDF5 Library. * **/ public static int H5Pset_local_heap_size_hint(long gcpl_id, long size_hint) throws HDF5LibraryException { if (size_hint < 0) { throw new HDF5FunctionArgumentException("size_hint must be non-negative"); } int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_local_heap_size_hint(gcpl_id, size_hint); if (retVal < 0) { h5libraryError(); } return retVal; } /** * @ingroup JH5P * * 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 HDF5 Library.
* @exception NullPointerException
* size is null.
*
**/
public static int H5Pget_link_phase_change(long gcpl_id, int[] links)
throws HDF5LibraryException, NullPointerException
{
int retVal = -1;
if (links == null || links.length < 2) {
throw new NullPointerException("links is null or has insufficient length");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment compact_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment dense_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_link_phase_change(gcpl_id, compact_segment,
dense_segment);
if (retVal < 0)
h5libraryError();
links[0] = compact_segment.get(ValueLayout.JAVA_INT, 0);
links[1] = dense_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid values of max_compact and min_dense.
*
**/
public static int H5Pset_link_phase_change(long gcpl_id, int max_compact, int min_dense)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (max_compact < 0 || min_dense < 0) {
throw new HDF5FunctionArgumentException("max_compact and min_dense must be non-negative");
}
if (max_compact < min_dense) {
throw new HDF5FunctionArgumentException("max_compact must be greater than or equal to min_dense");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_link_phase_change(gcpl_id, max_compact, min_dense);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* link_info is null.
*
**/
public static int H5Pget_est_link_info(long gcpl_id, int[] link_info)
throws HDF5LibraryException, NullPointerException
{
int retVal = -1;
if (link_info == null || link_info.length < 2) {
throw new NullPointerException("link_info is null or has insufficient length");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment est_num_entries_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment est_name_len_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_est_link_info(gcpl_id, est_num_entries_segment,
est_name_len_segment);
if (retVal < 0)
h5libraryError();
link_info[0] = est_num_entries_segment.get(ValueLayout.JAVA_INT, 0);
link_info[1] = est_name_len_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid values to est_num_entries and est_name_len.
*
**/
public static int H5Pset_est_link_info(long gcpl_id, int est_num_entries, int est_name_len)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (est_num_entries < 0 || est_name_len < 0) {
throw new HDF5FunctionArgumentException("est_num_entries and est_name_len must be non-negative");
}
int retVal =
org.hdfgroup.javahdf5.hdf5_h.H5Pset_est_link_info(gcpl_id, est_num_entries, est_name_len);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pget_link_creation_order(long gcpl_id) throws HDF5LibraryException
{
int crt_order_flags = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment crt_order_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_link_creation_order(gcpl_id, crt_order_segment) < 0)
h5libraryError();
crt_order_flags = crt_order_segment.get(ValueLayout.JAVA_INT, 0);
}
if (crt_order_flags < 0)
h5libraryError();
return crt_order_flags;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_link_creation_order(long gcpl_id, int crt_order_flags)
throws HDF5LibraryException
{
if (crt_order_flags < 0) {
throw new HDF5FunctionArgumentException("crt_order_flags must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_link_creation_order(gcpl_id, crt_order_flags);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
// /////// String creation property list (STRCPL) routines ///////
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pget_char_encoding(long plist_id) throws HDF5LibraryException
{
int encoding = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment encoding_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_char_encoding(plist_id, encoding_segment) < 0)
h5libraryError();
encoding = encoding_segment.get(ValueLayout.JAVA_INT, 0);
}
if (encoding < 0)
h5libraryError();
return encoding;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static void H5Pset_char_encoding(long plist_id, int encoding) throws HDF5LibraryException
{
if (encoding < 0) {
throw new HDF5FunctionArgumentException("encoding must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_char_encoding(plist_id, encoding);
if (retVal < 0) {
h5libraryError();
}
}
// /////// Link access property list (LAPL) routines ///////
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static long H5Pget_nlinks(long lapl_id) throws HDF5LibraryException
{
long nlinks = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment nlinks_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_nlinks(lapl_id, nlinks_segment) < 0)
h5libraryError();
nlinks = nlinks_segment.get(ValueLayout.JAVA_LONG, 0);
}
if (nlinks < 0)
h5libraryError();
return nlinks;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Argument is Illegal
*
**/
public static int H5Pset_nlinks(long lapl_id, long nlinks)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (nlinks < 0) {
throw new HDF5FunctionArgumentException("nlinks must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_nlinks(lapl_id, nlinks);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* prefix is null.
*
**/
public static long H5Pget_elink_prefix(long lapl_id, String[] prefix)
throws HDF5LibraryException, NullPointerException
{
if (prefix == null || prefix.length < 1) {
throw new NullPointerException("prefix is null or has insufficient length");
}
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Pget_elink_prefix(lapl_id, MemorySegment.NULL, 0);
if (buf_size < 0)
h5libraryError();
MemorySegment prefix_segment = arena.allocate(buf_size + 1);
buf_size =
org.hdfgroup.javahdf5.hdf5_h.H5Pget_elink_prefix(lapl_id, prefix_segment, buf_size + 1);
if (buf_size < 0)
h5libraryError();
prefix[0] = prefix_segment.getString(0, StandardCharsets.UTF_8);
}
return buf_size;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* prefix is null.
*
**/
public static int H5Pset_elink_prefix(long lapl_id, String prefix)
throws HDF5LibraryException, NullPointerException
{
if (prefix == null) {
throw new NullPointerException("prefix is null");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment prefix_segment = arena.allocateFrom(prefix);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_elink_prefix(lapl_id, prefix_segment);
if (retVal < 0) {
h5libraryError();
}
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static long H5Pget_elink_fapl(long lapl_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_elink_fapl(long lapl_id, long fapl_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_elink_fapl(lapl_id, fapl_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pget_elink_acc_flags(long lapl_id) throws HDF5LibraryException
{
int flags = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment flags_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_elink_acc_flags(lapl_id, flags_segment) < 0)
h5libraryError();
flags = flags_segment.get(ValueLayout.JAVA_INT, 0);
}
if (flags < 0)
h5libraryError();
return flags;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception HDF5FunctionArgumentException
* Invalid Flag values.
*
**/
public static int H5Pset_elink_acc_flags(long lapl_id, int flags)
throws HDF5LibraryException, HDF5FunctionArgumentException
{
if (flags < 0) {
throw new HDF5FunctionArgumentException("flags must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_elink_acc_flags(lapl_id, flags);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
// /////// Object copy property list (OCPYPL) routines ///////
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pget_copy_object(long ocp_plist_id) throws HDF5LibraryException
{
int copy_options = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment copy_options_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_copy_object(ocp_plist_id, copy_options_segment) < 0)
h5libraryError();
copy_options = copy_options_segment.get(ValueLayout.JAVA_INT, 0);
}
if (copy_options < 0)
h5libraryError();
return copy_options;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static void H5Pset_copy_object(long ocp_plist_id, int copy_options) throws HDF5LibraryException
{
if (copy_options < 0) {
throw new HDF5FunctionArgumentException("copy_options must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_copy_object(ocp_plist_id, copy_options);
if (retVal < 0) {
h5libraryError();
}
}
// /////// file drivers property list routines ///////
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* increment or backing_store is null.
*
**/
public static void H5Pget_fapl_core(long fapl_id, long[] increment, boolean[] backing_store)
throws HDF5LibraryException, NullPointerException
{
if (increment == null || increment.length < 1 || backing_store == null || backing_store.length < 1) {
throw new NullPointerException("increment or backing_store is null or has insufficient length");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment increment_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment backing_store_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pget_fapl_core(fapl_id, increment_segment,
backing_store_segment);
if (retVal < 0)
h5libraryError();
increment[0] = increment_segment.get(ValueLayout.JAVA_LONG, 0);
backing_store[0] = backing_store_segment.get(ValueLayout.JAVA_BOOLEAN, 0);
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_fapl_core(long fapl_id, long increment, boolean backing_store)
throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_fapl_core(fapl_id, increment, backing_store);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pget_fapl_direct(long fapl_id, long[] info) throws HDF5LibraryException
{
if (info == null || info.length < 3) {
throw new NullPointerException("info is null or has insufficient length (needs 3 elements)");
}
try {
// Use reflection to check if H5Pget_fapl_direct exists
java.lang.reflect.Method method = org.hdfgroup.javahdf5.hdf5_h.class.getMethod(
"H5Pget_fapl_direct", long.class, MemorySegment.class, MemorySegment.class,
MemorySegment.class);
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment alignment_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment block_size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment cbuf_size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((retVal = (int)method.invoke(null, fapl_id, alignment_segment, block_size_segment,
cbuf_size_segment)) < 0)
h5libraryError();
info[0] = alignment_segment.get(ValueLayout.JAVA_LONG, 0);
info[1] = block_size_segment.get(ValueLayout.JAVA_LONG, 0);
info[2] = cbuf_size_segment.get(ValueLayout.JAVA_LONG, 0);
}
return retVal;
}
catch (NoSuchMethodException e) {
throw new HDF5LibraryException(
"H5Pget_fapl_direct not available (Direct VFD not enabled in this build)");
}
catch (Exception e) {
throw new HDF5LibraryException("H5Pget_fapl_direct failed: " + e.getMessage());
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_fapl_direct(long fapl_id, long alignment, long block_size, long cbuf_size)
throws HDF5LibraryException
{
if (alignment < 0 || block_size < 0 || cbuf_size < 0) {
throw new HDF5FunctionArgumentException(
"alignment, block_size, and cbuf_size must be non-negative");
}
try {
// Use reflection to check if H5Pset_fapl_direct exists
java.lang.reflect.Method method = org.hdfgroup.javahdf5.hdf5_h.class.getMethod(
"H5Pset_fapl_direct", long.class, long.class, long.class, long.class);
int retVal = (int)method.invoke(null, fapl_id, alignment, block_size, cbuf_size);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
catch (NoSuchMethodException e) {
throw new HDF5LibraryException(
"H5Pset_fapl_direct not available (Direct VFD not enabled in this build)");
}
catch (Exception e) {
throw new HDF5LibraryException("H5Pset_fapl_direct failed: " + e.getMessage());
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* memb_size or memb_fapl_id is null.
*
**/
public static int H5Pget_fapl_family(long fapl_id, long[] memb_size, long[] memb_fapl_id)
throws HDF5LibraryException, NullPointerException
{
if (memb_size == null || memb_size.length < 1 || memb_fapl_id == null || memb_fapl_id.length < 1) {
throw new NullPointerException("memb_size or memb_fapl_id is null or has insufficient length");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment memb_size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
MemorySegment memb_fapl_id_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((org.hdfgroup.javahdf5.hdf5_h.H5Pget_fapl_family(fapl_id, memb_size_segment,
memb_fapl_id_segment)) < 0)
h5libraryError();
memb_size[0] = memb_size_segment.get(ValueLayout.JAVA_LONG, 0);
memb_fapl_id[0] = memb_fapl_id_segment.get(ValueLayout.JAVA_LONG, 0);
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_fapl_family(long fapl_id, long memb_size, long memb_fapl_id)
throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_fapl_family(fapl_id, memb_size, memb_fapl_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_fapl_hdfs(long fapl_id, Object fapl_conf)
throws HDF5LibraryException, NullPointerException
{
try {
// Check if H5Pset_fapl_hdfs exists using reflection
java.lang.reflect.Method method = org.hdfgroup.javahdf5.hdf5_h.class.getMethod(
"H5Pset_fapl_hdfs", long.class, MemorySegment.class);
// Method exists, but struct conversion not yet implemented
throw new HDF5LibraryException("H5Pset_fapl_hdfs struct conversion not yet implemented for FFM");
}
catch (NoSuchMethodException e) {
throw new HDF5LibraryException(
"H5Pset_fapl_hdfs not available (HDFS VFD not enabled in this build)");
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static Object H5Pget_fapl_hdfs(long fapl_id) throws HDF5LibraryException
{
try {
// Check if H5Pget_fapl_hdfs exists using reflection
java.lang.reflect.Method method = org.hdfgroup.javahdf5.hdf5_h.class.getMethod(
"H5Pget_fapl_hdfs", long.class, MemorySegment.class);
// Method exists, but struct conversion not yet implemented
throw new HDF5LibraryException("H5Pget_fapl_hdfs struct conversion not yet implemented for FFM");
}
catch (NoSuchMethodException e) {
throw new HDF5LibraryException(
"H5Pget_fapl_hdfs not available (HDFS VFD not enabled in this build)");
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* an array is null.
*
**/
public static boolean H5Pget_fapl_multi(long fapl_id, int[] memb_map, long[] memb_fapl,
String[] memb_name, long[] memb_addr)
throws HDF5LibraryException, NullPointerException
{
boolean relax = false; // Default to false
try (Arena arena = Arena.ofConfined()) {
MemorySegment map_segment = MemorySegment.NULL;
if (memb_map != null)
map_segment = arena.allocate(ValueLayout.JAVA_INT, HDF5Constants.H5FD_MEM_NTYPES);
MemorySegment fapl_segment = MemorySegment.NULL;
if (memb_fapl != null)
fapl_segment = arena.allocate(ValueLayout.JAVA_LONG, HDF5Constants.H5FD_MEM_NTYPES);
MemorySegment name_segment = MemorySegment.NULL;
if (memb_name != null) {
SequenceLayout stringArrayLayout =
MemoryLayout.sequenceLayout(HDF5Constants.H5FD_MEM_NTYPES, ValueLayout.ADDRESS);
name_segment = arena.allocate(stringArrayLayout, HDF5Constants.H5FD_MEM_NTYPES);
for (int i = 0; i < memb_name.length; i++) {
// allocateFrom converts the Java string to a null-terminated C string in off-heap memory
MemorySegment cString = MemorySegment.NULL;
if (memb_name[i] != null)
cString = arena.allocateFrom(memb_name[i], StandardCharsets.UTF_8);
// Store the address of the C string in the 'pointers' segment
name_segment.setAtIndex(ValueLayout.ADDRESS, i, cString);
}
}
MemorySegment addr_segment = MemorySegment.NULL;
if (memb_addr != null)
addr_segment = arena.allocate(ValueLayout.JAVA_LONG, HDF5Constants.H5FD_MEM_NTYPES);
MemorySegment relax_segment = arena.allocate(ValueLayout.JAVA_BOOLEAN, 1);
relax_segment.set(ValueLayout.JAVA_BOOLEAN, 0, relax); // Default to false
if (org.hdfgroup.javahdf5.hdf5_h.H5Pget_fapl_multi(fapl_id, map_segment, fapl_segment,
name_segment, addr_segment, relax_segment) < 0)
h5libraryError();
if (memb_map != null)
MemorySegment.copy(map_segment, ValueLayout.JAVA_INT, 0L, memb_map, 0,
HDF5Constants.H5FD_MEM_NTYPES);
if (memb_fapl != null)
MemorySegment.copy(fapl_segment, ValueLayout.JAVA_LONG, 0L, memb_fapl, 0,
HDF5Constants.H5FD_MEM_NTYPES);
if (memb_addr != null)
MemorySegment.copy(addr_segment, ValueLayout.JAVA_LONG, 0L, memb_addr, 0,
HDF5Constants.H5FD_MEM_NTYPES);
if (memb_name != null) {
for (int i = 0; i < HDF5Constants.H5FD_MEM_NTYPES; i++) {
MemorySegment cStringSegment = name_segment.getAtIndex(ValueLayout.ADDRESS, i);
memb_name[i] = null;
if (cStringSegment.address() != 0)
memb_name[i] = cStringSegment.reinterpret(Integer.MAX_VALUE)
.getString(0, StandardCharsets.UTF_8);
}
}
relax = relax_segment.get(ValueLayout.JAVA_BOOLEAN, 0); // Default to false
}
return relax;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* an array is null.
*
**/
public static void H5Pset_fapl_multi(long fapl_id, int[] memb_map, long[] memb_fapl, String[] memb_name,
long[] memb_addr, boolean relax)
throws HDF5LibraryException, NullPointerException
{
try (Arena arena = Arena.ofConfined()) {
MemorySegment memb_map_segment = MemorySegment.NULL;
if (memb_map != null)
memb_map_segment = arena.allocateFrom(ValueLayout.JAVA_INT, memb_map);
MemorySegment memb_fapl_segment = MemorySegment.NULL;
if (memb_fapl != null)
memb_fapl_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, memb_fapl);
MemorySegment memb_name_segment = MemorySegment.NULL;
if (memb_name != null) {
memb_name_segment = arena.allocate(ValueLayout.ADDRESS, memb_name.length);
for (int i = 0; i < memb_name.length; i++) {
// allocateFrom converts the Java string to a null-terminated C string in off-heap memory
MemorySegment cString = MemorySegment.NULL;
if (memb_name[i] != null)
cString = arena.allocateFrom(memb_name[i], StandardCharsets.UTF_8);
// Store the address of the C string in the 'pointers' segment
memb_name_segment.setAtIndex(ValueLayout.ADDRESS, i, cString);
}
}
MemorySegment memb_addr_segment = MemorySegment.NULL;
if (memb_addr != null)
memb_addr_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, memb_addr);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_fapl_multi(fapl_id, memb_map_segment, memb_fapl_segment,
memb_name_segment, memb_addr_segment,
relax) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* logfile is null.
**/
public static void H5Pset_fapl_log(long fapl_id, String logfile, long flags, long buf_size)
throws HDF5LibraryException, NullPointerException
{
if (logfile == null) {
throw new NullPointerException("logfile is null");
}
if (buf_size < 0) {
throw new HDF5FunctionArgumentException("buf_size must be non-negative");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment logfile_segment = arena.allocateFrom(logfile);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_fapl_log(fapl_id, logfile_segment, flags, buf_size) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_fapl_sec2(long fapl_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_fapl_sec2(fapl_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
* @exception NullPointerException
* meta_ext or raw_ext is null.
*
**/
public static void H5Pset_fapl_split(long fapl_id, String meta_ext, long meta_plist_id, String raw_ext,
long raw_plist_id) throws HDF5LibraryException, NullPointerException
{
if (meta_ext == null || raw_ext == null) {
throw new NullPointerException("meta_ext or raw_ext is null");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment meta_ext_segment = arena.allocateFrom(meta_ext);
MemorySegment raw_ext_segment = arena.allocateFrom(raw_ext);
if (org.hdfgroup.javahdf5.hdf5_h.H5Pset_fapl_split(fapl_id, meta_ext_segment, meta_plist_id,
raw_ext_segment, raw_plist_id) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_fapl_stdio(long fapl_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pset_fapl_stdio(fapl_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_fapl_windows(long fapl_id) throws HDF5LibraryException
{
try {
// Use reflection to check if H5Pset_fapl_windows exists
java.lang.reflect.Method method =
org.hdfgroup.javahdf5.hdf5_h.class.getMethod("H5Pset_fapl_windows", long.class);
int retVal = (int)method.invoke(null, fapl_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
catch (NoSuchMethodException e) {
throw new HDF5LibraryException(
"H5Pset_fapl_windows not available (Windows VFD not enabled in this build)");
}
catch (Exception e) {
throw new HDF5LibraryException("H5Pset_fapl_windows failed: " + e.getMessage());
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static int H5Pset_fapl_ros3(long fapl_id, hdf.hdf5lib.structs.H5FD_ros3_fapl_t fapl_conf)
throws HDF5LibraryException, NullPointerException
{
if (fapl_conf == null) {
throw new NullPointerException("fapl_conf is null");
}
try {
// Use reflection to access FFM ROS3 classes (they may not exist if ROS3 disabled)
Class ros3Class = Class.forName("org.hdfgroup.javahdf5.H5FD_ros3_fapl_t");
Class hdf5Class = org.hdfgroup.javahdf5.hdf5_h.class;
// Get method handles via reflection
java.lang.reflect.Method h5psetMethod =
hdf5Class.getMethod("H5Pset_fapl_ros3", long.class, MemorySegment.class);
java.lang.reflect.Method allocateMethod = ros3Class.getMethod("allocate", SegmentAllocator.class);
java.lang.reflect.Method versionMethod =
ros3Class.getMethod("version", MemorySegment.class, int.class);
java.lang.reflect.Method authenticateMethod =
ros3Class.getMethod("authenticate", MemorySegment.class, boolean.class);
java.lang.reflect.Method awsRegionMethod = ros3Class.getMethod("aws_region", MemorySegment.class);
java.lang.reflect.Method secretIdMethod = ros3Class.getMethod("secret_id", MemorySegment.class);
java.lang.reflect.Method secretKeyMethod = ros3Class.getMethod("secret_key", MemorySegment.class);
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate FFM struct using reflection
MemorySegment ffmConfig = (MemorySegment)allocateMethod.invoke(null, arena);
// Set version and authenticate fields
versionMethod.invoke(null, ffmConfig, fapl_conf.version);
authenticateMethod.invoke(null, ffmConfig, fapl_conf.authenticate);
// Get char array segments and copy strings
MemorySegment awsRegionSeg = (MemorySegment)awsRegionMethod.invoke(null, ffmConfig);
MemorySegment secretIdSeg = (MemorySegment)secretIdMethod.invoke(null, ffmConfig);
MemorySegment secretKeySeg = (MemorySegment)secretKeyMethod.invoke(null, ffmConfig);
copyStringToCharArray(arena, fapl_conf.aws_region, awsRegionSeg, 33);
copyStringToCharArray(arena, fapl_conf.secret_id, secretIdSeg, 129);
copyStringToCharArray(arena, fapl_conf.secret_key, secretKeySeg, 129);
// Call native H5Pset_fapl_ros3
retVal = (int)h5psetMethod.invoke(null, fapl_id, ffmConfig);
if (retVal < 0) {
h5libraryError();
}
}
return retVal;
}
catch (ClassNotFoundException e) {
throw new HDF5LibraryException(
"H5Pset_fapl_ros3 not available (ros3 VFD not enabled in this build)");
}
catch (NoSuchMethodException e) {
throw new HDF5LibraryException(
"H5Pset_fapl_ros3 not available (ros3 VFD not enabled in this build)");
}
catch (java.lang.reflect.InvocationTargetException e) {
Throwable cause = e.getCause();
if (cause instanceof HDF5LibraryException) {
throw (HDF5LibraryException)cause;
}
throw new HDF5LibraryException("H5Pset_fapl_ros3 failed: " + e.getMessage());
}
catch (Exception e) {
throw new HDF5LibraryException("H5Pset_fapl_ros3 failed: " + e.getMessage());
}
}
/**
* @ingroup JH5P
*
* 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 HDF5 Library.
*
**/
public static hdf.hdf5lib.structs.H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id)
throws HDF5LibraryException, NullPointerException
{
try {
// Use reflection to access FFM ROS3 classes (they may not exist if ROS3 disabled)
Class ros3Class = Class.forName("org.hdfgroup.javahdf5.H5FD_ros3_fapl_t");
Class hdf5Class = org.hdfgroup.javahdf5.hdf5_h.class;
// Get method handles via reflection
java.lang.reflect.Method h5pgetMethod =
hdf5Class.getMethod("H5Pget_fapl_ros3", long.class, MemorySegment.class);
java.lang.reflect.Method allocateMethod = ros3Class.getMethod("allocate", SegmentAllocator.class);
java.lang.reflect.Method versionGetMethod = ros3Class.getMethod("version", MemorySegment.class);
java.lang.reflect.Method authenticateGetMethod =
ros3Class.getMethod("authenticate", MemorySegment.class);
java.lang.reflect.Method awsRegionMethod = ros3Class.getMethod("aws_region", MemorySegment.class);
java.lang.reflect.Method secretIdMethod = ros3Class.getMethod("secret_id", MemorySegment.class);
java.lang.reflect.Method secretKeyMethod = ros3Class.getMethod("secret_key", MemorySegment.class);
hdf.hdf5lib.structs.H5FD_ros3_fapl_t faplConfig = new hdf.hdf5lib.structs.H5FD_ros3_fapl_t();
try (Arena arena = Arena.ofConfined()) {
// Allocate FFM struct using reflection
MemorySegment ffmConfig = (MemorySegment)allocateMethod.invoke(null, arena);
// Call native H5Pget_fapl_ros3
int status = (int)h5pgetMethod.invoke(null, fapl_id, ffmConfig);
if (status < 0) {
h5libraryError();
}
// Extract version and authenticate fields
faplConfig.version = (int)versionGetMethod.invoke(null, ffmConfig);
faplConfig.authenticate = (boolean)authenticateGetMethod.invoke(null, ffmConfig);
// Get char array segments and extract strings
MemorySegment awsRegionSeg = (MemorySegment)awsRegionMethod.invoke(null, ffmConfig);
MemorySegment secretIdSeg = (MemorySegment)secretIdMethod.invoke(null, ffmConfig);
MemorySegment secretKeySeg = (MemorySegment)secretKeyMethod.invoke(null, ffmConfig);
faplConfig.aws_region = extractStringFromCharArray(awsRegionSeg);
faplConfig.secret_id = extractStringFromCharArray(secretIdSeg);
faplConfig.secret_key = extractStringFromCharArray(secretKeySeg);
}
return faplConfig;
}
catch (ClassNotFoundException e) {
throw new HDF5LibraryException(
"H5Pget_fapl_ros3 not available (ros3 VFD not enabled in this build)");
}
catch (NoSuchMethodException e) {
throw new HDF5LibraryException(
"H5Pget_fapl_ros3 not available (ros3 VFD not enabled in this build)");
}
catch (java.lang.reflect.InvocationTargetException e) {
Throwable cause = e.getCause();
if (cause instanceof HDF5LibraryException) {
throw (HDF5LibraryException)cause;
}
throw new HDF5LibraryException("H5Pget_fapl_ros3 failed: " + e.getMessage());
}
catch (Exception e) {
throw new HDF5LibraryException("H5Pget_fapl_ros3 failed: " + e.getMessage());
}
}
// /////// 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 //
// //
// ////////////////////////////////////////////////////////////
/**
* @defgroup JH5PL Java Plugin (H5PL) Interface
*
* @see H5PL, C-API
*
* @see @ref H5PL_UG, User Guide
**/
/**
* @ingroup JH5PL
*
* 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 HDF5 Library.
**/
public static void H5PLset_loading_state(int plugin_flags) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5PLset_loading_state(plugin_flags);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5PL
*
* 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 HDF5 Library.
**/
public static int H5PLget_loading_state() throws HDF5LibraryException
{
int plugin_flags = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment flags_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5PLget_loading_state(flags_segment) < 0)
h5libraryError();
plugin_flags = flags_segment.get(ValueLayout.JAVA_INT, 0);
}
if (plugin_flags < 0) {
h5libraryError();
}
return plugin_flags;
}
/**
* @ingroup JH5PL
*
* 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 HDF5 Library.
* @exception NullPointerException
* plugin_path is null.
**/
public static void H5PLappend(String plugin_path) throws HDF5LibraryException, NullPointerException
{
if (plugin_path == null) {
throw new NullPointerException("plugin_path cannot be null");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment path_segment = arena.allocateFrom(plugin_path);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5PLappend(path_segment);
if (retVal < 0) {
h5libraryError();
}
}
}
/**
* @ingroup JH5PL
*
* 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 HDF5 Library.
* @exception NullPointerException
* plugin_path is null.
**/
public static void H5PLprepend(String plugin_path) throws HDF5LibraryException, NullPointerException
{
if (plugin_path == null) {
throw new NullPointerException("plugin_path cannot be null");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment path_segment = arena.allocateFrom(plugin_path);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5PLprepend(path_segment);
if (retVal < 0) {
h5libraryError();
}
}
}
/**
* @ingroup JH5PL
*
* 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 HDF5 Library.
* @exception NullPointerException
* plugin_path is null.
**/
public static void H5PLreplace(String plugin_path, int index)
throws HDF5LibraryException, NullPointerException
{
if (plugin_path == null) {
throw new NullPointerException("plugin_path cannot be null");
}
if (index < 0) {
throw new HDF5FunctionArgumentException("index must be non-negative");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment path_segment = arena.allocateFrom(plugin_path);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5PLreplace(path_segment, index);
if (retVal < 0) {
h5libraryError();
}
}
}
/**
* @ingroup JH5PL
*
* 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 HDF5 Library.
* @exception NullPointerException
* plugin_path is null.
**/
public static void H5PLinsert(String plugin_path, int index)
throws HDF5LibraryException, NullPointerException
{
if (plugin_path == null) {
throw new NullPointerException("plugin_path cannot be null");
}
if (index < 0) {
throw new HDF5FunctionArgumentException("index must be non-negative");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment path_segment = arena.allocateFrom(plugin_path);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5PLinsert(path_segment, index);
if (retVal < 0) {
h5libraryError();
}
}
}
/**
* @ingroup JH5PL
*
* H5PLremove removes the plugin path at the specified index.
*
* @param index
* IN: The table index (0-based).
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static void H5PLremove(int index) throws HDF5LibraryException
{
if (index < 0) {
throw new HDF5FunctionArgumentException("index must be non-negative");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5PLremove(index);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5PL
*
* 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 HDF5 Library.
**/
public static String H5PLget(int index) throws HDF5LibraryException
{
long buf_size = -1;
if (index < 0) {
throw new HDF5FunctionArgumentException("index must be non-negative");
}
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5PLget(index, MemorySegment.NULL, 0)) < 0)
h5libraryError();
String plugin_path = null;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment path_segment = arena.allocate(buf_size + 1);
/* Get the attribute name */
if (org.hdfgroup.javahdf5.hdf5_h.H5PLget(index, path_segment, buf_size + 1) < 0)
h5libraryError();
plugin_path = path_segment.getString(0, StandardCharsets.UTF_8);
}
return plugin_path;
}
/**
* @ingroup JH5PL
*
* 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 HDF5 Library.
**/
public static int H5PLsize() throws HDF5LibraryException
{
int size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5PLsize(size_segment) < 0)
h5libraryError();
size = size_segment.get(ValueLayout.JAVA_INT, 0);
}
if (size < 0) {
h5libraryError();
}
return size;
}
// ////////////////////////////////////////////////////////////
// //
// H5R: HDF5 1.8 Reference API Functions //
// //
// ////////////////////////////////////////////////////////////
/**
* @defgroup JH5R Java Reference (H5R) Interface
*
* @see H5R, C-API
*
* @see @ref H5R_UG, User Guide
* @deprecated As of HDF5 1.12.0 in favor of H5Rcreate_object(), H5Rcreate_region() and H5Rcreate_attr()
**/
@Deprecated
private static int H5Rcreate(byte[] ref, long loc_id, String name, int ref_type, long space_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (name == null) {
throw new NullPointerException("name is null");
}
if (ref == null) {
throw new NullPointerException("ref is null");
}
if ((ref_type == org.hdfgroup.javahdf5.hdf5_h.H5R_OBJECT() &&
ref.length != org.hdfgroup.javahdf5.hdf5_h.H5R_OBJ_REF_BUF_SIZE()) ||
(ref_type == org.hdfgroup.javahdf5.hdf5_h.H5R_DATASET_REGION() &&
ref.length != org.hdfgroup.javahdf5.hdf5_h.H5R_DSET_REG_REF_BUF_SIZE())) {
throw new HDF5FunctionArgumentException("ref length is invalid");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment = arena.allocateFrom(name);
MemorySegment ref_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Rcreate(ref_segment, loc_id, name_segment, ref_type,
space_id)) < 0)
h5libraryError();
// Read the data from the memory segment
for (int i = 0; i < ref.length; i++) {
ref[i] = ref_segment.get(ValueLayout.JAVA_BYTE, i);
}
}
return retVal;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
*
* @deprecated As of HDF5 1.12.0 in favor of H5Rcreate_object(), H5Rcreate_region() and H5Rcreate_attr()
**/
@Deprecated
public static byte[] H5Rcreate(long loc_id, String name, int ref_type, long space_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
byte rbuf[] = null;
if (ref_type == org.hdfgroup.javahdf5.hdf5_h.H5R_DATASET_REGION())
rbuf = new byte[(int)org.hdfgroup.javahdf5.hdf5_h.H5R_DSET_REG_REF_BUF_SIZE()];
else if (ref_type == org.hdfgroup.javahdf5.hdf5_h.H5R_OBJECT())
rbuf = new byte[(int)org.hdfgroup.javahdf5.hdf5_h.H5R_OBJ_REF_BUF_SIZE()];
else
throw new HDF5FunctionArgumentException("Invalid ref_type");
/* will raise an exception if fails */
hdf.hdf5lib.H5.H5Rcreate(rbuf, loc_id, name, ref_type, space_id);
return rbuf;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* output array is null.
* @exception HDF5FunctionArgumentException
* output array is invalid.
*
* @deprecated As of HDF5 1.12.0 in favor of H5Rcreate_object(), H5Rcreate_region() and H5Rcreate_attr()
**/
@Deprecated
public static long H5Rdereference(long dataset, long access_list, int ref_type, byte[] ref)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref == null) {
throw new NullPointerException("ref is null");
}
long id = H5I_INVALID_HID();
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref);
id = org.hdfgroup.javahdf5.hdf5_h.H5Rdereference2(dataset, access_list, ref_type, ref_segment);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Rdereference add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* size is null.
* @exception HDF5FunctionArgumentException
* Argument is illegal.
**/
public static long H5Rget_name(long loc_id, int ref_type, byte[] ref, String[] name, long size)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (name == null || size <= 0) {
throw new NullPointerException("name is null or size is invalid");
}
if (ref == null) {
throw new NullPointerException("ref is null");
}
if (ref.length != org.hdfgroup.javahdf5.hdf5_h.H5R_OBJ_REF_BUF_SIZE() &&
ref.length != org.hdfgroup.javahdf5.hdf5_h.H5R_DSET_REG_REF_BUF_SIZE()) {
throw new HDF5FunctionArgumentException("ref length is invalid");
}
long retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref);
MemorySegment name_segment = arena.allocateFrom(name[0]);
retVal =
org.hdfgroup.javahdf5.hdf5_h.H5Rget_name(loc_id, ref_type, ref_segment, name_segment, size);
if (retVal < 0)
h5libraryError();
// Read the data from the memory segment
name[0] = name_segment.getString(0, StandardCharsets.UTF_8);
}
return retVal;
}
/**
* @ingroup JH5R
*
* H5Rget_name_string 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.
*
* @return Returns the name if successful, returning null if no name is associated with
* the identifier.
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
* @exception NullPointerException
* size is null.
* @exception HDF5FunctionArgumentException
* Argument is illegal.
**/
public static String H5Rget_name_string(long loc_id, int ref_type, byte[] ref)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref == null) {
throw new NullPointerException("ref is null");
}
if (ref.length != org.hdfgroup.javahdf5.hdf5_h.H5R_OBJ_REF_BUF_SIZE() &&
ref.length != org.hdfgroup.javahdf5.hdf5_h.H5R_DSET_REG_REF_BUF_SIZE()) {
throw new HDF5FunctionArgumentException("ref length is invalid");
}
String name = null;
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref);
MemorySegment size_segment = arena.allocate(ValueLayout.JAVA_LONG, 1);
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Rget_name(loc_id, ref_type, ref_segment,
MemorySegment.NULL, 0)) < 0)
h5libraryError();
MemorySegment name_segment = arena.allocate(buf_size + 1); // +1 for null terminator
if (org.hdfgroup.javahdf5.hdf5_h.H5Rget_name(loc_id, ref_type, ref_segment, name_segment,
buf_size + 1) < 0)
h5libraryError();
// Read the data from the memory segment
name = name_segment.getString(0, StandardCharsets.UTF_8);
}
return name;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static int H5Rget_obj_type(long loc_id, int ref_type, byte ref[])
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref == null) {
throw new NullPointerException("ref is null");
}
int obj_type = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref);
MemorySegment obj_type_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Rget_obj_type2(loc_id, ref_type, ref_segment,
obj_type_segment) < 0)
h5libraryError();
obj_type = obj_type_segment.get(ValueLayout.JAVA_INT, 0);
}
return obj_type;
}
/**
* @ingroup JH5R
*
* 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 static int H5Rget_obj_type2(long loc_id, int ref_type, byte ref[], int[] obj_type)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref == null) {
throw new NullPointerException("ref is null");
}
throw new HDF5LibraryException("H5Rget_obj_type2 not implemented");
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static long H5Rget_region(long loc_id, int ref_type, byte[] ref)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref == null) {
throw new NullPointerException("ref is null");
}
long id = H5I_INVALID_HID();
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref);
id = org.hdfgroup.javahdf5.hdf5_h.H5Rget_region(loc_id, ref_type, ref_segment);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Rget_region add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
// ////////////////////////////////////////////////////////////
// //
// H5R: HDF5 1.12 Reference API Functions //
// //
// ////////////////////////////////////////////////////////////
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static byte[] H5Rcreate_object(long loc_id, String name, long access_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (name == null) {
throw new NullPointerException("name is null");
}
byte rbuf[] = new byte[org.hdfgroup.javahdf5.hdf5_h.H5R_REF_BUF_SIZE()];
try (Arena arena = Arena.ofConfined()) {
MemorySegment rbuf_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, rbuf);
MemorySegment name_segment = arena.allocateFrom(name);
if (org.hdfgroup.javahdf5.hdf5_h.H5Rcreate_object(loc_id, name_segment, access_id, rbuf_segment) <
0)
h5libraryError();
// Read the data from the memory segment
for (int i = 0; i < rbuf.length; i++) {
rbuf[i] = rbuf_segment.get(ValueLayout.JAVA_BYTE, i);
}
}
return rbuf;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static byte[] H5Rcreate_region(long loc_id, String name, long space_id, long access_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (name == null) {
throw new NullPointerException("name is null");
}
byte rbuf[] = new byte[org.hdfgroup.javahdf5.hdf5_h.H5R_REF_BUF_SIZE()];
try (Arena arena = Arena.ofConfined()) {
MemorySegment rbuf_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, rbuf);
MemorySegment name_segment = arena.allocateFrom(name);
if (org.hdfgroup.javahdf5.hdf5_h.H5Rcreate_region(loc_id, name_segment, space_id, access_id,
rbuf_segment) < 0)
h5libraryError();
// Read the data from the memory segment
for (int i = 0; i < rbuf.length; i++) {
rbuf[i] = rbuf_segment.get(ValueLayout.JAVA_BYTE, i);
}
}
return rbuf;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static byte[] H5Rcreate_attr(long loc_id, String name, String attr_name, long access_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (name == null || attr_name == null) {
throw new NullPointerException("name or attr_name is null");
}
byte rbuf[] = new byte[org.hdfgroup.javahdf5.hdf5_h.H5R_REF_BUF_SIZE()];
try (Arena arena = Arena.ofConfined()) {
MemorySegment rbuf_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, rbuf);
MemorySegment name_segment = arena.allocateFrom(name);
MemorySegment attr_name_segment = arena.allocateFrom(attr_name);
if (org.hdfgroup.javahdf5.hdf5_h.H5Rcreate_attr(loc_id, name_segment, attr_name_segment,
access_id, rbuf_segment) < 0)
h5libraryError();
// Read the data from the memory segment
for (int i = 0; i < rbuf.length; i++) {
rbuf[i] = rbuf_segment.get(ValueLayout.JAVA_BYTE, i);
}
}
return rbuf;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static void H5Rdestroy(byte[] ref_ptr)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref_ptr == null) {
throw new NullPointerException("ref_ptr is null");
}
if (ref_ptr.length != org.hdfgroup.javahdf5.hdf5_h.H5R_REF_BUF_SIZE()) {
throw new HDF5FunctionArgumentException("ref_ptr length is invalid");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_ptr_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref_ptr);
if (org.hdfgroup.javahdf5.hdf5_h.H5Rdestroy(ref_ptr_segment) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static int H5Rget_type(byte[] ref_ptr)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref_ptr == null) {
throw new NullPointerException("ref_ptr is null");
}
int ref_type = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_ptr_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref_ptr);
if ((ref_type = org.hdfgroup.javahdf5.hdf5_h.H5Rget_type(ref_ptr_segment)) < 0)
h5libraryError();
}
return ref_type;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static boolean H5Requal(byte[] ref1_ptr, byte[] ref2_ptr)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref1_ptr == null || ref2_ptr == null) {
throw new NullPointerException("ref1_ptr or ref2_ptr is null");
}
boolean equal = false;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref1_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref1_ptr);
MemorySegment ref2_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref2_ptr);
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Requal(ref1_segment, ref2_segment);
if (retVal < 0)
h5libraryError();
if (retVal > 0)
equal = true;
else
equal = false;
}
return equal;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static byte[] H5Rcopy(byte[] src_ref_ptr)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (src_ref_ptr == null) {
throw new NullPointerException("src_ref_ptr is null");
}
if (src_ref_ptr.length != org.hdfgroup.javahdf5.hdf5_h.H5R_REF_BUF_SIZE()) {
throw new HDF5FunctionArgumentException("src_ref_ptr length is invalid");
}
byte[] dest_ref_ptr = new byte[org.hdfgroup.javahdf5.hdf5_h.H5R_REF_BUF_SIZE()];
try (Arena arena = Arena.ofConfined()) {
MemorySegment src_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, src_ref_ptr);
MemorySegment dest_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, dest_ref_ptr);
if (org.hdfgroup.javahdf5.hdf5_h.H5Rcopy(src_segment, dest_segment) < 0)
h5libraryError();
}
return dest_ref_ptr;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref_ptr == null) {
throw new NullPointerException("ref_ptr is null");
}
long id = H5I_INVALID_HID();
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_ptr_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref_ptr);
id = org.hdfgroup.javahdf5.hdf5_h.H5Ropen_object(ref_ptr_segment, rapl_id, oapl_id);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Ropen_object add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref_ptr == null) {
throw new NullPointerException("ref_ptr is null");
}
long id = H5I_INVALID_HID();
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_ptr_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref_ptr);
id = org.hdfgroup.javahdf5.hdf5_h.H5Ropen_region(ref_ptr_segment, rapl_id, oapl_id);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Ropen_region add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* an input array is null.
* @exception HDF5FunctionArgumentException
* an input array is invalid.
**/
public static long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref_ptr == null) {
throw new NullPointerException("ref_ptr is null");
}
long id = H5I_INVALID_HID();
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_ptr_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref_ptr);
id = org.hdfgroup.javahdf5.hdf5_h.H5Ropen_attr(ref_ptr_segment, rapl_id, aapl_id);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Ropen_attr add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* array is null.
* @exception HDF5FunctionArgumentException
* array is invalid.
**/
public static int H5Rget_obj_type3(byte[] ref_ptr, long rapl_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref_ptr == null) {
throw new NullPointerException("ref_ptr is null");
}
int obj_type = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_ptr_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref_ptr);
MemorySegment obj_type_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if (org.hdfgroup.javahdf5.hdf5_h.H5Rget_obj_type3(ref_ptr_segment, rapl_id, obj_type_segment) < 0)
h5libraryError();
obj_type = obj_type_segment.get(ValueLayout.JAVA_INT, 0);
}
return obj_type;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* array is null.
* @exception HDF5FunctionArgumentException
* array is invalid.
**/
public static String H5Rget_file_name(byte[] ref_ptr)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref_ptr == null) {
throw new NullPointerException("ref_ptr is null");
}
String fileName = null;
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_ptr_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref_ptr);
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Rget_file_name(ref_ptr_segment, MemorySegment.NULL,
0)) < 0)
h5libraryError();
MemorySegment name_segment = arena.allocate(buf_size + 1); // +1 for null terminator
if (org.hdfgroup.javahdf5.hdf5_h.H5Rget_file_name(ref_ptr_segment, name_segment, buf_size + 1) <
0)
h5libraryError();
// Read the data from the memory segment
fileName = name_segment.getString(0, StandardCharsets.UTF_8);
}
return fileName;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* array is null.
* @exception HDF5FunctionArgumentException
* array is invalid.
**/
public static String H5Rget_obj_name(byte[] ref_ptr, long rapl_id)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref_ptr == null) {
throw new NullPointerException("ref_ptr is null");
}
String objName = null;
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_ptr_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref_ptr);
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Rget_obj_name(ref_ptr_segment, rapl_id,
MemorySegment.NULL, 0)) < 0)
h5libraryError();
MemorySegment name_segment = arena.allocate(buf_size + 1); // +1 for null terminator
if (org.hdfgroup.javahdf5.hdf5_h.H5Rget_obj_name(ref_ptr_segment, rapl_id, name_segment,
buf_size + 1) < 0)
h5libraryError();
// Read the data from the memory segment
objName = name_segment.getString(0, StandardCharsets.UTF_8);
}
return objName;
}
/**
* @ingroup JH5R
*
* 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 HDF5 Library.
* @exception NullPointerException
* array is null.
* @exception HDF5FunctionArgumentException
* array is invalid.
**/
public static String H5Rget_attr_name(byte[] ref_ptr)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (ref_ptr == null) {
throw new NullPointerException("ref_ptr is null");
}
String attrName = null;
long buf_size = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment ref_ptr_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, ref_ptr);
if ((buf_size = org.hdfgroup.javahdf5.hdf5_h.H5Rget_attr_name(ref_ptr_segment, MemorySegment.NULL,
0)) < 0)
h5libraryError();
MemorySegment name_segment = arena.allocate(buf_size + 1); // +1 for null terminator
if (org.hdfgroup.javahdf5.hdf5_h.H5Rget_attr_name(ref_ptr_segment, name_segment, buf_size + 1) <
0)
h5libraryError();
// Read the data from the memory segment
attrName = name_segment.getString(0, StandardCharsets.UTF_8);
}
return attrName;
}
// ////////////////////////////////////////////////////////////
// //
// H5S: Dataspace Interface Functions //
// //
// ////////////////////////////////////////////////////////////
/**
* @defgroup JH5S Java Dataspace (H5S) Interface
*
* @see H5S, C-API
*
* @see @ref H5S_UG, User Guide
**/
/**
* @defgroup JH5S Java Dataspace (H5S) Interface
**/
/**************** Operations on dataspaces ********************/
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static long H5Screate(int type) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.H5Screate(type);
if (id > 0) {
log.trace("OPEN_IDS: H5Screate add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
* @exception NullPointerException
* dims or maxdims is null.
**/
public static long H5Screate_simple(int rank, long[] dims, long[] maxdims)
throws HDF5Exception, NullPointerException
{
long id = H5I_INVALID_HID();
if (dims == null) {
throw new NullPointerException("Null dims array");
}
if (rank < 0) {
throw new HDF5FunctionArgumentException("Negative rank");
}
if (dims.length != rank) {
throw new HDF5FunctionArgumentException("Invalid dims array");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment dims_segment = arena.allocate(ValueLayout.JAVA_LONG, rank);
MemorySegment.copy((Object)dims, 0, dims_segment, ValueLayout.JAVA_LONG, 0, rank);
MemorySegment maxdims_segment = MemorySegment.NULL;
if (maxdims != null) {
maxdims_segment = arena.allocate(ValueLayout.JAVA_LONG, rank);
MemorySegment.copy((Object)maxdims, 0, maxdims_segment, ValueLayout.JAVA_LONG, 0, rank);
}
id = org.hdfgroup.javahdf5.hdf5_h.H5Screate_simple(rank, dims_segment, maxdims_segment);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Screate_simple add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static long H5Sset_extent_simple(long space_id, int rank, long[] current_size, long[] maximum_size)
throws HDF5LibraryException, NullPointerException
{
if (current_size == null || maximum_size == null) {
throw new NullPointerException("current_size or maximum_size is null");
}
if (current_size.length != rank || maximum_size.length != rank) {
throw new HDF5FunctionArgumentException("current_size or maximum_size length is invalid");
}
long id = H5I_INVALID_HID();
try (Arena arena = Arena.ofConfined()) {
MemorySegment cs_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, current_size);
MemorySegment maxs_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, maximum_size);
if ((id = org.hdfgroup.javahdf5.hdf5_h.H5Sset_extent_simple(space_id, rank, cs_segment,
maxs_segment)) < 0)
h5libraryError();
}
return id;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public 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 hdf.hdf5lib.H5.H5Sset_extent_simple(space_id, rank, lacs, lamaxs);
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static long H5Scopy(long space_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.H5Scopy(space_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Scopy add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5S
*
* H5Sclose releases a dataspace.
*
* @param space_id
* Identifier of dataspace to release.
*
* @return a non-negative value if successful
**/
public static int H5Sclose(long space_id)
{
log.trace("OPEN_IDS: H5Sclose remove {}", space_id);
OPEN_IDS.remove(space_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Sclose(space_id);
if (retVal < 0)
h5libraryError();
return retVal;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static byte[] H5Sencode(long obj_id) throws HDF5LibraryException
{
byte[] buf = null;
try (Arena arena = Arena.ofConfined()) {
// Allocate a buffer for the size
MemorySegment nalloc_segment = arena.allocate(ValueLayout.JAVA_LONG);
org.hdfgroup.javahdf5.hdf5_h.H5Sencode2(obj_id, MemorySegment.NULL, nalloc_segment,
H5P_DEFAULT());
long buf_size = nalloc_segment.get(ValueLayout.JAVA_LONG, 0);
MemorySegment buf_segment = arena.allocate(buf_size);
if (org.hdfgroup.javahdf5.hdf5_h.H5Sencode2(obj_id, buf_segment, nalloc_segment, H5P_DEFAULT()) <
0)
h5libraryError();
buf = buf_segment.toArray(ValueLayout.JAVA_BYTE);
}
if (buf == null || buf.length == 0) {
throw new HDF5LibraryException("Failed to encode dataspace");
}
return buf;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
* @exception NullPointerException
* buf is null.
**/
public static long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("buf is null");
}
long id = H5I_INVALID_HID();
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, buf);
id = org.hdfgroup.javahdf5.hdf5_h.H5Sdecode(buf_segment);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Sdecode add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException
{
long npoints = org.hdfgroup.javahdf5.hdf5_h.H5Sget_simple_extent_npoints(space_id);
if (npoints < 0) {
h5libraryError();
}
return npoints;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException
{
int ndims = org.hdfgroup.javahdf5.hdf5_h.H5Sget_simple_extent_ndims(space_id);
if (ndims < 0) {
h5libraryError();
}
return ndims;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
* @exception NullPointerException
* dims or maxdims is null.
**/
public static int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims)
throws HDF5LibraryException, NullPointerException
{
if (dims != null && dims.length < 0) {
throw new NullPointerException("dims length is invalid");
}
if (maxdims != null && maxdims.length < 0) {
throw new NullPointerException("maxdims length is invalid");
}
int ndims = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment dims_segment = MemorySegment.NULL;
if (dims != null)
dims_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, dims);
MemorySegment maxdims_segment = MemorySegment.NULL;
if (maxdims != null)
maxdims_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, maxdims);
if ((ndims = org.hdfgroup.javahdf5.hdf5_h.H5Sget_simple_extent_dims(space_id, dims_segment,
maxdims_segment)) < 0)
h5libraryError();
}
return ndims;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static boolean H5Sis_simple(long space_id) throws HDF5LibraryException
{
boolean isSimple = false;
int status = org.hdfgroup.javahdf5.hdf5_h.H5Sis_simple(space_id);
if (status < 0) {
h5libraryError();
}
isSimple = (status > 0);
return isSimple;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException
{
int type = org.hdfgroup.javahdf5.hdf5_h.H5Sget_simple_extent_type(space_id);
if (type < 0) {
h5libraryError();
}
return type;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static int H5Sset_extent_none(long space_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Sset_extent_none(space_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static int H5Sextent_copy(long dest_space_id, long source_space_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Sextent_copy(dest_space_id, source_space_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static boolean H5Sextent_equal(long first_space_id, long second_space_id)
throws HDF5LibraryException
{
boolean isEqual = false;
int status = org.hdfgroup.javahdf5.hdf5_h.H5Sextent_equal(first_space_id, second_space_id);
if (status < 0) {
h5libraryError();
}
isEqual = (status > 0);
return isEqual;
}
/***************** Operations on dataspace selections *****************/
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static int H5Sget_select_type(long space_id) throws HDF5LibraryException
{
int type = org.hdfgroup.javahdf5.hdf5_h.H5Sget_select_type(space_id);
if (type < 0) {
h5libraryError();
}
return type;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static long H5Sget_select_npoints(long space_id) throws HDF5LibraryException
{
long npoints = org.hdfgroup.javahdf5.hdf5_h.H5Sget_select_npoints(space_id);
if (npoints < 0) {
h5libraryError();
}
return npoints;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static void H5Sselect_copy(long dst_id, long src_id) throws HDF5LibraryException
{
if (org.hdfgroup.javahdf5.hdf5_h.H5Sselect_copy(dst_id, src_id) < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static boolean H5Sselect_valid(long space_id) throws HDF5LibraryException
{
boolean isValid = false;
int status = org.hdfgroup.javahdf5.hdf5_h.H5Sselect_valid(space_id);
if (status < 0) {
h5libraryError();
}
isValid = (status > 0);
return isValid;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
* @exception NullPointerException
* offset is null.
**/
public static void H5Sselect_adjust(long space_id, long[][] offset)
throws HDF5LibraryException, NullPointerException
{
if (offset == null) {
throw new NullPointerException("offset is null");
}
if (offset.length == 0 || offset[0].length == 0) {
throw new HDF5FunctionArgumentException("offset array is empty");
}
int rank = -1;
if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0)
h5libraryError();
if (offset.length != rank)
throw new HDF5FunctionArgumentException("offset array rank does not match rank");
try (Arena arena = Arena.ofConfined()) {
SequenceLayout offset_layout = MemoryLayout.sequenceLayout(
offset.length, MemoryLayout.sequenceLayout(offset[0].length, ValueLayout.JAVA_LONG));
MemorySegment offset_segment = arena.allocate(offset_layout);
for (int i = 0; i < offset.length; i++) {
MemorySegment row_segment =
offset_segment.asSlice(i * offset[0].length * Long.BYTES, offset[0].length * Long.BYTES);
for (int j = 0; j < offset[i].length; j++) {
row_segment.set(ValueLayout.JAVA_LONG, j * Long.BYTES, offset[i][j]);
}
}
if (org.hdfgroup.javahdf5.hdf5_h.H5Sselect_adjust(space_id, offset_segment) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library. * @exception NullPointerException * start or end is null. **/ public static int H5Sget_select_bounds(long space_id, long[] start, long[] end) throws HDF5LibraryException, NullPointerException { if (start == null || end == null) { throw new NullPointerException("Negative ID or null array"); } if (start.length != end.length) { throw new HDF5FunctionArgumentException("start and end length is invalid"); } int status = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment start_segment = arena.allocate(ValueLayout.JAVA_LONG, start.length); MemorySegment end_segment = arena.allocate(ValueLayout.JAVA_LONG, end.length); if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Sget_select_bounds(space_id, start_segment, end_segment)) < 0) h5libraryError(); MemorySegment.copy(start_segment, ValueLayout.JAVA_LONG, 0L, start, 0, start.length); MemorySegment.copy(end_segment, ValueLayout.JAVA_LONG, 0L, end, 0, end.length); } return status; } /** * @ingroup JH5S * * 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 HDF5 Library. **/ public static boolean H5Sselect_shape_same(long space1_id, long space2_id) throws HDF5LibraryException { boolean isSame = false; int status = org.hdfgroup.javahdf5.hdf5_h.H5Sselect_shape_same(space1_id, space2_id); if (status < 0) { h5libraryError(); } isSame = (status > 0); return isSame; } /** * @ingroup JH5S * * 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 HDF5 Library. * @exception NullPointerException * offset is null. **/ public static boolean H5Sselect_intersect_block(long space_id, long[] start, long[] end) throws HDF5LibraryException, NullPointerException { if (start == null || end == null) { throw new NullPointerException("start or end is null"); } if (start.length != end.length) { throw new HDF5FunctionArgumentException("start and end length is invalid"); } boolean isIntersect = false; int status = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment start_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, start); MemorySegment end_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, end); if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Sselect_intersect_block(space_id, start_segment, end_segment)) < 0) h5libraryError(); } isIntersect = (status > 0); return isIntersect; } /** * @ingroup JH5S * * 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 HDF5 Library. * @exception NullPointerException * offset array is null. **/ public static int H5Soffset_simple(long space_id, byte[] offset) throws HDF5LibraryException, NullPointerException { if (offset == null) { throw new NullPointerException("offset array is null"); } if (offset.length == 0) { throw new HDF5FunctionArgumentException("offset array is empty"); } int status = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment offset_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, offset); if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Soffset_simple(space_id, offset_segment)) < 0) h5libraryError(); } return status; } /** * @ingroup JH5S * * 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 HDF5 Library. * @exception NullPointerException * offset array is null. **/ public static int H5Soffset_simple(long space_id, long[] offset) throws HDF5Exception, NullPointerException { if (offset == null) throw new NullPointerException("offset array is null"); HDFArray theArray = new HDFArray(offset); byte[] theArr = theArray.byteify(); int retVal = H5Soffset_simple(space_id, theArr); theArr = null; theArray = null; return retVal; } /** * @ingroup JH5S * * 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 HDF5 Library. **/ public static int H5Sselect_all(long space_id) throws HDF5LibraryException { int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Sselect_all(space_id); if (retVal < 0) { h5libraryError(); } return retVal; } /** * @ingroup JH5S * * 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 HDF5 Library. **/ public static int H5Sselect_none(long space_id) throws HDF5LibraryException { int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Sselect_none(space_id); if (retVal < 0) { h5libraryError(); } return retVal; } /** * @ingroup JH5S * * 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 HDF5 Library. **/ private static int H5Sselect_elements(long space_id, int op, int num_elements, byte[] coord) throws HDF5LibraryException, NullPointerException { int retVal = -1; if (coord == null) { throw new NullPointerException("coord array is null"); } if (coord.length == 0) { throw new HDF5FunctionArgumentException("coord array is empty"); } try (Arena arena = Arena.ofConfined()) { MemorySegment coord_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, coord); if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Sselect_elements(space_id, op, (long)num_elements, coord_segment)) < 0) h5libraryError(); } return retVal; } /** * @ingroup JH5S * * 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 HDF5 Library. * @exception NullPointerException * cord array is **/ public static int H5Sselect_elements(long space_id, int op, int num_elements, long[][] coord2D) throws HDF5Exception, HDF5LibraryException, NullPointerException { if (coord2D == null) throw new NullPointerException("coord2D array is null"); if (coord2D.length != num_elements) throw new HDF5FunctionArgumentException("coord2D length does not match num_elements"); int rows = coord2D.length; int cols = coord2D[0].length; int totalLongs = rows * cols; // Create a 1D long array to hold the flattened data. long[] flattenedArray = new long[totalLongs]; int index = 0; for (int i = 0; i < rows; i++) { System.arraycopy(coord2D[i], 0, flattenedArray, index, cols); index += cols; } ByteBuffer byteBuffer = ByteBuffer.allocate(flattenedArray.length * Long.BYTES); byteBuffer.order(ByteOrder.nativeOrder()); LongBuffer longBuffer = byteBuffer.asLongBuffer(); longBuffer.put(flattenedArray); byte[] coord = byteBuffer.array(); int retVal = H5Sselect_elements(space_id, op, num_elements, coord); coord = null; return retVal; } /** * @ingroup JH5S * * 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 HDF5 Library. **/ public static long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException { if (spaceid < 0) { throw new HDF5FunctionArgumentException("Negative ID"); } long npoints = org.hdfgroup.javahdf5.hdf5_h.H5Sget_select_elem_npoints(spaceid); if (npoints < 0) { h5libraryError(); } return npoints; } /** * @ingroup JH5S * * 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 HDF5 Library. * @exception NullPointerException * buf is null. **/ public static int H5Sget_select_elem_pointlist(long spaceid, long startpoint, long numpoints, long[] buf) throws HDF5LibraryException, NullPointerException { if (buf == null) { throw new NullPointerException("buf is null"); } if (spaceid < 0) { throw new HDF5FunctionArgumentException("Negative ID"); } if (buf.length == 0) { throw new HDF5FunctionArgumentException("buf array is empty"); } int rank = -1; if ((rank = H5Sget_simple_extent_ndims(spaceid)) < 0) h5libraryError(); if (rank == 0) rank = 1; if (buf.length < (numpoints * rank)) throw new HDF5FunctionArgumentException("buffer input array too small"); int status = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_LONG, numpoints * rank); if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Sget_select_elem_pointlist( spaceid, startpoint, numpoints, buf_segment)) < 0) h5libraryError(); MemorySegment.copy(buf_segment, ValueLayout.JAVA_LONG, 0L, buf, 0, (int)numpoints * rank); } return status; } /** * @ingroup JH5S * * 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 HDF5 Library. * @exception NullPointerException * an input array is null. * @exception HDF5FunctionArgumentException * an input array is invalid. **/ public static int H5Sselect_hyperslab(long space_id, int op, byte[] start, byte[] stride, byte[] count, byte[] block) throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException { 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); } /** * @ingroup JH5S * * 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 HDF5 Library. * @exception NullPointerException * an input array is null. * @exception HDF5FunctionArgumentException * an input array is invalid. **/ public static int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException { if (start == null || count == null) { throw new NullPointerException("start, stride, count, or block is null"); } if (start.length != count.length) { throw new HDF5FunctionArgumentException("start, stride, count, and block length is invalid"); } int status = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment start_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, start); MemorySegment count_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, count); MemorySegment stride_segment = MemorySegment.NULL; if (stride != null) { stride_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, stride); } MemorySegment block_segment = MemorySegment.NULL; if (block != null) { block_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, block); } if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Sselect_hyperslab( space_id, op, start_segment, stride_segment, count_segment, block_segment)) < 0) h5libraryError(); } return status; } /** * @ingroup JH5S * * 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 HDF5 Library. * @exception NullPointerException * an input array is null. * @exception HDF5FunctionArgumentException * an input array is invalid. **/ public static long H5Scombine_hyperslab(long space_id, int op, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException { if (start == null || count == null) { throw new NullPointerException("start or count is null"); } if (start.length != count.length) { throw new HDF5FunctionArgumentException("startand count length is invalid"); } if (stride != null && start.length != stride.length) throw new HDF5FunctionArgumentException("start and stride length is invalid"); if (block != null && start.length != block.length) throw new HDF5FunctionArgumentException("start and block length is invalid"); long retVal = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment start_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, start); MemorySegment count_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, count); MemorySegment stride_segment = MemorySegment.NULL; if (stride != null) { stride_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, stride); } MemorySegment block_segment = MemorySegment.NULL; if (block != null) { block_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, block); } retVal = org.hdfgroup.javahdf5.hdf5_h.H5Scombine_hyperslab( space_id, op, start_segment, stride_segment, count_segment, block_segment); if (retVal < 0) { h5libraryError(); } } return retVal; } /** * @ingroup JH5S * * 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 HDF5 Library. **/ public static void H5Smodify_select(long space1_id, int op, long space2_id) throws HDF5LibraryException { if (org.hdfgroup.javahdf5.hdf5_h.H5Smodify_select(space1_id, op, space2_id) < 0) { h5libraryError(); } } /** * @ingroup JH5S * * 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 HDF5 Library. **/ public static long H5Scombine_select(long space1_id, int op, long space2_id) throws HDF5LibraryException { long retVal = org.hdfgroup.javahdf5.hdf5_h.H5Scombine_select(space1_id, op, space2_id); if (retVal < 0) { h5libraryError(); } return retVal; } /** * @ingroup JH5S * * 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 HDF5 Library. **/ public static boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException { boolean isRegular = false; int status = org.hdfgroup.javahdf5.hdf5_h.H5Sis_regular_hyperslab(space_id); if (status < 0) { h5libraryError(); } isRegular = (status > 0); return isRegular; } /** * @ingroup JH5S * * 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 HDF5 Library. * @exception NullPointerException * an output array is null. * @exception HDF5FunctionArgumentException * an output array is invalid. **/ public static void H5Sget_regular_hyperslab(long space_id, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException { int rank = -1; if ((rank = H5Sget_simple_extent_ndims(space_id)) < 0) h5libraryError(); try (Arena arena = Arena.ofConfined()) { MemorySegment start_segment = MemorySegment.NULL; if (start != null) start_segment = arena.allocate(ValueLayout.JAVA_LONG, rank); MemorySegment count_segment = MemorySegment.NULL; if (count != null) count_segment = arena.allocate(ValueLayout.JAVA_LONG, rank); MemorySegment stride_segment = MemorySegment.NULL; if (stride != null) stride_segment = arena.allocate(ValueLayout.JAVA_LONG, rank); MemorySegment block_segment = MemorySegment.NULL; if (block != null) block_segment = arena.allocate(ValueLayout.JAVA_LONG, rank); if (org.hdfgroup.javahdf5.hdf5_h.H5Sget_regular_hyperslab(space_id, start_segment, stride_segment, count_segment, block_segment) < 0) h5libraryError(); MemorySegment.copy(start_segment, ValueLayout.JAVA_LONG, 0L, start, 0, start.length); MemorySegment.copy(count_segment, ValueLayout.JAVA_LONG, 0L, count, 0, count.length); MemorySegment.copy(stride_segment, ValueLayout.JAVA_LONG, 0L, stride, 0, stride.length); MemorySegment.copy(block_segment, ValueLayout.JAVA_LONG, 0L, block, 0, block.length); } } /** * @ingroup JH5S * * 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 HDF5 Library. **/ public static long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException { if (spaceid < 0) { throw new HDF5FunctionArgumentException("Negative ID"); } long nblocks = org.hdfgroup.javahdf5.hdf5_h.H5Sget_select_hyper_nblocks(spaceid); if (nblocks < 0) { h5libraryError(); } return nblocks; } /** * @ingroup JH5S * * 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 HDF5 Library.
* @exception NullPointerException
* buf is null.
**/
public static int H5Sget_select_hyper_blocklist(long spaceid, long startblock, long numblocks, long[] buf)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("buf is null");
}
if (spaceid < 0) {
throw new HDF5FunctionArgumentException("Negative ID or null buf");
}
if (buf.length == 0) {
throw new HDF5FunctionArgumentException("buf array is empty");
}
int rank = -1;
if ((rank = H5Sget_simple_extent_ndims(spaceid)) < 0)
h5libraryError();
if (rank == 0)
rank = 1;
if (buf.length < (numblocks * rank))
throw new HDF5FunctionArgumentException("buffer input array too small");
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_segment = arena.allocate(ValueLayout.JAVA_LONG, numblocks * rank * 2);
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Sget_select_hyper_blocklist(
spaceid, startblock, numblocks, buf_segment)) < 0)
h5libraryError();
MemorySegment.copy(buf_segment, ValueLayout.JAVA_LONG, 0L, buf, 0, (int)numblocks * rank * 2);
}
return status;
}
/**
* @ingroup JH5S
*
* 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 HDF5 Library.
**/
public static long H5Sselect_project_intersection(long src_space_id, long dst_space_id,
long src_intersect_space_id) throws HDF5LibraryException
{
long retVal = org.hdfgroup.javahdf5.hdf5_h.H5Sselect_project_intersection(src_space_id, dst_space_id,
src_intersect_space_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
// /////// unimplemented ////////
///// Operations on dataspace selections /////
//
///// Operations on dataspace selection iterators /////
// public static H5Ssel_iter_create(hid_t spaceid, size_t elmt_size, unsigned
// flags); public static 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 static H5Ssel_iter_reset(hid_t sel_iter_id, hid_t space_id);
// public static H5Ssel_iter_close(hid_t sel_iter_id);
// ////////////////////////////////////////////////////////////
// //
// H5T: Datatype Interface Functions //
// //
// ////////////////////////////////////////////////////////////
/**
* @defgroup JH5T Java Datatype (H5T) Interface
*
* @see H5T, C-API
*
* @see @ref H5T_UG, User Guide
**/
/**
* @defgroup JH5T Java Datatype (H5T) Interface
**/
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* dim is null.
**/
public static long H5Tarray_create(long base_id, int ndims, long[] dim)
throws HDF5LibraryException, NullPointerException
{
if (dim == null)
throw new NullPointerException("dim is null");
long id = HDF5Constants.H5I_INVALID_HID;
try (Arena arena = Arena.ofConfined()) {
MemorySegment dim_segment = arena.allocateFrom(ValueLayout.JAVA_LONG, dim);
id = org.hdfgroup.javahdf5.hdf5_h.H5Tarray_create2(base_id, ndims, dim_segment);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Tarray_create add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* H5Tclose releases a datatype.
*
* @param type_id
* IN: Identifier of datatype to release.
*
* @return a non-negative value if successful
**/
public static int H5Tclose(long type_id)
{
log.trace("OPEN_IDS: H5Tclose remove {}", type_id);
OPEN_IDS.remove(type_id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tclose(type_id);
if (retVal < 0)
h5libraryError();
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static void H5Tcommit(long loc_id, String name, long type_id, long lcpl_id, long tcpl_id,
long tapl_id) throws HDF5LibraryException, NullPointerException
{
if (name == null) {
throw new NullPointerException("name is null");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment = arena.allocateFrom(name);
if (org.hdfgroup.javahdf5.hdf5_h.H5Tcommit2(loc_id, name_segment, type_id, lcpl_id, tcpl_id,
tapl_id) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static void H5Tcommit_anon(long loc_id, long type_id, long tcpl_id, long tapl_id)
throws HDF5LibraryException
{
if (org.hdfgroup.javahdf5.hdf5_h.H5Tcommit_anon(loc_id, type_id, tcpl_id, tapl_id) < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static boolean H5Tcommitted(long type_id) throws HDF5LibraryException
{
boolean isCommitted = false;
int result = org.hdfgroup.javahdf5.hdf5_h.H5Tcommitted(type_id);
if (result < 0) {
h5libraryError();
}
else if (result > 0) {
isCommitted = true;
}
else {
isCommitted = false;
}
return isCommitted;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static boolean H5Tcompiler_conv(long src_id, long dst_id) throws HDF5LibraryException
{
boolean hardconvert = false;
int result = org.hdfgroup.javahdf5.hdf5_h.H5Tcompiler_conv(src_id, dst_id);
if (result < 0) {
h5libraryError();
}
else if (result > 0) {
hardconvert = true;
}
else {
hardconvert = false;
}
return hardconvert;
}
/**
* @ingroup JH5T
*
* H5Tcomplex_create creates a new complex number datatype object.
*
* @param base_id
* IN: Datatype identifier for the complex number base datatype.
* Must be a floating-point datatype.
*
* @return a valid datatype identifier
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static long H5Tcomplex_create(long base_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.H5Tcomplex_create(base_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Tcomplex_create add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* buf is null.
**/
public static void H5Tconvert(long src_id, long dst_id, long nelmts, byte[] buf, byte[] background,
long plist_id) throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("buf is null");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, buf);
MemorySegment background_segment = MemorySegment.NULL;
if (background != null)
background_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, background);
if (org.hdfgroup.javahdf5.hdf5_h.H5Tconvert(src_id, dst_id, nelmts, buf_segment,
background_segment, plist_id) < 0)
h5libraryError();
for (int i = 0; i < buf.length; i++) {
buf[i] = buf_segment.get(ValueLayout.JAVA_BYTE, i);
}
}
}
// int H5Tconvert(int src_id, int dst_id, long nelmts, Pointer buf, Pointer background, int plist_id);
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static long H5Tcopy(long type_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.H5Tcopy(type_id);
if (id > 0) {
log.trace("OPEN_IDS: H5Tcopy add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* H5Tcreate creates a new datatype 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 HDF5 Library.
**/
public static long H5Tcreate(int tclass, long size) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.H5Tcreate(tclass, size);
if (id > 0) {
log.trace("OPEN_IDS: H5Tcreate add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* 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.
*
* @param buf_size
* IN: Size of the buffer.
*
* @return a new object handle
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
* @exception NullPointerException
* buf is null.
**/
public static long H5Tdecode(byte[] buf, long buf_size) throws HDF5LibraryException, NullPointerException
{
long id = H5I_INVALID_HID();
if (buf == null) {
throw new NullPointerException("buf is null");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment buf_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, buf);
id = org.hdfgroup.javahdf5.hdf5_h.H5Tdecode2(buf_segment, buf_size);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Tdecode add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static boolean H5Tdetect_class(long type_id, int cls) throws HDF5LibraryException
{
boolean isClass = false;
int result = org.hdfgroup.javahdf5.hdf5_h.H5Tdetect_class(type_id, cls);
if (result < 0) {
h5libraryError();
}
else if (result > 0) {
isClass = true;
}
else {
isClass = false;
}
return isClass;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* buf is null.
**/
public static int H5Tencode(long obj_id, byte[] buf, long nalloc)
throws HDF5LibraryException, NullPointerException
{
if (buf == null) {
throw new NullPointerException("buf is null");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a buffer for the size
MemorySegment nalloc_segment = arena.allocate(ValueLayout.JAVA_LONG);
org.hdfgroup.javahdf5.hdf5_h.H5Tencode(obj_id, MemorySegment.NULL, nalloc_segment);
MemorySegment buf_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, buf);
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Tencode(obj_id, buf_segment, nalloc_segment)) < 0)
h5libraryError();
nalloc = nalloc_segment.get(ValueLayout.JAVA_LONG, 0);
}
return status;
}
// /*
// * @ingroup JH5T
// *
// * 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 HDF5 Library.
// **/
// public static byte[] H5Tencode(int obj_id)
// throws HDF5LibraryException {}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static long H5Tenum_create(long base_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static void H5Tenum_insert(long type, String name, byte[] value)
throws HDF5LibraryException, NullPointerException
{
if (name == null) {
throw new NullPointerException("name is null");
}
if (value == null) {
throw new NullPointerException("value is null");
}
if (type < 0) {
throw new HDF5FunctionArgumentException("Negative type id value");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment = arena.allocateFrom(name);
MemorySegment value_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, value);
if (org.hdfgroup.javahdf5.hdf5_h.H5Tenum_insert(type, name_segment, value_segment) < 0)
h5libraryError();
}
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static int H5Tenum_insert(long type, String name, int[] value)
throws HDF5LibraryException, NullPointerException
{
if (value == null) {
throw new NullPointerException("value is null");
}
return hdf.hdf5lib.H5.H5Tenum_insert_int(type, name, value);
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static int H5Tenum_insert(long type, String name, int value)
throws HDF5LibraryException, NullPointerException
{
int[] val = {value};
return hdf.hdf5lib.H5.H5Tenum_insert_int(type, name, val);
}
private static int H5Tenum_insert_int(long type, String name, int[] intvalue)
throws HDF5LibraryException, NullPointerException
{
if (name == null) {
throw new NullPointerException("name is null");
}
if (intvalue == null) {
throw new NullPointerException("intvalue is null");
}
if (type < 0) {
throw new HDF5FunctionArgumentException("Negative type id value");
}
byte[] byteArray = new byte[intvalue.length * 4]; // Each int is 4 bytes
for (int i = 0; i < intvalue.length; i++) {
int value = intvalue[i];
// Extract bytes using bit shifts and store them in the byte array
byteArray[i * 4] = (byte)((value >> 24) & 0xFF);
byteArray[i * 4 + 1] = (byte)((value >> 16) & 0xFF);
byteArray[i * 4 + 2] = (byte)((value >> 8) & 0xFF);
byteArray[i * 4 + 3] = (byte)(value & 0xFF);
}
hdf.hdf5lib.H5.H5Tenum_insert(type, name, byteArray);
return 0;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* value is null.
**/
public static String H5Tenum_nameof(long type, byte[] value, long size)
throws HDF5LibraryException, NullPointerException
{
if (value == null) {
throw new NullPointerException("value is null");
}
if (type < 0) {
throw new HDF5FunctionArgumentException("Negative type id value");
}
String name = new String();
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment = arena.allocate(size + 1);
MemorySegment value_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, value);
if (org.hdfgroup.javahdf5.hdf5_h.H5Tenum_nameof(type, value_segment, name_segment, size) < 0)
h5libraryError();
name = name_segment.getString(0, StandardCharsets.UTF_8);
}
return name;
}
// int H5Tenum_nameof(int type, Pointer value, Buffer name/* out */, long size);
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static int H5Tenum_nameof(long type, int[] value, String[] name, int size)
throws HDF5LibraryException, NullPointerException
{
if (value == null) {
throw new NullPointerException("value is null");
}
if (type < 0) {
throw new HDF5FunctionArgumentException("Negative type id value");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment = arena.allocate(size + 1);
MemorySegment value_segment = arena.allocateFrom(ValueLayout.JAVA_INT, value);
if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Tenum_nameof(type, value_segment, name_segment,
size)) < 0)
h5libraryError();
name[0] = name_segment.getString(0, StandardCharsets.UTF_8);
}
return status;
}
private static int H5Tenum_nameof_int(long type, int[] value, String[] name, int size)
throws HDF5LibraryException, NullPointerException
{
return hdf.hdf5lib.H5.H5Tenum_nameof(type, value, name, size);
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static void H5Tenum_valueof(long type, String name, byte[] value)
throws HDF5LibraryException, NullPointerException
{
if (name == null) {
throw new NullPointerException("name is null");
}
if (value == null) {
throw new NullPointerException("value is null");
}
if (type < 0) {
throw new HDF5FunctionArgumentException("Negative type id value");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment = arena.allocateFrom(name);
MemorySegment value_segment = arena.allocate(ValueLayout.JAVA_BYTE, value.length);
if (org.hdfgroup.javahdf5.hdf5_h.H5Tenum_valueof(type, name_segment, value_segment) < 0)
h5libraryError();
MemorySegment.copy(value_segment, ValueLayout.JAVA_BYTE, 0L, value, 0, value.length);
}
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static int H5Tenum_valueof(long type, String name, int[] value)
throws HDF5LibraryException, NullPointerException
{
hdf.hdf5lib.H5.H5Tenum_valueof_int(type, name, value);
return 0;
}
private static int H5Tenum_valueof_int(long type, String name, int[] value)
throws HDF5LibraryException, NullPointerException
{
if (name == null) {
throw new NullPointerException("name is null");
}
if (value == null) {
throw new NullPointerException("value is null");
}
if (type < 0) {
throw new HDF5FunctionArgumentException("Negative type id value");
}
byte[] byteArray = new byte[value.length * 4]; // Each int is 4 bytes
hdf.hdf5lib.H5.H5Tenum_valueof(type, name, byteArray);
ByteBuffer buffer = ByteBuffer.wrap(byteArray);
for (int i = 0; i < value.length; i++) {
value[i] = buffer.getInt();
}
return 0;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static boolean H5Tequal(long type_id1, long type_id2) throws HDF5LibraryException
{
if (type_id1 < 0 || type_id2 < 0) {
throw new HDF5FunctionArgumentException("Negative type id value");
}
boolean isEqual = false;
int result = org.hdfgroup.javahdf5.hdf5_h.H5Tequal(type_id1, type_id2);
if (result < 0) {
h5libraryError();
}
else if (result > 0) {
isEqual = true;
}
else {
isEqual = false;
}
return isEqual;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* dims is null.
**/
public static int H5Tget_array_dims(long type_id, long[] dims)
throws HDF5LibraryException, NullPointerException
{
return hdf.hdf5lib.H5.H5Tget_array_dims2(type_id, dims);
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* dims is null.
**/
public static int H5Tget_array_dims2(long type_id, long[] dims)
throws HDF5LibraryException, NullPointerException
{
if (dims == null) {
throw new NullPointerException("dims is null");
}
int ndims = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment dims_segment = arena.allocate(ValueLayout.JAVA_LONG, dims.length);
ndims = org.hdfgroup.javahdf5.hdf5_h.H5Tget_array_dims2(type_id, dims_segment);
if (ndims < 0)
h5libraryError();
for (int i = 0; i < ndims; i++)
dims[i] = dims_segment.get(ValueLayout.JAVA_LONG, i * Long.BYTES);
}
return ndims;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_array_ndims(long type_id) throws HDF5LibraryException
{
int ndims = org.hdfgroup.javahdf5.hdf5_h.H5Tget_array_ndims(type_id);
if (ndims < 0) {
h5libraryError();
}
return ndims;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_class(long type_id) throws HDF5LibraryException
{
int class_id = org.hdfgroup.javahdf5.hdf5_h.H5Tget_class(type_id);
if (class_id < 0) {
h5libraryError();
}
return class_id;
}
/**
* @ingroup JH5T
*
* 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 if (HDF5Constants.H5T_COMPLEX == class_id) /* Complex number types */
retValue = "H5T_COMPLEX";
else
retValue = "H5T_NO_CLASS";
return retValue;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static long H5Tget_create_plist(long type_id) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_cset(long type_id) throws HDF5LibraryException
{
int cset = org.hdfgroup.javahdf5.hdf5_h.H5Tget_cset(type_id);
if (cset < 0) {
h5libraryError();
}
return cset;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_cset(long type_id, int cset) throws HDF5LibraryException
{
if (cset < 0) {
throw new HDF5FunctionArgumentException("Negative character set value");
}
int status = org.hdfgroup.javahdf5.hdf5_h.H5Tset_cset(type_id, cset);
if (status < 0) {
h5libraryError();
}
return status;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_ebias(long type_id) throws HDF5LibraryException
{
int ebias = (int)hdf.hdf5lib.H5.H5Tget_ebias_long(type_id);
return ebias;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_ebias(long type_id, int ebias) throws HDF5LibraryException
{
int status = org.hdfgroup.javahdf5.hdf5_h.H5Tset_ebias(type_id, (long)ebias);
if (status < 0) {
h5libraryError();
}
return status;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static long H5Tget_ebias_long(long type_id) throws HDF5LibraryException
{
long ebias = org.hdfgroup.javahdf5.hdf5_h.H5Tget_ebias(type_id);
if (ebias == 0) {
h5libraryError();
}
return ebias;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static void H5Tset_ebias(long type_id, long ebias) throws HDF5LibraryException
{
int status = org.hdfgroup.javahdf5.hdf5_h.H5Tset_ebias(type_id, ebias);
if (status < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* fields is null.
* @exception HDF5FunctionArgumentException
* fields array is invalid.
**/
public static int H5Tget_fields(long type_id, int[] fields)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
return H5Tget_fields_int(type_id, fields);
}
private static int H5Tget_fields_int(long type_id, int[] fields)
throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException
{
if (fields == null) {
throw new NullPointerException("fields is null");
}
if (fields.length < 5) {
throw new HDF5FunctionArgumentException("fields array is invalid");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment spos_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment epos_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment esize_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment mpos_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment msize_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
status = org.hdfgroup.javahdf5.hdf5_h.H5Tget_fields(type_id, spos_segment, epos_segment,
esize_segment, mpos_segment, msize_segment);
if (status < 0)
h5libraryError();
fields[0] = spos_segment.get(ValueLayout.JAVA_INT, 0);
fields[1] = epos_segment.get(ValueLayout.JAVA_INT, 0);
fields[2] = esize_segment.get(ValueLayout.JAVA_INT, 0);
fields[3] = mpos_segment.get(ValueLayout.JAVA_INT, 0);
fields[4] = msize_segment.get(ValueLayout.JAVA_INT, 0);
}
return status;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static void H5Tset_fields(long type_id, long spos, long epos, long esize, long mpos, long msize)
throws HDF5LibraryException
{
int status = org.hdfgroup.javahdf5.hdf5_h.H5Tset_fields(type_id, spos, epos, esize, mpos, msize);
if (status < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_fields(long type_id, int spos, int epos, int esize, int mpos, int msize)
throws HDF5LibraryException
{
hdf.hdf5lib.H5.H5Tset_fields(type_id, (long)spos, (long)epos, (long)esize, (long)mpos, (long)msize);
return 0;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_inpad(long type_id) throws HDF5LibraryException
{
int inpad = org.hdfgroup.javahdf5.hdf5_h.H5Tget_inpad(type_id);
if (inpad < 0) {
h5libraryError();
}
return inpad;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_inpad(long type_id, int inpad) throws HDF5LibraryException
{
int status = org.hdfgroup.javahdf5.hdf5_h.H5Tset_inpad(type_id, inpad);
if (status < 0) {
h5libraryError();
}
return status;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_member_class(long type_id, int membno) throws HDF5LibraryException
{
int classId = org.hdfgroup.javahdf5.hdf5_h.H5Tget_member_class(type_id, membno);
if (classId < 0) {
h5libraryError();
}
return classId;
}
/**
* @ingroup JH5T
*
* H5Tget_member_index retrieves the index of a field of a compound datatype.
*
* @param type_id
* IN: Identifier of datatype to query.
* @param field_name
* IN: Field name of the field index to retrieve.
*
* @return if field is defined, the index; else negative.
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static int H5Tget_member_index(long type_id, String field_name) throws HDF5LibraryException
{
if (field_name == null) {
throw new NullPointerException("field_name is null");
}
int index = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment field_name_segment = arena.allocateFrom(field_name);
index = org.hdfgroup.javahdf5.hdf5_h.H5Tget_member_index(type_id, field_name_segment);
}
if (index < 0) {
h5libraryError();
}
return index;
}
/**
* @ingroup JH5T
*
* H5Tget_member_name retrieves the name of a field of a compound datatype or an element of an enumeration
* datatype.
*
* @param type_id
* IN: Identifier of datatype to query.
* @param field_idx
* IN: Field index (0-based) of the field name to retrieve.
*
* @return a valid pointer to the name if successful; otherwise null.
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static String H5Tget_member_name(long type_id, int field_idx) throws HDF5LibraryException
{
String name = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment = org.hdfgroup.javahdf5.hdf5_h.H5Tget_member_name(type_id, field_idx);
if (name_segment == null)
h5libraryError();
name = name_segment.getString(0, StandardCharsets.UTF_8);
}
return name;
}
/**
* @ingroup JH5T
*
* H5Tget_member_offset returns the byte offset of the specified member of the compound datatype. This is
* the byte offset in the HDF5 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.
**/
public static long H5Tget_member_offset(long type_id, int membno)
{
long offset = org.hdfgroup.javahdf5.hdf5_h.H5Tget_member_offset(type_id, membno);
if (offset < 0) {
h5libraryError();
}
return offset;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static long H5Tget_member_type(long type_id, int field_idx) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* value is null.
**/
public static void H5Tget_member_value(long type_id, int membno, byte[] value)
throws HDF5LibraryException, NullPointerException
{
if (value == null) {
throw new NullPointerException("value is null");
}
if (value.length != 4) {
throw new HDF5FunctionArgumentException("value array must have length 4");
}
try (Arena arena = Arena.ofConfined()) {
MemorySegment value_segment = arena.allocate(value.length * ValueLayout.JAVA_BYTE.byteSize());
if (org.hdfgroup.javahdf5.hdf5_h.H5Tget_member_value(type_id, membno, value_segment) < 0)
h5libraryError();
for (int i = 0; i < value.length; i++) {
value[i] = value_segment.get(ValueLayout.JAVA_BYTE, i);
}
}
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* value is null.
**/
public static int H5Tget_member_value(long type_id, int membno, int[] value)
throws HDF5LibraryException, NullPointerException
{
return hdf.hdf5lib.H5.H5Tget_member_value_int(type_id, membno, value);
}
private static int H5Tget_member_value_int(long type_id, int membno, int[] value)
throws HDF5LibraryException, NullPointerException
{
if (value == null) {
throw new NullPointerException("value is null");
}
if (value.length != 1) {
throw new HDF5FunctionArgumentException("value array must have length 1");
}
int status = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment value_segment = arena.allocate(ValueLayout.JAVA_INT, value.length);
status = org.hdfgroup.javahdf5.hdf5_h.H5Tget_member_value(type_id, membno, value_segment);
if (status < 0)
h5libraryError();
for (int i = 0; i < value.length; i++) {
value[i] = value_segment.get(ValueLayout.JAVA_INT, i * Integer.BYTES);
}
}
return status;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static long H5Tget_native_type(long type_id) throws HDF5LibraryException
{
return hdf.hdf5lib.H5.H5Tget_native_type(type_id, HDF5Constants.H5T_DIR_ASCEND);
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static long H5Tget_native_type(long type_id, int direction) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_nmembers(long type_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tget_nmembers(type_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_norm(long type_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tget_norm(type_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_norm(long type_id, int norm) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tset_norm(type_id, norm);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_offset(long type_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tget_offset(type_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_offset(long type_id, int offset) throws HDF5LibraryException
{
hdf.hdf5lib.H5.H5Tset_offset(type_id, (long)offset);
return 0;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static void H5Tset_offset(long type_id, long offset) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tset_offset(type_id, offset);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_order(long type_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tget_order(type_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_order(long type_id, int order) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tset_order(type_id, order);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* pad is null.
**/
public static int H5Tget_pad(long type_id, int[] pad) throws HDF5LibraryException, NullPointerException
{
if (pad == null || pad.length < 2) {
throw new NullPointerException("pad is null or has less than 2 elements");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
// Allocate a MemorySegment to hold the string bytes
MemorySegment lsb_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
MemorySegment msb_segment = arena.allocate(ValueLayout.JAVA_INT, 1);
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tget_pad(type_id, lsb_segment, msb_segment)) < 0)
h5libraryError();
pad[0] = lsb_segment.get(ValueLayout.JAVA_INT, 0);
pad[1] = msb_segment.get(ValueLayout.JAVA_INT, 0);
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_pad(long type_id, int lsb, int msb) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tset_pad(type_id, lsb, msb);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_precision(long type_id) throws HDF5LibraryException
{
int retVal = (int)hdf.hdf5lib.H5.H5Tget_precision_long(type_id);
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_precision(long type_id, int precision) throws HDF5LibraryException
{
hdf.hdf5lib.H5.H5Tset_precision(type_id, (long)precision);
return 0;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static long H5Tget_precision_long(long type_id) throws HDF5LibraryException
{
long retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tget_precision(type_id);
if (retVal == 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static void H5Tset_precision(long type_id, long precision) throws HDF5LibraryException
{
if (precision < 0) {
throw new HDF5FunctionArgumentException("Negative precision value");
}
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tset_precision(type_id, precision);
if (retVal < 0) {
h5libraryError();
}
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_sign(long type_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tget_sign(type_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* H5Tset_sign sets the sign property 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 HDF5 Library.
**/
public static int H5Tset_sign(long type_id, int sign) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tset_sign(type_id, sign);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static long H5Tget_size(long type_id) throws HDF5FunctionArgumentException
{
long retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tget_size(type_id);
if (retVal == 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_size(long type_id, long size) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tset_size(type_id, size);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tget_strpad(long type_id) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tget_strpad(type_id);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_strpad(long type_id, int strpad) throws HDF5LibraryException
{
int retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tset_strpad(type_id, strpad);
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static long H5Tget_super(long type) throws HDF5LibraryException
{
long id = org.hdfgroup.javahdf5.hdf5_h.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());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* H5Tget_tag returns the tag associated with datatype type_id.
*
* @param type
* IN: Identifier of datatype.
*
* @return the tag
*
* @exception HDF5LibraryException
* Error from the HDF5 Library.
**/
public static String H5Tget_tag(long type) throws HDF5LibraryException
{
if (type < 0) {
throw new HDF5FunctionArgumentException("Negative type id value");
}
String tag = null;
try (Arena arena = Arena.ofConfined()) {
MemorySegment tag_segment = org.hdfgroup.javahdf5.hdf5_h.H5Tget_tag(type);
if (tag_segment != null) {
tag = tag_segment.getString(0, StandardCharsets.UTF_8);
}
}
if (tag == null) {
h5libraryError();
}
return tag;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tset_tag(long type, String tag) throws HDF5LibraryException
{
if (tag == null) {
throw new NullPointerException("tag is null");
}
if (type < 0) {
throw new HDF5FunctionArgumentException("Negative type id value");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment tag_segment = arena.allocateFrom(tag);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tset_tag(type, tag_segment);
}
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static int H5Tinsert(long type_id, String name, long offset, long field_id)
throws HDF5LibraryException, NullPointerException
{
if (name == null) {
throw new NullPointerException("name is null");
}
int retVal = -1;
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment = arena.allocateFrom(name);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tinsert(type_id, name_segment, offset, field_id);
}
if (retVal < 0) {
h5libraryError();
}
return retVal;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static boolean H5Tis_variable_str(long type_id) throws HDF5LibraryException
{
boolean is_vstr = false;
int retVal = -1;
if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5Tis_variable_str(type_id)) < 0)
h5libraryError();
if (retVal > 0) {
is_vstr = true;
}
return is_vstr;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
**/
public static int H5Tlock(long type_id) throws HDF5LibraryException
{
int ret = org.hdfgroup.javahdf5.hdf5_h.H5Tlock(type_id);
if (ret < 0) {
h5libraryError();
}
return ret;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library.
* @exception NullPointerException
* name is null.
**/
public static long H5Topen(long loc_id, String name, long tapl_id)
throws HDF5LibraryException, NullPointerException
{
if (name == null) {
throw new NullPointerException("name is null");
}
long id = H5I_INVALID_HID();
try (Arena arena = Arena.ofConfined()) {
MemorySegment name_segment = arena.allocateFrom(name);
id = org.hdfgroup.javahdf5.hdf5_h.H5Topen2(loc_id, name_segment, tapl_id);
}
if (id > 0) {
log.trace("OPEN_IDS: H5Topen add {}", id);
OPEN_IDS.add(id);
log.trace("OPEN_IDS: {}", OPEN_IDS.size());
}
else
h5libraryError();
return id;
}
/**
* @ingroup JH5T
*
* 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 HDF5 Library. **/ public static int H5Tpack(long type_id) throws HDF5LibraryException { int ret = org.hdfgroup.javahdf5.hdf5_h.H5Tpack(type_id); if (ret < 0) { h5libraryError(); } return ret; } /** * @ingroup JH5T * * 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 HDF5 Library. * @exception NullPointerException * buf is null. **/ public static void H5Treclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { if (buf == null) { throw new NullPointerException("buf is null"); } int retVal = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment buf_segment = arena.allocateFrom(ValueLayout.JAVA_BYTE, buf); retVal = org.hdfgroup.javahdf5.hdf5_h.H5Treclaim(type_id, space_id, xfer_plist_id, buf_segment); } if (retVal < 0) { h5libraryError(); } } /** * @ingroup JH5T * * H5Tvlen_create creates a new variable-length (VL) datatype. * * @param base_id * IN: Identifier of parent datatype. * * @return a non-negative value if successful * * @exception HDF5LibraryException * Error from the HDF5 Library. **/ public static long H5Tvlen_create(long base_id) throws HDF5LibraryException { long id = org.hdfgroup.javahdf5.hdf5_h.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()); } else h5libraryError(); return id; } /** * @ingroup JH5T * * 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 HDF5 Library. **/ public static void H5Tflush(long dtype_id) throws HDF5LibraryException { if (org.hdfgroup.javahdf5.hdf5_h.H5Tflush(dtype_id) < 0) { h5libraryError(); } } /** * @ingroup JH5T * * 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 HDF5 Library. **/ public static void H5Trefresh(long dtype_id) throws HDF5LibraryException { if (org.hdfgroup.javahdf5.hdf5_h.H5Trefresh(dtype_id) < 0) { h5libraryError(); } } // /////// unimplemented //////// // H5T_conv_t H5Tfind(int src_id, int dst_id, H5T_cdata_t *pcdata); // public static int H5Tregister(H5T_pers_t pers, String name, int src_id, int dst_id, // H5T_conv_t func) // throws HDF5LibraryException, NullPointerException {} // public static 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 // // // // //////////////////////////////////////////////////////////// /** * @defgroup JH5VL Java VOL Connector (H5VL) Interface * * @see H5VL, C-API * * @see @ref H5VL_UG, User Guide **/ /** * @defgroup JH5VL Java VOL Connector (H5VL) Interface **/ /** * @ingroup JH5VL * * 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 HDF5 Library. **/ public static long H5VLregister_connector_by_name(String connector_name, long vipl_id) throws HDF5LibraryException { long id = H5I_INVALID_HID(); if (connector_name == null) { throw new NullPointerException("Connector name cannot be null"); } try (Arena arena = Arena.ofConfined()) { MemorySegment connector_name_segment = arena.allocateFrom(connector_name); id = org.hdfgroup.javahdf5.hdf5_h.H5VLregister_connector_by_name(connector_name_segment, vipl_id); } if (id > 0) { log.trace("OPEN_IDS: H5VLregister_connector_by_name add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } else h5libraryError(); return id; } /** * @ingroup JH5VL * * 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 HDF5 Library. **/ public static long H5VLregister_connector_by_value(int connector_value, long vipl_id) throws HDF5LibraryException { long id = org.hdfgroup.javahdf5.hdf5_h.H5VLregister_connector_by_value(connector_value, vipl_id); if (id > 0) { log.trace("OPEN_IDS: H5VLregister_connector_by_value add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } else h5libraryError(); return id; } /** * @ingroup JH5VL * * 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 HDF5 Library. **/ public static boolean H5VLis_connector_registered_by_name(String name) throws HDF5LibraryException { if (name == null) { throw new NullPointerException("Connector name cannot be null"); } boolean is_registered = false; int retVal = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment name_segment = arena.allocateFrom(name); if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5VLis_connector_registered_by_name(name_segment)) < 0) h5libraryError(); } if (retVal > 0) { is_registered = true; } return is_registered; } /** * @ingroup JH5VL * * 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 HDF5 Library. **/ public static boolean H5VLis_connector_registered_by_value(int connector_value) throws HDF5LibraryException { int retVal = -1; if (connector_value < 0) { throw new HDF5LibraryException("Invalid connector value: " + connector_value); } boolean is_registered = false; if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5VLis_connector_registered_by_value(connector_value)) < 0) h5libraryError(); if (retVal > 0) { is_registered = true; } return is_registered; } /** * @ingroup JH5VL * * 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 HDF5 Library. **/ public static long H5VLget_connector_id(long object_id) throws HDF5LibraryException { long id = org.hdfgroup.javahdf5.hdf5_h.H5VLget_connector_id(object_id); if (id > 0) { log.trace("OPEN_IDS: H5VLget_connector_id add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } else h5libraryError(); return id; } /** * @ingroup JH5VL * * 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 HDF5 Library. **/ public static long H5VLget_connector_id_by_name(String name) throws HDF5LibraryException { if (name == null) { throw new NullPointerException("Connector name cannot be null"); } long id = H5I_INVALID_HID(); try (Arena arena = Arena.ofConfined()) { MemorySegment name_segment = arena.allocateFrom(name); id = org.hdfgroup.javahdf5.hdf5_h.H5VLget_connector_id_by_name(name_segment); } if (id > 0) { log.trace("OPEN_IDS: H5VLget_connector_id_by_name add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } else h5libraryError(); return id; } /** * @ingroup JH5VL * * 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 HDF5 Library. **/ public static long H5VLget_connector_id_by_value(int connector_value) throws HDF5LibraryException { long id = org.hdfgroup.javahdf5.hdf5_h.H5VLget_connector_id_by_value(connector_value); if (id > 0) { log.trace("OPEN_IDS: H5VLget_connector_id_by_value add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } else h5libraryError(); return id; } /** * @ingroup JH5VL * * 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 HDF5 Library. **/ public static String H5VLget_connector_name(long object_id) throws HDF5LibraryException { long buf_size = -1; buf_size = org.hdfgroup.javahdf5.hdf5_h.H5VLget_connector_name(object_id, MemorySegment.NULL, 0); String ret_name = null; try (Arena arena = Arena.ofConfined()) { MemorySegment name_segment = arena.allocate(buf_size + 1); if (org.hdfgroup.javahdf5.hdf5_h.H5VLget_connector_name(object_id, name_segment, buf_size + 1) < 0) h5libraryError(); ret_name = name_segment.getString(0, StandardCharsets.UTF_8); } return ret_name; } /** * @ingroup JH5VL * * H5VLclose closes a VOL connector ID. * * @param connector_id * IN: Identifier of the connector. * * @exception HDF5LibraryException * Error from the HDF5 Library. **/ public static void H5VLclose(long connector_id) throws HDF5LibraryException { int retVal = org.hdfgroup.javahdf5.hdf5_h.H5VLclose(connector_id); log.trace("OPEN_IDS: H5VLclose remove {}", connector_id); OPEN_IDS.remove(connector_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); if (retVal < 0) { h5libraryError(); } } /** * @ingroup JH5VL * * H5VLunregister_connector removes a VOL connector ID from the library. * * @param connector_id * IN: Identifier of the connector. * * @exception HDF5LibraryException * Error from the HDF5 Library. **/ public static void H5VLunregister_connector(long connector_id) throws HDF5LibraryException { if (org.hdfgroup.javahdf5.hdf5_h.H5VLunregister_connector(connector_id) < 0) { h5libraryError(); } log.trace("OPEN_IDS: H5VLunregister_connector remove {}", connector_id); OPEN_IDS.remove(connector_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } /** * @ingroup JH5VL * * H5VLcmp_connector_cls Determines whether two connector identifiers refer to the same connector. * * @param conn_id1 * IN: Identifier of connector to compare. * @param conn_id2 * IN: Identifier of connector to compare. * * @return true if the connector identifiers refer to the same connector, else false. * * @exception HDF5LibraryException * Error from the HDF5 Library. **/ public static boolean H5VLcmp_connector_cls(long conn_id1, long conn_id2) throws HDF5LibraryException { if (conn_id1 < 0 || conn_id2 < 0) { throw new HDF5LibraryException("Invalid connector ID: " + conn_id1 + ", " + conn_id2); } boolean is_equal = false; int cmp_value = 0; int retVal = -1; try (Arena arena = Arena.ofConfined()) { MemorySegment cmp_value_segment = arena.allocate(ValueLayout.JAVA_INT, 1); if ((retVal = org.hdfgroup.javahdf5.hdf5_h.H5VLcmp_connector_cls(cmp_value_segment, conn_id1, conn_id2)) < 0) h5libraryError(); cmp_value = cmp_value_segment.get(ValueLayout.JAVA_INT, 0); } if (cmp_value == 0) { is_equal = true; } return is_equal; } // /////// unimplemented //////// // hid_t H5VLregister_connector(const H5VL_class_t *cls, hid_t vipl_id); // //////////////////////////////////////////////////////////// // // // H5Z: Filter Interface Functions // // // // //////////////////////////////////////////////////////////// /** * @defgroup JH5Z Java Filter (H5Z) Interface * * @see H5Z, C-API * * @see @ref H5Z_UG, User Guide **/ /** * @ingroup JH5Z * * 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 HDF5 Library. **/ public static int H5Zfilter_avail(int filter) throws HDF5LibraryException { int status = -1; if (filter < 0) { throw new HDF5LibraryException("Invalid filter number: " + filter); } if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Zfilter_avail(filter)) < 0) { h5libraryError(); } return status; } /** * @ingroup JH5Z * * 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 HDF5 Library. **/ public static int H5Zget_filter_info(int filter) throws HDF5LibraryException { int flags = -1; if (filter < 0) { throw new HDF5LibraryException("Invalid filter number: " + filter); } try (Arena arena = Arena.ofConfined()) { MemorySegment flags_segment = arena.allocate(ValueLayout.JAVA_INT, 1); if (org.hdfgroup.javahdf5.hdf5_h.H5Zget_filter_info(filter, flags_segment) < 0) h5libraryError(); flags = flags_segment.get(ValueLayout.JAVA_INT, 0); } return flags; } /** * @ingroup JH5Z * * H5Zunregister unregisters a filter. * * @param filter * IN: filter number. * * @return a non-negative value if successful * * @exception HDF5LibraryException * Error from the HDF5 Library. **/ public static int H5Zunregister(int filter) throws HDF5LibraryException { int status = -1; if (filter < 0) { throw new HDF5LibraryException("Invalid filter number: " + filter); } if ((status = org.hdfgroup.javahdf5.hdf5_h.H5Zunregister(filter)) < 0) { h5libraryError(); } return status; } // /////// unimplemented //////// // herr_t H5Zregister(const void *cls); }