/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ package hdf.hdf5lib; import java.io.File; import java.nio.ByteBuffer; import java.util.Collection; import java.util.LinkedHashSet; import hdf.hdf5lib.callbacks.H5A_iterate_cb; import hdf.hdf5lib.callbacks.H5A_iterate_t; import hdf.hdf5lib.callbacks.H5D_iterate_cb; import hdf.hdf5lib.callbacks.H5D_iterate_t; import hdf.hdf5lib.callbacks.H5E_walk_cb; import hdf.hdf5lib.callbacks.H5E_walk_t; import hdf.hdf5lib.callbacks.H5L_iterate_cb; import hdf.hdf5lib.callbacks.H5L_iterate_t; import hdf.hdf5lib.callbacks.H5O_iterate_cb; import hdf.hdf5lib.callbacks.H5O_iterate_t; import hdf.hdf5lib.callbacks.H5P_cls_close_func_cb; import hdf.hdf5lib.callbacks.H5P_cls_close_func_t; import hdf.hdf5lib.callbacks.H5P_cls_copy_func_cb; import hdf.hdf5lib.callbacks.H5P_cls_copy_func_t; import hdf.hdf5lib.callbacks.H5P_cls_create_func_cb; import hdf.hdf5lib.callbacks.H5P_cls_create_func_t; import hdf.hdf5lib.callbacks.H5P_prp_set_func_cb; import hdf.hdf5lib.callbacks.H5P_prp_get_func_cb; import hdf.hdf5lib.callbacks.H5P_prp_delete_func_cb; import hdf.hdf5lib.callbacks.H5P_prp_copy_func_cb; import hdf.hdf5lib.callbacks.H5P_prp_compare_func_cb; import hdf.hdf5lib.callbacks.H5P_prp_close_func_cb; import hdf.hdf5lib.callbacks.H5P_prp_create_func_cb; import hdf.hdf5lib.callbacks.H5P_iterate_cb; import hdf.hdf5lib.callbacks.H5P_iterate_t; import hdf.hdf5lib.exceptions.HDF5Exception; import hdf.hdf5lib.exceptions.HDF5JavaException; import hdf.hdf5lib.exceptions.HDF5LibraryException; import hdf.hdf5lib.structs.H5AC_cache_config_t; import hdf.hdf5lib.structs.H5A_info_t; import hdf.hdf5lib.structs.H5E_error2_t; import hdf.hdf5lib.structs.H5F_info2_t; import hdf.hdf5lib.structs.H5G_info_t; import hdf.hdf5lib.structs.H5L_info_t; import hdf.hdf5lib.structs.H5O_info_t; /** * This class is the Java interface for the HDF5 library. *

* This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps a single * HDF5 entry point, generally with the arguments and return codes analogous to the C interface. *

* For details of the HDF5 library, see the HDF5 Documentation at: http://hdfgroup.org/HDF5/ *

*

* Mapping of arguments for Java * *

* In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF * Reference Manual. * *

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
HDF-5 C types to Java types
HDF-5Java
H5T_NATIVE_INTint, Integer
H5T_NATIVE_SHORTshort, Short
H5T_NATIVE_FLOATfloat, Float
H5T_NATIVE_DOUBLEdouble, Double
H5T_NATIVE_CHARbyte, Byte
H5T_C_S1java.lang.String
void *
* (i.e., pointer to `Any')		Special -- see HDFArray
*
*
General Rules for Passing Arguments and Results
*

* In general, arguments passed IN to Java are the analogous basic types, as above. The exception is for arrays, * which are discussed below. *

* The return value of Java methods is also the analogous type, as above. A major exception to that rule is that * all HDF functions that return SUCCEED/FAIL are declared boolean in the Java version, rather than int as * in the C. Functions that return a value or else FAIL are declared the equivalent to the C function. However, in most * cases the Java method will raise an exception instead of returning an error code. See Errors and * Exceptions below. *

* Java does not support pass by reference of arguments, so arguments that are returned through OUT parameters * must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in arrays. *

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

 *       h_err_t HDF5dummy( int *a1, int *a2)
 *
* * For the Java interface, this would be declared: * * 
 * public synchronized static native int HDF5dummy(int args[]);
 *
* * where a1 is args[0] and a2 is args[1], and would be invoked: * * 
 * H5.HDF5dummy(a);
 *
* *

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

* Arrays *

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

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

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

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

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

 * public synchronized static native int H5Dread(long fid, long filetype, long memtype, long memspace, Object data);
 *
* OPEN_IDS.addElement(id); * and the parameter data can be any multi-dimensional array of numbers, such as float[][], or int[][][], or * Double[][]. *

* HDF-5 Constants *

* The HDF-5 API defines a set of constants and enumerated values. Most of these values are available to Java programs * via the class HDF5Constants. For example, the parameters for * the h5open() call include two numeric values, HDFConstants.H5F_ACC_RDWR and * HDF5Constants.H5P_DEFAULT. As would be expected, these numbers correspond to the C constants * H5F_ACC_RDWR and H5P_DEFAULT. *

* The HDF-5 API defines a set of values that describe number types and sizes, such as "H5T_NATIVE_INT" and "hsize_t". * These values are determined at run time by the HDF-5 C library. To support these parameters, the Java class HDF5CDataTypes looks up the values when initiated. The values * can be accessed as public variables of the Java class, such as: * * 

 * long data_type = HDF5CDataTypes.JH5T_NATIVE_INT;
 *
* * The Java application uses both types of constants the same way, the only difference is that the * HDF5CDataTypes may have different values on different platforms. *

* Error handling and Exceptions *

* The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5 library. This API is omitted from the * JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is very natural * for Java programming. *

* The exceptions of the JHI5 are organized as sub-classes of the class HDF5Exception. There are two subclasses of * HDF5Exception, HDF5LibraryException * and HDF5JavaException. The sub-classes of the * former represent errors from the HDF-5 C library, while sub-classes of the latter represent errors in the JHI5 * wrapper and support code. *

* The super-class HDF5LibraryException implements the method 'printStackTrace()', which * prints out the HDF-5 error stack, as described in the HDF-5 C API H5Eprint(). This may be used by Java * exception handlers to print out the HDF-5 error stack. *

* * @version HDF5 1.10.3
* See also: hdf.hdf5lib.HDFArray
* hdf.hdf5lib.HDF5Constants
* hdf.hdf5lib.HDF5CDataTypes
* hdf.hdf5lib.HDF5Exception
* http://hdfgroup.org/HDF5" **/ public class H5 implements java.io.Serializable { /** * */ private static final long serialVersionUID = 6129888282117053288L; private final static org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(H5.class); /** * The version number of the HDF5 library: * LIB_VERSION[0]: The major version of the library. * LIB_VERSION[1]: The minor version of the library. * LIB_VERSION[2]: The release number of the library. * * Make sure to update the versions number when a different library is used. */ public final static int LIB_VERSION[] = { 1, 10, 3 }; public final static String H5PATH_PROPERTY_KEY = "hdf.hdf5lib.H5.hdf5lib"; // add system property to load library by name from library path, via // System.loadLibrary() public final static String H5_LIBRARY_NAME_PROPERTY_KEY = "hdf.hdf5lib.H5.loadLibraryName"; private static String s_libraryName; private static boolean isLibraryLoaded = false; private final static boolean IS_CRITICAL_PINNING = true; // change from Vector to LinkedHashSet - jp 6-Oct-2014 private final static LinkedHashSet OPEN_IDS = new LinkedHashSet(); static { loadH5Lib(); } public static void loadH5Lib() { // Make sure that the library is loaded only once if (isLibraryLoaded) return; // first try loading library by name from user supplied library path s_libraryName = System.getProperty(H5_LIBRARY_NAME_PROPERTY_KEY, null); String mappedName = null; if ((s_libraryName != null) && (s_libraryName.length() > 0)) { try { mappedName = System.mapLibraryName(s_libraryName); System.loadLibrary(s_libraryName); isLibraryLoaded = true; } catch (Throwable err) { err.printStackTrace(); isLibraryLoaded = false; } finally { log.info("HDF5 library: " + s_libraryName); log.debug(" resolved to: " + mappedName + "; "); log.info((isLibraryLoaded ? "" : " NOT") + " successfully loaded from system property"); } } if (!isLibraryLoaded) { // else try loading library via full path String filename = System.getProperty(H5PATH_PROPERTY_KEY, null); if ((filename != null) && (filename.length() > 0)) { File h5dll = new File(filename); if (h5dll.exists() && h5dll.canRead() && h5dll.isFile()) { try { System.load(filename); isLibraryLoaded = true; } catch (Throwable err) { err.printStackTrace(); isLibraryLoaded = false; } finally { log.info("HDF5 library: "); log.debug(filename); log.info((isLibraryLoaded ? "" : " NOT") + " successfully loaded."); } } else { isLibraryLoaded = false; throw (new UnsatisfiedLinkError("Invalid HDF5 library, " + filename)); } } } // else load standard library if (!isLibraryLoaded) { try { s_libraryName = "hdf5_java"; mappedName = System.mapLibraryName(s_libraryName); System.loadLibrary("hdf5_java"); isLibraryLoaded = true; } catch (Throwable err) { err.printStackTrace(); isLibraryLoaded = false; } finally { log.info("HDF5 library: " + s_libraryName); log.debug(" resolved to: " + mappedName + "; "); log.info((isLibraryLoaded ? "" : " NOT") + " successfully loaded from java.library.path"); } } /* Important! Exit quietly */ try { H5.H5dont_atexit(); } catch (HDF5LibraryException e) { System.exit(1); } /* Important! Disable error output to C stdout */ if (!log.isDebugEnabled()) H5.H5error_off(); /* * Optional: confirm the version This will crash immediately if not the specified version. */ Integer majnum = Integer.getInteger("hdf.hdf5lib.H5.hdf5maj", null); Integer minnum = Integer.getInteger("hdf.hdf5lib.H5.hdf5min", null); Integer relnum = Integer.getInteger("hdf.hdf5lib.H5.hdf5rel", null); if ((majnum != null) && (minnum != null) && (relnum != null)) { H5.H5check_version(majnum.intValue(), minnum.intValue(), relnum.intValue()); } } // //////////////////////////////////////////////////////////// // // // H5: General Library Functions // // // // //////////////////////////////////////////////////////////// /** * Get number of open IDs. * * @return Returns a count of open IDs */ public final static int getOpenIDCount() { return OPEN_IDS.size(); } /** * Get the open IDs * * @return Returns a collection of open IDs */ public final static Collection getOpenIDs() { return OPEN_IDS; } /** * H5check_version verifies that the arguments match the version numbers compiled into the library. * * @param majnum * The major version of the library. * @param minnum * The minor version of the library. * @param relnum * The release number of the library. * @return a non-negative value if successful. Upon failure (when the versions do not match), this function causes * the application to abort (i.e., crash) * * See C API function: herr_t H5check_version() **/ public synchronized static native int H5check_version(int majnum, int minnum, int relnum); /** * H5close flushes all data to disk, closes all file identifiers, and cleans up all memory used by the library. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5close() throws HDF5LibraryException; /** * H5open initialize the library. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5open() throws HDF5LibraryException; /** * H5dont_atexit indicates to the library that an atexit() cleanup routine should not be installed. In order to be * effective, this routine must be called before any other HDF function calls, and must be called each time the * library is loaded/linked into the application (the first time and after it's been unloaded). *

* This is called by the static initializer, so this should never need to be explicitly called by a Java program. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ private synchronized static native int H5dont_atexit() throws HDF5LibraryException; /** * Turn off error handling. By default, the C library prints the error stack of the HDF-5 C library on stdout. This * behavior may be disabled by calling H5error_off(). * * @return a non-negative value if successful */ public synchronized static native int H5error_off(); /** * Turn on error handling. By default, the C library prints the error stack of the HDF-5 C library on stdout. This * behavior may be reenabled by calling H5error_on(). */ public synchronized static native void H5error_on(); /** * H5garbage_collect collects on all free-lists of all types. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5garbage_collect() throws HDF5LibraryException; /** * H5get_libversion retrieves the major, minor, and release numbers of the version of the HDF library which is * linked to the application. * * @param libversion * The version information of the HDF library. * * 

     *      libversion[0] = The major version of the library.
     *      libversion[1] = The minor version of the library.
     *      libversion[2] = The release number of the library.
     *
* @return a non-negative value if successful, along with the version information. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5get_libversion(int[] libversion) throws HDF5LibraryException; public synchronized static native int H5set_free_list_limits(int reg_global_lim, int reg_list_lim, int arr_global_lim, int arr_list_lim, int blk_global_lim, int blk_list_lim) throws HDF5LibraryException; /** * H5export_dataset is a utility function to save data in a file. * * @param file_export_name * The file name to export data into. * @param file_name * The name of the HDF5 file containing the dataset. * @param object_path * The full path of the dataset to be exported. * @param binary_order * 99 - export data as text. * 1 - export data as binary Native Order. * 2 - export data as binary Little Endian. * 3 - export data as binary Big Endian. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5export_dataset(String file_export_name, String file_name, String object_path, int binary_order) throws HDF5LibraryException; /** * H5is_library_threadsafe Checks to see if the library was built with thread-safety enabled. * * @return true if hdf5 library implements threadsafe * **/ private synchronized static native boolean H5is_library_threadsafe(); // /////// unimplemented //////// // H5_DLL herr_t H5free_memory(void *mem); // H5_DLL void *H5allocate_memory(size_t size, hbool_t clear); // H5_DLL void *H5resize_memory(void *mem, size_t size); // //////////////////////////////////////////////////////////// // // // H5A: HDF5 1.8 Attribute Interface API Functions // // // // //////////////////////////////////////////////////////////// /** * H5Aclose terminates access to the attribute specified by its identifier, attr_id. * * @param attr_id * IN: Attribute to release access to. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Aclose(long attr_id) throws HDF5LibraryException { if (attr_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; log.trace("OPEN_IDS: H5Aclose remove {}", attr_id); OPEN_IDS.remove(attr_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); return _H5Aclose(attr_id); } private synchronized static native int _H5Aclose(long attr_id) throws HDF5LibraryException; /** * H5Acopy copies the content of one attribute to another. * * @param src_aid * the identifier of the source attribute * @param dst_aid * the identifier of the destination attribute * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native int H5Acopy(long src_aid, long dst_aid) throws HDF5LibraryException; /** * H5Acreate creates an attribute, attr_name, which is attached to the object specified by the identifier loc_id. * * @param loc_id * IN: Location or object identifier; may be dataset or group * @param attr_name * IN: Attribute name * @param type_id * IN: Attribute datatype identifier * @param space_id * IN: Attribute dataspace identifier * @param acpl_id * IN: Attribute creation property list identifier * @param aapl_id * IN: Attribute access property list identifier * * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - Name is null. **/ public static long H5Acreate(long loc_id, String attr_name, long type_id, long space_id, long acpl_id, long aapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Acreate2(loc_id, attr_name, type_id, space_id, acpl_id, aapl_id); if (id > 0) { log.trace("OPEN_IDS: H5A create add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } /** * H5Acreate2 an attribute, attr_name, which is attached to the object specified by the identifier loc_id. * * @see public static long H5Acreate( long loc_id, String attr_name, long type_id, long space_id, long acpl_id, long * aapl_id ) **/ private synchronized static native long _H5Acreate2(long loc_id, String attr_name, long type_id, long space_id, long acpl_id, long aapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Acreate_by_name creates an attribute, attr_name, which is attached to the object specified by loc_id and * obj_name. * * @param loc_id * IN: Location or object identifier; may be dataset or group * @param obj_name * IN: Name, relative to loc_id, of object that attribute is to be attached to * @param attr_name * IN: Attribute name * @param type_id * IN: Attribute datatype identifier * @param space_id * IN: Attribute dataspace identifier * @param acpl_id * IN: Attribute creation property list identifier (currently not used). * @param aapl_id * IN: Attribute access property list identifier (currently not used). * @param lapl_id * IN: Link access property list * * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static long H5Acreate_by_name(long loc_id, String obj_name, String attr_name, long type_id, long space_id, long acpl_id, long aapl_id, long lapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Acreate_by_name(loc_id, obj_name, attr_name, type_id, space_id, acpl_id, aapl_id, lapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Acreate_by_name add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Acreate_by_name(long loc_id, String obj_name, String attr_name, long type_id, long space_id, long acpl_id, long aapl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Adelete removes the attribute specified by its name, name, from a dataset, group, or named datatype. * * @param loc_id * IN: Identifier of the dataset, group, or named datatype. * @param name * IN: Name of the attribute to delete. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Adelete(long loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Adelete_by_idx removes an attribute, specified by its location in an index, from an object. * * @param loc_id * IN: Location or object identifier; may be dataset or group * @param obj_name * IN: Name of object, relative to location, from which attribute is to be removed * @param idx_type * IN: Type of index * @param order * IN: Order in which to iterate over index * @param n * IN: Offset within index * @param lapl_id * IN: Link access property list identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - obj_name is null. **/ public synchronized static native void H5Adelete_by_idx(long loc_id, String obj_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Adelete_by_name removes the attribute attr_name from an object specified by location and name, loc_id and * obj_name, respectively. * * @param loc_id * IN: Location or object identifier; may be dataset or group * @param obj_name * IN: Name of object, relative to location, from which attribute is to be removed * @param attr_name * IN: Name of attribute to delete * @param lapl_id * IN: Link access property list identifier. * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Adelete_by_name(long loc_id, String obj_name, String attr_name, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aexists determines whether the attribute attr_name exists on the object specified by obj_id. * * @param obj_id * IN: Object identifier. * @param attr_name * IN: Name of the attribute. * * @return boolean true if an attribute with a given name exists. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - attr_name is null. **/ public synchronized static native boolean H5Aexists(long obj_id, String attr_name) throws HDF5LibraryException, NullPointerException; /** * H5Aexists_by_name determines whether the attribute attr_name exists on an object. That object is specified by its * location and name, loc_id and obj_name, respectively. * * @param loc_id * IN: Location of object to which attribute is attached . * @param obj_name * IN: Name, relative to loc_id, of object that attribute is attached to. * @param attr_name * IN: Name of attribute. * @param lapl_id * IN: Link access property list identifier. * * @return boolean true if an attribute with a given name exists, otherwise returns false. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native boolean H5Aexists_by_name(long loc_id, String obj_name, String attr_name, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aget_info retrieves attribute information, by attribute identifier. * * @param attr_id * IN: Attribute identifier * * @return A buffer(H5A_info_t) for Attribute information * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native H5A_info_t H5Aget_info(long attr_id) throws HDF5LibraryException; /** * H5Aget_info_by_idx Retrieves attribute information, by attribute index position. * * @param loc_id * IN: Location of object to which attribute is attached * @param obj_name * IN: Name of object to which attribute is attached, relative to location * @param idx_type * IN: Type of index * @param order * IN: Index traversal order * @param n * IN: Attribute's position in index * @param lapl_id * IN: Link access property list * * @return A buffer(H5A_info_t) for Attribute information * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - obj_name is null. **/ public synchronized static native H5A_info_t H5Aget_info_by_idx(long loc_id, String obj_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aget_info_by_name Retrieves attribute information, by attribute name. * * @param loc_id * IN: Location of object to which attribute is attached * @param obj_name * IN: Name of object to which attribute is attached, relative to location * @param attr_name * IN: Attribute name * @param lapl_id * IN: Link access property list * * @return A buffer(H5A_info_t) for Attribute information * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - obj_name is null. **/ public synchronized static native H5A_info_t H5Aget_info_by_name(long loc_id, String obj_name, String attr_name, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aget_name retrieves the name of an attribute specified by the identifier, attr_id. * * @param attr_id * IN: Identifier of the attribute. * * @return String for Attribute name. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5Aget_name(long attr_id) throws HDF5LibraryException; /** * H5Aget_name_by_idx retrieves the name of an attribute that is attached to an object, which is specified by its * location and name, loc_id and obj_name, respectively. * * @param attr_id * IN: Attribute identifier * @param obj_name * IN: Name of object to which attribute is attached, relative to location * @param idx_type * IN: Type of index * @param order * IN: Index traversal order * @param n * IN: Attribute's position in index * @param lapl_id * IN: Link access property list * * @return String for Attribute name. * * @exception HDF5LibraryException * - Error from the HDF5 Library. * @exception NullPointerException * - obj_name is null. **/ public synchronized static native String H5Aget_name_by_idx(long attr_id, String obj_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aget_space retrieves a copy of the dataspace for an attribute. * * @param attr_id * IN: Identifier of an attribute. * * @return attribute dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Aget_space(long attr_id) throws HDF5LibraryException { long id = _H5Aget_space(attr_id); if (id > 0) { log.trace("OPEN_IDS: H5Aget_space add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Aget_space(long attr_id) throws HDF5LibraryException; /** * H5Aget_storage_size returns the amount of storage that is required for the specified attribute, attr_id. * * @param attr_id * IN: Identifier of the attribute to query. * * @return the amount of storage size allocated for the attribute; otherwise returns 0 (zero) * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Aget_storage_size(long attr_id) throws HDF5LibraryException; /** * H5Aget_type retrieves a copy of the datatype for an attribute. * * @param attr_id * IN: Identifier of an attribute. * * @return a datatype identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Aget_type(long attr_id) throws HDF5LibraryException { long id = _H5Aget_type(attr_id); if (id > 0) { log.trace("OPEN_IDS: H5Aget_type add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Aget_type(long attr_id) throws HDF5LibraryException; /** * H5Aopen opens an existing attribute, attr_name, that is attached to an object specified an object identifier, * object_id. * * @param obj_id * IN: Identifier for object to which attribute is attached * @param attr_name * IN: Name of attribute to open * @param aapl_id * IN: Attribute access property list identifier * * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - Name is null. **/ public static long H5Aopen(long obj_id, String attr_name, long aapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Aopen(obj_id, attr_name, aapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Aopen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Aopen(long obj_id, String attr_name, long aapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aopen_by_idx opens an existing attribute that is attached to an object specified by location and name, loc_id * and obj_name, respectively * * @param loc_id * IN: Location of object to which attribute is attached * @param obj_name * IN: Name of object to which attribute is attached, relative to location * @param idx_type * IN: Type of index * @param order * IN: Index traversal order * @param n * IN: Attribute's position in index * @param aapl_id * IN: Attribute access property list * @param lapl_id * IN: Link access property list * * @return An attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - Name is null. **/ public static long H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, int order, long n, long aapl_id, long lapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Aopen_by_idx(loc_id, obj_name, idx_type, order, n, aapl_id, lapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Aopen_by_idx add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Aopen_by_idx(long loc_id, String obj_name, int idx_type, int order, long n, long aapl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aopen_by_name Opens an attribute for an object by object name and attribute name * * @param loc_id * IN: Location from which to find object to which attribute is attached * @param obj_name * IN: Name of object to which attribute is attached, relative to loc_id * @param attr_name * IN: Name of attribute to open * @param aapl_id * IN: Attribute access property list * @param lapl_id * IN: Link access property list identifier * * @return Returns an attribute identifier if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - obj_name is null. **/ public static long H5Aopen_by_name(long loc_id, String obj_name, String attr_name, long aapl_id, long lapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Aopen_by_name(loc_id, obj_name, attr_name, aapl_id, lapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Aopen_by_name add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Aopen_by_name(long loc_id, String obj_name, String attr_name, long aapl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with * mem_type_id. The entire attribute is read into buf from the file. * * @param attr_id * IN: Identifier of an attribute to read. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). * @param buf * IN: Buffer for data to be read. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data buffer is null. **/ public synchronized static native int H5Aread(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Aread reads an attribute, specified with attr_id. The attribute's memory datatype is specified with * mem_type_id. The entire attribute is read into data object from the file. * * @param attr_id * IN: Identifier of an attribute to read. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). * @param obj * IN: Object for data to be read. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data buffer is null. See public synchronized static native int H5Aread( ) **/ public synchronized static int H5Aread(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, NullPointerException { HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.emptyBytes(); // This will raise an exception if there is an error int status = H5Aread(attr_id, mem_type_id, buf); // No exception: status really ought to be OK if (status >= 0) { obj = theArray.arrayify(buf); } return status; } public synchronized static native int H5AreadVL(long attr_id, long mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5AreadComplex(long attr_id, long mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Arename changes the name of attribute that is attached to the object specified by loc_id. The attribute named * old_attr_name is renamed new_attr_name. * * @param loc_id * IN: Location or object identifier; may be dataset or group * @param old_attr_name * IN: Prior attribute name * @param new_attr_name * IN: New attribute name * * @return A non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - Name is null. **/ public synchronized static native int H5Arename(long loc_id, String old_attr_name, String new_attr_name) throws HDF5LibraryException, NullPointerException; /** * H5Arename_by_name changes the name of attribute that is attached to the object specified by loc_id and obj_name. * The attribute named old_attr_name is renamed new_attr_name. * * @param loc_id * IN: Location or object identifier; may be dataset or group * @param obj_name * IN: Name of object, relative to location, whose attribute is to be renamed * @param old_attr_name * IN: Prior attribute name * @param new_attr_name * IN: New attribute name * @param lapl_id * IN: Link access property list * * @return A non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - Name is null. **/ public synchronized static native int H5Arename_by_name(long loc_id, String obj_name, String old_attr_name, String new_attr_name, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with * mem_type_id. The entire attribute is written from buf to the file. * * @param attr_id * IN: Identifier of an attribute to write. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). * @param buf * IN: Data to be written. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data is null. **/ public synchronized static native int H5Awrite(long attr_id, long mem_type_id, byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Awrite writes an attribute, specified with attr_id. The attribute's memory datatype is specified with * mem_type_id. The entire attribute is written from data object to the file. * * @param attr_id * IN: Identifier of an attribute to write. * @param mem_type_id * IN: Identifier of the attribute datatype (in memory). * @param obj * IN: Data object to be written. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data object is null. See public synchronized static native int H5Awrite(int attr_id, int * mem_type_id, byte[] buf); **/ public synchronized static int H5Awrite(long attr_id, long mem_type_id, Object obj) throws HDF5Exception, NullPointerException { HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.byteify(); int retVal = H5Awrite(attr_id, mem_type_id, buf); buf = null; theArray = null; return retVal; } public synchronized static native int H5AwriteVL(long attr_id, long mem_type_id, String[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Aget_create_plist retrieves a copy of the attribute creation property list identifier. * * @param attr_id * IN: Identifier of an attribute. * * @return identifier for the attribute's creation property list if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Aget_create_plist(long attr_id) throws HDF5LibraryException { long id = _H5Aget_create_plist(attr_id); if (id > 0) { log.trace("OPEN_IDS: H5Aget_create_plist add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Aget_create_plist(long attr_id) throws HDF5LibraryException; /** * H5Aiterate2 iterates over the attributes attached to a dataset, named datatype, or group, as * specified by obj_id. For each attribute, user-provided data, op_data, with additional information * as defined below, is passed to a user-defined function, op, which operates on that attribute. * * @param loc_id * IN: Identifier for object to which attributes are attached; may be group, dataset, or named datatype. * @param idx_type * IN: The type of index specified by idx_type can be one of the following: * H5_INDEX_NAME An alpha-numeric index by attribute name. * H5_INDEX_CRT_ORDER An index by creation order. * @param order * IN: The order in which the index is to be traversed, as specified by order, can be one of the following: * H5_ITER_INC Iteration is from beginning to end, i.e., a top-down iteration * incrementing the index position at each step. * H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration * decrementing the index position at each step. * H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided * as to the order, but HDF5 ensures that each element in the index will be * visited if the iteration completes successfully. * @param idx * IN/OUT: Initial and returned offset within index. * @param op * IN: Callback function to operate on each value. * @param op_data * IN/OUT: Pointer to any user-efined data for use by operator function. * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native int H5Aiterate(long loc_id, int idx_type, int order, long idx, H5A_iterate_cb op, H5A_iterate_t op_data) throws HDF5LibraryException, NullPointerException; /** * H5Aiterate_by_name iterates over the attributes attached to the dataset or group specified with loc_id * and obj_name. For each attribute, user-provided data, op_data, with additional information as defined * below, is passed to a user-defined function, op, which operates on that attribute. * * @param loc_id * IN: Identifier for object to which attributes are attached; may be group, dataset, or named datatype. * @param obj_name * IN: Name of object, relative to location. * @param idx_type * IN: The type of index specified by idx_type can be one of the following: * H5_INDEX_NAME An alpha-numeric index by attribute name. * H5_INDEX_CRT_ORDER An index by creation order. * @param order * IN: The order in which the index is to be traversed, as specified by order, can be one of the following: * H5_ITER_INC Iteration is from beginning to end, i.e., a top-down iteration * incrementing the index position at each step. * H5_ITER_DEC Iteration starts at the end of the index, i.e., a bottom-up iteration * decrementing the index position at each step. * H5_ITER_NATIVE HDF5 iterates in the fastest-available order. No information is provided * as to the order, but HDF5 ensures that each element in the index will be * visited if the iteration completes successfully. * @param idx * IN/OUT: Initial and returned offset within index. * @param op * IN: Callback function to operate on each value. * @param op_data * IN/OUT: Pointer to any user-efined data for use by operator function. * @param lapl_id * IN: Link access property list * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native int H5Aiterate_by_name(long loc_id, String obj_name, int idx_type, int order, long idx, H5A_iterate_cb op, H5A_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException; // //////////////////////////////////////////////////////////// // // // H5AC: Cache Interface Functions // // // // //////////////////////////////////////////////////////////// // No public Functions // //////////////////////////////////////////////////////////// // // // H5B: B-link-tree Interface Functions // // // // //////////////////////////////////////////////////////////// // No public Functions // //////////////////////////////////////////////////////////// // // // H5B2: v2 B-tree Interface Functions // // // // //////////////////////////////////////////////////////////// // No public Functions // //////////////////////////////////////////////////////////// // // // H5C: Cache Interface Functions // // // // //////////////////////////////////////////////////////////// // No public Functions // //////////////////////////////////////////////////////////// // // // H5D: Datasets Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Dcopy copies the content of one dataset to another dataset. * * @param src_did * the identifier of the source dataset * @param dst_did * the identifier of the destinaiton dataset * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native int H5Dcopy(long src_did, long dst_did) throws HDF5LibraryException; /** * H5Dclose ends access to a dataset specified by dataset_id and releases resources used by it. * * @param dataset_id * Identifier of the dataset to finish access to. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Dclose(long dataset_id) throws HDF5LibraryException { if (dataset_id < 0) return 0; // throw new HDF5LibraryException("Negative ID"); log.trace("OPEN_IDS: H5Dclose remove {}", dataset_id); OPEN_IDS.remove(dataset_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); return _H5Dclose(dataset_id); } private synchronized static native int _H5Dclose(long dataset_id) throws HDF5LibraryException; /** * H5Dcreate creates a new dataset named name at the location specified by loc_id. * * @param loc_id * IN: Location identifier * @param name * IN: Dataset name * @param type_id * IN: Datatype identifier * @param space_id * IN: Dataspace identifier * @param lcpl_id * IN: Identifier of link creation property list. * @param dcpl_id * IN: Identifier of dataset creation property list. * @param dapl_id * IN: Identifier of dataset access property list. * * @return a dataset identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static long H5Dcreate(long loc_id, String name, long type_id, long space_id, long lcpl_id, long dcpl_id, long dapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Dcreate2(loc_id, name, type_id, space_id, lcpl_id, dcpl_id, dapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Dcreate add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } /** * H5Dcreate2 creates a new dataset named name at the location specified by loc_id. * * @see public static int H5Dcreate(int loc_id, String name, int type_id, int space_id, int lcpl_id, int dcpl_id, * int dapl_id) **/ private synchronized static native long _H5Dcreate2(long loc_id, String name, long type_id, long space_id, long lcpl_id, long dcpl_id, long dapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Dcreate_anon creates a dataset in the file specified by loc_id. * * @param loc_id * IN: Location identifier * @param type_id * IN: Datatype identifier * @param space_id * IN: Dataspace identifier * @param dcpl_id * IN: Identifier of dataset creation property list. * @param dapl_id * IN: Identifier of dataset access property list. * * @return a dataset identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Dcreate_anon(long loc_id, long type_id, long space_id, long dcpl_id, long dapl_id) throws HDF5LibraryException { long id = _H5Dcreate_anon(loc_id, type_id, space_id, dcpl_id, dapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Dcreate_anon add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Dcreate_anon(long loc_id, long type_id, long space_id, long dcpl_id, long dapl_id) throws HDF5LibraryException; /** * H5Dfill explicitly fills the dataspace selection in memory, space_id, with the fill value specified in fill. * * @param fill * IN: Pointer to the fill value to be used. * @param fill_type * IN: Fill value datatype identifier. * @param buf * IN/OUT: Pointer to the memory buffer containing the selection to be filled. * @param buf_type * IN: Datatype of dataspace elements to be filled. * @param space_id * IN: Dataspace describing memory buffer and containing the selection to be filled. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native void H5Dfill(byte[] fill, long fill_type, byte[] buf, long buf_type, long space_id) throws HDF5LibraryException, NullPointerException; /** * H5Dget_access_plist returns an identifier for a copy of the dataset access property list for a dataset. * * @param dset_id * IN: Identifier of the dataset to query. * * @return a dataset access property list identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Dget_access_plist(long dset_id) throws HDF5LibraryException; /** * H5Dget_create_plist returns an identifier for a copy of the dataset creation property list for a dataset. * * @param dataset_id * Identifier of the dataset to query. * @return a dataset creation property list identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Dget_create_plist(long dataset_id) throws HDF5LibraryException { long id = _H5Dget_create_plist(dataset_id); if (id > 0) { log.trace("OPEN_IDS: H5Dget_create_plist add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Dget_create_plist(long dataset_id) throws HDF5LibraryException; /** * H5Dget_offset returns the address in the file of the dataset dset_id. * * @param dset_id * IN: Identifier of the dataset in question * * @return the offset in bytes. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Dget_offset(long dset_id) throws HDF5LibraryException; /** * H5Dget_space returns an identifier for a copy of the dataspace for a dataset. * * @param dataset_id * Identifier of the dataset to query. * * @return a dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Dget_space(long dataset_id) throws HDF5LibraryException { long id = _H5Dget_space(dataset_id); if (id > 0) { log.trace("OPEN_IDS: H5Dget_space add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Dget_space(long dataset_id) throws HDF5LibraryException; /** * H5Dget_space_status determines whether space has been allocated for the dataset dset_id. * * @param dset_id * IN: Identifier of the dataset to query. * * @return the space allocation status * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Dget_space_status(long dset_id) throws HDF5LibraryException; /** * H5Dget_storage_size returns the amount of storage that is required for the dataset. * * @param dataset_id * Identifier of the dataset in question * * @return he amount of storage space allocated for the dataset. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Dget_storage_size(long dataset_id) throws HDF5LibraryException, IllegalArgumentException; /** * H5Dget_type returns an identifier for a copy of the datatype for a dataset. * * @param dataset_id * Identifier of the dataset to query. * * @return a datatype identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Dget_type(long dataset_id) throws HDF5LibraryException { long id = _H5Dget_type(dataset_id); if (id > 0) { log.trace("OPEN_IDS: H5Dget_type add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Dget_type(long dataset_id) throws HDF5LibraryException; /** * H5Diterate iterates over all the data elements in the memory buffer buf, executing the callback function operator * once for each such data element. * * @param buf * IN/OUT: Pointer to the memory containing the elements to iterate over. * @param buf_type * IN: Buffer datatype identifier. * @param space_id * IN: Dataspace describing memory buffer. * @param op * IN: Callback function to operate on each value. * @param op_data * IN/OUT: Pointer to any user-efined data for use by operator function. * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native int H5Diterate(byte[] buf, long buf_type, long space_id, H5D_iterate_cb op, H5D_iterate_t op_data) throws HDF5LibraryException, NullPointerException; /** * H5Dopen opens the existing dataset specified by a location identifier and name, loc_id and name, respectively. * * @param loc_id * IN: Location identifier * @param name * IN: Dataset name * @param dapl_id * IN: Identifier of dataset access property list. * * @return a dataset identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static long H5Dopen(long loc_id, String name, long dapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Dopen2(loc_id, name, dapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Dopen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } /** * H5Dopen2 opens the existing dataset specified by a location identifier and name, loc_id and name, respectively. * * @see public static int H5Dopen(int loc_id, String name, int dapl_id) **/ private synchronized static native long _H5Dopen2(long loc_id, String name, long dapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application * memory buffer buf. * * @param dataset_id * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. * @param mem_space_id * Identifier of the memory dataspace. * @param file_space_id * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param obj * Buffer to store data read from the file. * @param isCriticalPinning * request lock on data reference. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data buffer is null. **/ public synchronized static native int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, byte[] obj, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { return H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true); } /** * H5Dread reads a (partial) dataset, specified by its identifier dataset_id, from the file into the application * data object. * * @param dataset_id * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. * @param mem_space_id * Identifier of the memory dataspace. * @param file_space_id * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param obj * Object to store data read from the file. * @param isCriticalPinning * request lock on data reference. * * @return a non-negative value if successful * * @exception HDF5Exception * - Failure in the data conversion. * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data object is null. **/ public synchronized static int H5Dread(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException, NullPointerException { int status = -1; boolean is1D = false; Class dataClass = obj.getClass(); if (!dataClass.isArray()) { throw (new HDF5JavaException("H5Dread: data is not an array")); } String cname = dataClass.getName(); is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); char dname = cname.charAt(cname.lastIndexOf("[") + 1); log.trace("H5Dread: cname={} is1D={} dname={}", cname, is1D, dname); if (is1D && (dname == 'B')) { log.trace("H5Dread_dname_B"); status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[]) obj, isCriticalPinning); } else if (is1D && (dname == 'S')) { log.trace("H5Dread_dname_S"); status = H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (short[]) obj, isCriticalPinning); } else if (is1D && (dname == 'I')) { log.trace("H5Dread_dname_I"); status = H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (int[]) obj, isCriticalPinning); } else if (is1D && (dname == 'J')) { log.trace("H5Dread_dname_J"); status = H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj); } else if (is1D && (dname == 'F')) { log.trace("H5Dread_dname_F"); status = H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj, isCriticalPinning); } else if (is1D && (dname == 'D')) { log.trace("H5Dread_dname_D"); status = H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (double[]) obj, isCriticalPinning); } else if (H5.H5Tequal(mem_type_id, HDF5Constants.H5T_STD_REF_DSETREG)) { log.trace("H5Dread_reg_ref"); status = H5Dread_reg_ref(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (String[]) obj); } else if (is1D && (dataClass.getComponentType() == String.class)) { log.trace("H5Dread_string type"); if (H5.H5Tis_variable_str(mem_type_id)) { status = H5Dread_VLStrings(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[]) obj); } else { status = H5Dread_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (String[]) obj); } } else { // Create a data buffer to hold the data into a Java Array HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.emptyBytes(); 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; } public synchronized static native int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dread_reg_ref(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Dread_reg_ref_data(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dread_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5DreadVL(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Dread_string(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Dread_VLStrings(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Dset_extent sets the current dimensions of the chunked dataset dset_id to the sizes specified in size. * * @param dset_id * IN: Chunked dataset identifier. * @param size * IN: Array containing the new magnitude of each dimension of the dataset. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. **/ public synchronized static native void H5Dset_extent(long dset_id, long size[]) throws HDF5LibraryException, NullPointerException; /** * H5Dvlen_get_buf_size determines the number of bytes required to store the VL data from the dataset, using the * space_id for the selection in the dataset on disk and the type_id for the memory representation of the VL data in * memory. * * @param dset_id * IN: Identifier of the dataset read from. * @param type_id * IN: Identifier of the datatype. * @param space_id * IN: Identifier of the dataspace. * * @return the size in bytes of the memory buffer required to store the VL data. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native long H5Dvlen_get_buf_size(long dset_id, long type_id, long space_id) throws HDF5LibraryException; /** * H5Dvlen_reclaim reclaims buffer used for VL data. * * @param type_id * Identifier of the datatype. * @param space_id * Identifier of the dataspace. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param buf * Buffer with data to be reclaimed. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native int H5Dvlen_reclaim(long type_id, long space_id, long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory buffer * buf into the file. * * @param dataset_id * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. * @param mem_space_id * Identifier of the memory dataspace. * @param file_space_id * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param buf * Buffer with data to be written to the file. * @param isCriticalPinning * request lock on data reference. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, byte[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, byte[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object obj) throws HDF5Exception, HDF5LibraryException, NullPointerException { return H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, obj, true); } /** * H5Dwrite writes a (partial) dataset, specified by its identifier dataset_id, from the application memory data * object into the file. * * @param dataset_id * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. * @param mem_space_id * Identifier of the memory dataspace. * @param file_space_id * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param obj * Object with data to be written to the file. * @param isCriticalPinning * request lock on data reference. * * @return a non-negative value if successful * * @exception HDF5Exception * - Failure in the data conversion. * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - data object is null. **/ public synchronized static int H5Dwrite(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object obj, boolean isCriticalPinning) throws HDF5Exception, HDF5LibraryException, NullPointerException { int status = -1; boolean is1D = false; Class dataClass = obj.getClass(); if (!dataClass.isArray()) { throw (new HDF5JavaException("H5Dread: data is not an array")); } String cname = dataClass.getName(); is1D = (cname.lastIndexOf('[') == cname.indexOf('[')); char dname = cname.charAt(cname.lastIndexOf("[") + 1); if (is1D && (dname == 'B')) { status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (byte[]) obj, isCriticalPinning); } else if (is1D && (dname == 'S')) { status = H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (short[]) obj, isCriticalPinning); } else if (is1D && (dname == 'I')) { status = H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (int[]) obj, isCriticalPinning); } else if (is1D && (dname == 'J')) { status = H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (long[]) obj, isCriticalPinning); } else if (is1D && (dname == 'F')) { status = H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (float[]) obj, isCriticalPinning); } else if (is1D && (dname == 'D')) { status = H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (double[]) obj, isCriticalPinning); } else if (is1D && (dataClass.getComponentType() == String.class)) { log.trace("H5Dwrite_string type"); if (H5.H5Tis_variable_str(mem_type_id)) { status = H5Dwrite_VLStrings(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (Object[]) obj); } else { status = H5Dwrite_string(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, (String[]) obj); } } else { HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.byteify(); // will raise exception on error status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, isCriticalPinning); // clean up these: assign 'null' as hint to gc() buf = null; theArray = null; } return status; } public synchronized static native int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite_double(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, double[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_double(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite_float(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, float[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_float(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite_int(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, int[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_int(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite_long(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, long[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_long(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf, boolean isCriticalPinning) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Dwrite_short(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, short[] buf) throws HDF5LibraryException, NullPointerException { return H5Dwrite_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); } public synchronized static native int H5Dwrite_string(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Dwrite_VLStrings writes a (partial) variable length String dataset, specified by its identifier dataset_id, from * the application memory buffer buf into the file. * * ---- contributed by Rosetta Biosoftware * * @param dataset_id * Identifier of the dataset read from. * @param mem_type_id * Identifier of the memory datatype. * @param mem_space_id * Identifier of the memory dataspace. * @param file_space_id * Identifier of the dataset's dataspace in the file. * @param xfer_plist_id * Identifier of a transfer property list for this I/O operation. * @param buf * Buffer with data to be written to the file. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Dwrite_VLStrings(long dataset_id, long mem_type_id, long mem_space_id, long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Dflush causes all buffers associated with a dataset to be immediately flushed to disk without removing the * data from the cache. * * @param dset_id * IN: Identifier of the dataset to be flushed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Dflush(long dset_id) throws HDF5LibraryException; /** * H5Drefresh causes all buffers associated with a dataset to be cleared and immediately re-loaded with updated * contents from disk. This function essentially closes the dataset, evicts all metadata associated with it * from the cache, and then re-opens the dataset. The reopened dataset is automatically re-registered with the same ID. * * @param dset_id * IN: Identifier of the dataset to be refreshed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Drefresh(long dset_id) throws HDF5LibraryException; // /////// unimplemented //////// // H5_DLL herr_t H5Ddebug(hid_t dset_id); // H5_DLL herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes); // H5_DLL herr_t H5Dformat_convert(hid_t dset_id); // H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type); // herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id, // size_t dst_buf_size, void *dst_buf, H5D_gather_func_t op, void *op_data); // herr_t H5Dscatter(H5D_scatter_func_t op, void *op_data, hid_t type_id, hid_t dst_space_id, void *dst_buf); // //////////////////////////////////////////////////////////// // // // H5E: Error Stack // // // // //////////////////////////////////////////////////////////// /** * H5Eauto_is_v2 determines whether the error auto reporting function for an error stack conforms to the H5E_auto2_t * typedef or the H5E_auto1_t typedef. * * @param stack_id * IN: Error stack identifier. * * @return boolean true if the error stack conforms to H5E_auto2_t and false if it conforms to H5E_auto1_t. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Eauto_is_v2(long stack_id) throws HDF5LibraryException; /** * H5Eclear clears the error stack for the current thread. H5Eclear can fail if there are problems initializing the * library. *

* This may be used by exception handlers to assure that the error condition in the HDF-5 library has been reset. * * @return Returns a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Eclear() throws HDF5LibraryException { H5Eclear2(HDF5Constants.H5E_DEFAULT); return 0; } /** * H5Eclear clears the error stack specified by estack_id, or, if estack_id is set to H5E_DEFAULT, the error stack * for the current thread. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static void H5Eclear(long stack_id) throws HDF5LibraryException { H5Eclear2(stack_id); } /** * H5Eclear2 clears the error stack specified by estack_id, or, if estack_id is set to H5E_DEFAULT, the error stack * for the current thread. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eclear2(long stack_id) throws HDF5LibraryException; /** * H5Eclose_msg closes an error message identifier, which can be either a major or minor message. * * @param err_id * IN: Error message identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eclose_msg(long err_id) throws HDF5LibraryException; /** * H5Eclose_stack closes the object handle for an error stack and releases its resources. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eclose_stack(long stack_id) throws HDF5LibraryException; /** * H5Ecreate_msg adds an error message to an error class defined by client library or application program. * * @param cls_id * IN: Error class identifier. * @param msg_type * IN: The type of the error message. * @param msg * IN: The error message. * * @return a message identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - msg is null. **/ public synchronized static native long H5Ecreate_msg(long cls_id, int msg_type, String msg) throws HDF5LibraryException, NullPointerException; /** * H5Ecreate_stack creates a new empty error stack and returns the new stack's identifier. * * @return an error stack identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Ecreate_stack() throws HDF5LibraryException; /** * H5Eget_class_name retrieves the name of the error class specified by the class identifier. * * @param class_id * IN: Error class identifier. * * @return the name of the error class * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5Eget_class_name(long class_id) throws HDF5LibraryException, NullPointerException; /** * H5Eget_current_stack copies the current error stack and returns an error stack identifier for the new copy. * * @return an error stack identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Eget_current_stack() throws HDF5LibraryException; /** * H5Eset_current_stack replaces the content of the current error stack with a copy of the content of the error * stack specified by estack_id. * * @param stack_id * IN: Error stack identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eset_current_stack(long stack_id) throws HDF5LibraryException; /** * H5Eget_msg retrieves the error message including its length and type. * * @param msg_id * IN: Name of the error class. * @param type_list * OUT: The type of the error message. Valid values are H5E_MAJOR and H5E_MINOR. * * @return the error message * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5Eget_msg(long msg_id, int[] type_list) throws HDF5LibraryException; /** * H5Eget_num retrieves the number of error records in the error stack specified by estack_id (including major, * minor messages and description). * * @param stack_id * IN: Error stack identifier. * * @return the number of error messages * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Eget_num(long stack_id) throws HDF5LibraryException, NullPointerException; /** * H5Eprint2 prints the error stack specified by estack_id on the specified stream, stream. * * @param stack_id * IN: Error stack identifier.If the identifier is H5E_DEFAULT, the current error stack will be printed. * @param stream * IN: File pointer, or stderr if null. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eprint2(long stack_id, Object stream) throws HDF5LibraryException; /** * H5Epop deletes the number of error records specified in count from the top of the error stack specified by * estack_id (including major, minor messages and description). * * @param stack_id * IN: Error stack identifier. * @param count * IN: Version of the client library or application to which the error class belongs. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Epop(long stack_id, long count) throws HDF5LibraryException; /** * H5Epush2 pushes a new error record onto the error stack specified by estack_id. * * @param stack_id * IN: Error stack identifier. * @param file * IN: Name of the file in which the error was detected. * @param func * IN: Name of the function in which the error was detected. * @param line * IN: Line number within the file at which the error was detected. * @param cls_id * IN: Error class identifier. * @param maj_id * IN: Major error identifier. * @param min_id * IN: Minor error identifier. * @param msg * IN: Error description string. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - file, func, or msg is null. **/ public 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); } public synchronized static native void H5Epush2(long stack_id, String file, String func, int line, long cls_id, long maj_id, long min_id, String msg) throws HDF5LibraryException, NullPointerException; /** * H5Eregister_class registers a client library or application program to the HDF5 error API so that the client * library or application program can report errors together with HDF5 library. * * @param cls_name * IN: Name of the error class. * @param lib_name * IN: Name of the client library or application to which the error class belongs. * @param version * IN: Version of the client library or application to which the error class belongs. * * @return a class identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native long H5Eregister_class(String cls_name, String lib_name, String version) throws HDF5LibraryException, NullPointerException; /** * H5Eunregister_class removes the error class specified by class_id. * * @param class_id * IN: Error class identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Eunregister_class(long class_id) throws HDF5LibraryException; /** * H5Ewalk walks the error stack specified by estack_id for the current thread and calls the * function specified in func for each error along the way. * * @param stack_id * IN: Error stack identifier. * @param direction * IN: Direction in which the error stack is to be walked. * @param func * IN: Function to be called for each error encountered. * @param client_data * IN: Data to be passed with func. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - func is null. **/ public static void H5Ewalk(long stack_id, long direction, H5E_walk_cb func, H5E_walk_t client_data) throws HDF5LibraryException, NullPointerException { H5Ewalk2(stack_id, direction, func, client_data); } public synchronized static native void H5Ewalk2(long stack_id, long direction, H5E_walk_cb func, H5E_walk_t client_data) throws HDF5LibraryException, NullPointerException; // /////// unimplemented //////// // public interface H5E_auto2_t extends Callback // { // int callback(int estack, Pointer client_data); // } // int H5Eget_auto(long estack_id, H5E_auto2_t func, PointerByReference client_data); // { // return H5Eget_auto2(estack_id, func, client_data); // } // int H5Eget_auto2(long estack_id, H5E_auto2_t func, PointerByReference client_data); // int H5Eset_auto(long estack_id, H5E_auto2_t func, Pointer client_data); // { // return H5Eset_auto2(estack_id, func, client_data); // } // int H5Eset_auto2(long estack_id, H5E_auto2_t func, Pointer client_data); // public static void H5Epush(long err_stack, String file, String func, int line, // long cls_id, long maj_id, long min_id, String msg, ...) // { // H5Epush2(err_stack, file, func, line, cls_id, maj_id, min_id, msg, ...); // } // public synchronized static native void H5Epush2(long err_stack, String file, String func, int line, // long cls_id, long maj_id, long min_id, String msg, ...); // //////////////////////////////////////////////////////////// // // // H5F: File Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Fclose terminates access to an HDF5 file. * * @param file_id * Identifier of a file to terminate access to. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Fclose(long file_id) throws HDF5LibraryException { if (file_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; log.trace("OPEN_IDS: H5Fclose remove {}", file_id); OPEN_IDS.remove(file_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); return _H5Fclose(file_id); } private synchronized static native int _H5Fclose(long file_id) throws HDF5LibraryException; /** * H5Fopen opens an existing file and is the primary function for accessing existing HDF5 files. * * @param name * Name of the file to access. * @param flags * File access flags. * @param access_id * Identifier for the file access properties list. * * @return a file identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static long H5Fopen(String name, int flags, long access_id) throws HDF5LibraryException, NullPointerException { long id = _H5Fopen(name, flags, access_id); if (id > 0) { log.trace("OPEN_IDS: H5Fopen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Fopen(String name, int flags, long access_id) throws HDF5LibraryException, NullPointerException; /** * H5Freopen reopens an HDF5 file. * * @param file_id * Identifier of a file to terminate and reopen access to. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @return a new file identifier if successful **/ public static long H5Freopen(long file_id) throws HDF5LibraryException { long id = _H5Freopen(file_id); if (id > 0) { log.trace("OPEN_IDS: H5Freopen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Freopen(long file_id) throws HDF5LibraryException; /** * H5Fcreate is the primary function for creating HDF5 files. * * @param name * Name of the file to access. * @param flags * File access flags. Possible values include: *

    *
  • * H5F_ACC_RDWR Allow read and write access to file.
    • *
  • * H5F_ACC_RDONLY Allow read-only access to file.
    • *
  • * H5F_ACC_TRUNC Truncate file, if it already exists, erasing all data previously stored in the file.
    • *
  • * H5F_ACC_EXCL Fail if file already exists.
    • *
  • * H5P_DEFAULT Apply default file access and creation properties.
    • *
* * @param create_id * File creation property list identifier, used when modifying default file meta-data. Use H5P_DEFAULT * for default access properties. * @param access_id * File access property list identifier. If parallel file access is desired, this is a collective call * according to the communicator stored in the access_id (not supported in Java). Use H5P_DEFAULT for * default access properties. * * @return a file identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static long H5Fcreate(String name, int flags, long create_id, long access_id) throws HDF5LibraryException, NullPointerException { long id = _H5Fcreate(name, flags, create_id, access_id); if (id > 0) { log.trace("OPEN_IDS: H5Fcreate add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Fcreate(String name, int flags, long create_id, long access_id) throws HDF5LibraryException, NullPointerException; /** * H5Fflush causes all buffers associated with a file or object to be immediately flushed (written) to disk without * removing the data from the (memory) cache. *

* After this call completes, the file (or object) is in a consistent state and all data written to date is assured * to be permanent. * * @param object_id * Identifier of object used to identify the file. object_id can be any object associated with the * file, including the file itself, a dataset, a group, an attribute, or a named data type. * @param scope * specifies the scope of the flushing action, in the case that the HDF-5 file is not a single physical * file. *

* Valid values are: *

    *
  • * H5F_SCOPE_GLOBAL Flushes the entire virtual file.
    • *
  • * H5F_SCOPE_LOCAL Flushes only the specified file.
    • *
* * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Fflush(long object_id, int scope) throws HDF5LibraryException; /** * H5Fget_access_plist returns the file access property list identifier of the specified file. * * @param file_id * Identifier of file to get access property list of * * @return a file access property list identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Fget_access_plist(long file_id) throws HDF5LibraryException { long id = _H5Fget_access_plist(file_id); if (id > 0) { log.trace("OPEN_IDS: H5Fget_access_plist add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Fget_access_plist(long file_id) throws HDF5LibraryException; /** * H5Fget_create_plist returns a file creation property list identifier identifying the creation properties used to * create this file. * * @param file_id * Identifier of the file to get creation property list * * @return a file creation property list identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Fget_create_plist(long file_id) throws HDF5LibraryException { long id = _H5Fget_create_plist(file_id); if (id > 0) { log.trace("OPEN_IDS: H5Fget_create_plist add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Fget_create_plist(long file_id) throws HDF5LibraryException; public synchronized static native long H5Fget_filesize(long file_id) throws HDF5LibraryException; /** * H5Fget_freespace returns the amount of space that is unused by any objects in the file. * * @param file_id * IN: File identifier for a currently-open HDF5 file * * @return the amount of free space in the file * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Fget_freespace(long file_id) throws HDF5LibraryException; /** * H5Fget_intent retrieves the intended access mode flag passed with H5Fopen when the file was opened. * * @param file_id * IN: File identifier for a currently-open HDF5 file * * @return the intended access mode flag, as originally passed with H5Fopen. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Fget_intent(long file_id) throws HDF5LibraryException; /** * H5Fget_mdc_hit_rate queries the metadata cache of the target file to obtain its hit rate (cache hits / (cache * hits + cache misses)) since the last time hit rate statistics were reset. * * @param file_id * IN: Identifier of the target file. * * @return the double in which the hit rate is returned. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native double H5Fget_mdc_hit_rate(long file_id) throws HDF5LibraryException; /** * H5Fget_mdc_size queries the metadata cache of the target file for the desired size information. * * @param file_id * IN: Identifier of the target file. * @param metadata_cache * OUT: Current metadata cache information *
    *
  • metadata_cache[0] = max_size_ptr // current cache maximum size
    • *
  • metadata_cache[1] = min_clean_size_ptr // current cache minimum clean size
    • *
  • metadata_cache[2] = cur_size_ptr // current cache size
    • *
* * @return current number of entries in the cache * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - metadata_cache is null. **/ public synchronized static native int H5Fget_mdc_size(long file_id, long[] metadata_cache) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Fget_name retrieves the name of the file to which the object obj_id belongs. * * @param obj_id * IN: Identifier of the object for which the associated filename is sought. * * @return the filename. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5Fget_name(long obj_id) throws HDF5LibraryException; /** * H5Fget_obj_count returns the number of open object identifiers for the file. * * @param file_id * IN: File identifier for a currently-open HDF5 file * @param types * IN: Type of object for which identifiers are to be returned. *
    *
  • H5F_OBJ_FILE Files only
    • *
  • H5F_OBJ_DATASET Datasets only
    • *
  • H5F_OBJ_GROUP Groups only
    • *
  • H5F_OBJ_DATATYPE Named datatypes only
    • *
  • H5F_OBJ_ATTR Attributes only
    • *
  • H5F_OBJ_ALL All of the above
    • *
  • H5F_OBJ_LOCAL Restrict search to objects opened through current file identifier.
    • *
* * @return the number of open objects. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Fget_obj_count(long file_id, int types) throws HDF5LibraryException; /** * H5Fget_obj_ids returns the list of identifiers for all open HDF5 objects fitting the specified criteria. * * @param file_id * IN: File identifier for a currently-open HDF5 file * @param types * IN: Type of object for which identifiers are to be returned. * @param max_objs * IN: Maximum number of object identifiers to place into obj_id_list. * @param obj_id_list * OUT: Pointer to the returned list of open object identifiers. * * @return the number of objects placed into obj_id_list. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - obj_id_list is null. **/ public synchronized static native long H5Fget_obj_ids(long file_id, int types, long max_objs, long[] obj_id_list) throws HDF5LibraryException, NullPointerException; /** * H5Fis_hdf5 determines whether a file is in the HDF5 format. * * @param name * File name to check format. * * @return true if is HDF-5, false if not. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native boolean H5Fis_hdf5(String name) throws HDF5LibraryException, NullPointerException; /** * H5Fmount mounts the file specified by child_id onto the group specified by loc_id and name using the mount * properties plist_id. * * @param loc_id * The identifier for the group onto which the file specified by child_id is to be mounted. * @param name * The name of the group onto which the file specified by child_id is to be mounted. * @param child_id * The identifier of the file to be mounted. * @param plist_id * The identifier of the property list to be used. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Fmount(long loc_id, String name, long child_id, long plist_id) throws HDF5LibraryException, NullPointerException; /** * Given a mount point, H5Funmount dissassociates the mount point's file from the file mounted there. * * @param loc_id * The identifier for the location at which the specified file is to be unmounted. * @param name * The name of the file to be unmounted. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Funmount(long loc_id, String name) throws HDF5LibraryException, NullPointerException; /** * H5Freset_mdc_hit_rate_stats resets the hit rate statistics counters in the metadata cache associated with the * specified file. * * @param file_id * IN: Identifier of the target file. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Freset_mdc_hit_rate_stats(long file_id) throws HDF5LibraryException; /** * H5Fget_info returns global information for the file associated with the * object identifier obj_id. * * @param obj_id IN: Object identifier for any object in the file. * * @return A buffer(H5F_info2_t) for current "global" information about file * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native H5F_info2_t H5Fget_info(long obj_id) throws HDF5LibraryException; /** * H5Fclear_elink_file_cache evicts all the cached child files in the specified file's external file * cache, causing them to be closed if there is nothing else holding them open. * * @param file_id * IN: Identifier of the target file. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Fclear_elink_file_cache(long file_id) throws HDF5LibraryException; /** * H5Fstart_swmr_write will activate SWMR writing mode for a file associated with file_id. This routine will * prepare and ensure the file is safe for SWMR writing. * * @param file_id * IN: Identifier of the target file. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Fstart_swmr_write(long file_id) throws HDF5LibraryException; /** * H5Fstart_mdc_logging starts logging metadata cache events if logging was previously enabled. * * @param file_id * IN: Identifier of the target file. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Fstart_mdc_logging(long file_id) throws HDF5LibraryException; /** * H5Fstop_mdc_logging stops logging metadata cache events if logging was previously enabled and is currently ongoing. * * @param file_id * IN: Identifier of the target file. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Fstop_mdc_logging(long file_id) throws HDF5LibraryException; /** * H5Fget_mdc_logging_status gets the current metadata cache logging status. * * @param file_id * IN: Identifier of the target file. * * @param mdc_logging_status * the status * mdc_logging_status[0] = is_enabled, whether logging is enabled * mdc_logging_status[1] = is_currently_logging, whether events are currently being logged * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - mdc_logging_status is null. **/ public synchronized static native void H5Fget_mdc_logging_status(long file_id, boolean[] mdc_logging_status) throws HDF5LibraryException, NullPointerException; // /////// unimplemented //////// // H5_DLL herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa); // H5_DLL herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment); // ssize_t H5Fget_file_image(hid_t file_id, void * buf_ptr, size_t buf_len); // herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info); // ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type, size_t nsects, H5F_sect_info_t *sect_info/*out*/); // H5_DLL herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver_t high); // H5_DLL herr_t H5Fformat_convert(hid_t fid); // H5_DLL herr_t H5Freset_page_buffering_stats(hid_t file_id); // H5_DLL herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2], // unsigned hits[2], unsigned misses[2], unsigned evictions[2], unsigned bypasses[2]); // H5_DLL herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t *image_size); // #ifdef H5_HAVE_PARALLEL // H5_DLL herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag); // H5_DLL herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag); // #endif /* H5_HAVE_PARALLEL */ // /** // * H5Fget_vfd_handle returns a pointer to the file handle from the // low-level file driver // * currently being used by the HDF5 library for file I/O. // * // * @param file_id IN: Identifier of the file to be queried. // * @param fapl IN: File access property list identifier. // * // * @return a pointer to the file handle being used by the low-level // virtual file driver. // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // **/ // public synchronized static native Pointer file_handle // H5Fget_vfd_handle(int file_id, int fapl) // throws HDF5LibraryException; // /** // * H5Fget_mdc_config loads the current metadata cache configuration into // * the instance of H5AC_cache_config_t pointed to by the config_ptr // parameter. // * // * @param file_id IN: Identifier of the target file // * @param config_ptr IN/OUT: Pointer to the instance of // H5AC_cache_config_t in which the current metadata cache configuration is to be reported. // * // * @return none // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // * @exception NullPointerException - config_ptr is null. // **/ // public synchronized static native void H5Fget_mdc_config(int file_id, H5AC_cache_config_t config_ptr) // throws HDF5LibraryException, NullPointerException; // /** // * H5Fset_mdc_config attempts to configure the file's metadata cache // according to the configuration supplied. // * // * @param file_id IN: Identifier of the target file // * @param config_ptr IN: Pointer to the instance of H5AC_cache_config_t // containing the desired configuration. // * // * @return none // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // * @exception NullPointerException - config_ptr is null. // **/ // public synchronized static native int H5Fset_mdc_config(int file_id, H5AC_cache_config_t config_ptr) // throws HDF5LibraryException, NullPointerException; // //////////////////////////////////////////////////////////// // // // H5FD: File Driver Interface Functions // // // // //////////////////////////////////////////////////////////// // /////// unimplemented //////// // H5_DLL hid_t H5FDregister(const H5FD_class_t *cls); // H5_DLL herr_t H5FDunregister(hid_t driver_id); // H5_DLL H5FD_t *H5FDopen(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr); // H5_DLL herr_t H5FDclose(H5FD_t *file); // H5_DLL int H5FDcmp(const H5FD_t *f1, const H5FD_t *f2); // H5_DLL int H5FDquery(const H5FD_t *f, unsigned long *flags); // H5_DLL haddr_t H5FDalloc(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, hsize_t size); // H5_DLL herr_t H5FDfree(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size); // H5_DLL haddr_t H5FDget_eoa(H5FD_t *file, H5FD_mem_t type); // H5_DLL herr_t H5FDset_eoa(H5FD_t *file, H5FD_mem_t type, haddr_t eoa); // H5_DLL haddr_t H5FDget_eof(H5FD_t *file, H5FD_mem_t type); // H5_DLL herr_t H5FDget_vfd_handle(H5FD_t *file, hid_t fapl, void**file_handle); // H5_DLL herr_t H5FDread(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, void *buf/*out*/); // H5_DLL herr_t H5FDwrite(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, const void *buf); // H5_DLL herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, hbool_t closing); // H5_DLL herr_t H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing); // H5_DLL herr_t H5FDlock(H5FD_t *file, hbool_t rw); // H5_DLL herr_t H5FDunlock(H5FD_t *file); // H5_DLL herr_t H5FDdriver_query(hid_t driver_id, unsigned long *flags/*out*/); // //////////////////////////////////////////////////////////// // // // H5FS: File Free Space Interface Functions // // // // //////////////////////////////////////////////////////////// // No public Functions // //////////////////////////////////////////////////////////// // // // H5G: Group Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Gclose releases resources used by a group which was opened by a call to H5Gcreate() or H5Gopen(). * * @param group_id * Group identifier to release. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Gclose(long group_id) throws HDF5LibraryException { if (group_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; log.trace("OPEN_IDS: H5Gclose remove {}", group_id); OPEN_IDS.remove(group_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); return _H5Gclose(group_id); } private synchronized static native int _H5Gclose(long group_id) throws HDF5LibraryException; /** * H5Gcreate creates a new group with the specified name at the specified location, loc_id. * * @param loc_id * IN: The file or group identifier. * @param name * IN: The absolute or relative name of the new group. * @param lcpl_id * IN: Identifier of link creation property list. * @param gcpl_id * IN: Identifier of group creation property list. * @param gapl_id * IN: Identifier of group access property list. (No group access properties have been implemented at * this time; use H5P_DEFAULT.) * * @return a valid group identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static long H5Gcreate(long loc_id, String name, long lcpl_id, long gcpl_id, long gapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Gcreate2(loc_id, name, lcpl_id, gcpl_id, gapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Gcreate add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Gcreate2(long loc_id, String name, long lcpl_id, long gcpl_id, long gapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Gcreate_anon creates a new empty group in the file specified by loc_id. * * @param loc_id * IN: File or group identifier specifying the file in which the new group is to be created. * @param gcpl_id * IN: Identifier of group creation property list. * @param gapl_id * IN: Identifier of group access property list. (No group access properties have been implemented at * this time; use H5P_DEFAULT.) * * @return a valid group identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Gcreate_anon(long loc_id, long gcpl_id, long gapl_id) throws HDF5LibraryException { long id = _H5Gcreate_anon(loc_id, gcpl_id, gapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Gcreate_anon add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Gcreate_anon(long loc_id, long gcpl_id, long gapl_id) throws HDF5LibraryException; /** * H5Gget_create_plist returns an identifier for the group creation property list associated with the group * specified by group_id. * * @param group_id * IN: Identifier of the group. * * @return an identifier for the group's creation property list * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Gget_create_plist(long group_id) throws HDF5LibraryException; /** * H5Gget_info retrieves information about the group specified by group_id. The information is returned in the * group_info struct. * * @param group_id * IN: Identifier of the group. * * @return a structure in which group information is returned * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native H5G_info_t H5Gget_info(long group_id) throws HDF5LibraryException; /** * H5Gget_info_by_idx retrieves information about a group, according to the group's position within an index. * * @param group_id * IN: File or group identifier. * @param group_name * IN: Name of group for which information is to be retrieved. * @param idx_type * IN: Type of index by which objects are ordered * @param order * IN: Order of iteration within index * @param n * IN: Attribute's position in index * @param lapl_id * IN: Link access property list. * * @return a structure in which group information is returned * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native H5G_info_t H5Gget_info_by_idx(long group_id, String group_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Gget_info_by_name retrieves information about the group group_name located in the file or group specified by * loc_id. * * @param group_id * IN: File or group identifier. * @param name * IN: Name of group for which information is to be retrieved. * @param lapl_id * IN: Link access property list. * * @return a structure in which group information is returned * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native H5G_info_t H5Gget_info_by_name(long group_id, String name, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * retrieves information of all objects under the group (name) located in the file or group specified by loc_id. * * @param loc_id * IN: File or group identifier * @param name * IN: Name of group for which information is to be retrieved * @param objNames * OUT: Names of all objects under the group, name. * @param objTypes * OUT: Types of all objects under the group, name. * @param objRef * OUT: Reference number of all objects under the group, name. * * @return the number of items found * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. */ public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] objNames, int[] objTypes, long[] objRef) throws HDF5LibraryException, NullPointerException { if (objNames == null) { throw new NullPointerException("H5Gget_obj_info_all(): name array is null"); } return H5Gget_obj_info_all(loc_id, name, objNames, objTypes, null, null, objRef, HDF5Constants.H5_INDEX_NAME); } public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype, int[] ltype, long[] ref, int indx_type) throws HDF5LibraryException, NullPointerException { return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, null, ref, indx_type, -1); } public synchronized static int H5Gget_obj_info_all(long loc_id, String name, String[] oname, int[] otype, int[] ltype, long[] fno, long[] ref, int indx_type) throws HDF5LibraryException, NullPointerException { return H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, ref, oname.length, indx_type, -1); } public synchronized static int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype, int[] ltype, long[] fno, long[] ref, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException { if (oname == null) { throw new NullPointerException("H5Gget_obj_info_full(): name array is null"); } if (otype == null) { throw new NullPointerException("H5Gget_obj_info_full(): object type array is null"); } if (oname.length == 0) { throw new HDF5LibraryException("H5Gget_obj_info_full(): array size is zero"); } if (oname.length != otype.length) { throw new HDF5LibraryException("H5Gget_obj_info_full(): name and type array sizes are different"); } if (ltype == null) ltype = new int[otype.length]; if (fno == null) fno = new long[ref.length]; if (indx_type < 0) indx_type = HDF5Constants.H5_INDEX_NAME; if (indx_order < 0) indx_order = HDF5Constants.H5_ITER_INC; log.trace("H5Gget_obj_info_full: oname_len={}", oname.length); int status = H5Gget_obj_info_full(loc_id, name, oname, otype, ltype, fno, ref, oname.length, indx_type, indx_order); for (int indx = 0; indx < oname.length; indx++) log.trace("H5Gget_obj_info_full: oname={}", oname[indx]); return status; } private synchronized static native int H5Gget_obj_info_full(long loc_id, String name, String[] oname, int[] otype, int[] ltype, long[] fno, long[] ref, int n, int indx_type, int indx_order) throws HDF5LibraryException, NullPointerException; /** * H5Gget_obj_info_idx report the name and type of object with index 'idx' in a Group. The 'idx' corresponds to the * index maintained by H5Giterate. Each link is returned, so objects with multiple links will be counted once for * each link. * * @param loc_id * IN: file or group ID. * @param name * IN: name of the group to iterate, relative to the loc_id * @param idx * IN: the index of the object to iterate. * @param oname * the name of the object [OUT] * @param type * the type of the object [OUT] * * @return non-negative if successful, -1 if not. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. */ public synchronized static int H5Gget_obj_info_idx(long loc_id, String name, int idx, String[] oname, int[] type) throws HDF5LibraryException, NullPointerException { String n[] = new String[1]; n[0] = new String(""); oname[0] = H5Lget_name_by_idx(loc_id, name, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, idx, HDF5Constants.H5P_DEFAULT); H5L_info_t info = H5Lget_info_by_idx(loc_id, name, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, idx, HDF5Constants.H5P_DEFAULT); type[0] = info.type; return 0; } /* * Add these methods so that we don't need to call * in a loop to get information for all the object in a group, which takes * a lot of time to finish if the number of objects is more than 10,000 */ /** * retrieves information of all objects (recurvisely) under the group (name) located in the file or group specified * by loc_id upto maximum specified by objMax. * * @param loc_id * IN: File or group identifier * @param objNames * OUT: Names of all objects under the group, name. * @param objTypes * OUT: Types of all objects under the group, name. * @param lnkTypes * OUT: Types of all links under the group, name. * @param objRef * OUT: Reference number of all objects under the group, name. * @param objMax * IN: Maximum number of all objects under the group, name. * * @return the number of items found * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. */ public synchronized static int H5Gget_obj_info_max(long loc_id, String[] objNames, int[] objTypes, int[] lnkTypes, long[] objRef, long objMax) throws HDF5LibraryException, NullPointerException { if (objNames == null) { throw new NullPointerException("H5Gget_obj_info_max(): name array is null"); } if (objTypes == null) { throw new NullPointerException("H5Gget_obj_info_max(): object type array is null"); } if (lnkTypes == null) { throw new NullPointerException("H5Gget_obj_info_max(): link type array is null"); } if (objNames.length <= 0) { throw new HDF5LibraryException("H5Gget_obj_info_max(): array size is zero"); } if (objMax <= 0) { throw new HDF5LibraryException("H5Gget_obj_info_max(): maximum array size is zero"); } if (objNames.length != objTypes.length) { throw new HDF5LibraryException("H5Gget_obj_info_max(): name and type array sizes are different"); } return H5Gget_obj_info_max(loc_id, objNames, objTypes, lnkTypes, objRef, objMax, objNames.length); } private synchronized static native int H5Gget_obj_info_max(long loc_id, String[] oname, int[] otype, int[] ltype, long[] ref, long amax, int n) throws HDF5LibraryException, NullPointerException; /** * H5Gn_members report the number of objects in a Group. The 'objects' include everything that will be visited by * H5Giterate. Each link is returned, so objects with multiple links will be counted once for each link. * * @param loc_id * file or group ID. * @param name * name of the group to iterate, relative to the loc_id * * @return the number of members in the group or -1 if error. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. */ public synchronized static long H5Gn_members(long loc_id, String name) throws HDF5LibraryException, NullPointerException { long grp_id = H5Gopen(loc_id, name, HDF5Constants.H5P_DEFAULT); long n = -1; try { H5G_info_t info = H5.H5Gget_info(grp_id); n = info.nlinks; } finally { H5Gclose(grp_id); } return n; } /** * H5Gopen opens an existing group, name, at the location specified by loc_id. * * @param loc_id * IN: File or group identifier specifying the location of the group to be opened. * @param name * IN: Name of group to open. * @param gapl_id * IN: Identifier of group access property list. * * @return a valid group identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static long H5Gopen(long loc_id, String name, long gapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Gopen2(loc_id, name, gapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Gopen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Gopen2(long loc_id, String name, long gapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Gflush causes all buffers associated with a group to be immediately flushed to disk without * removing the data from the cache. * * @param group_id * IN: Identifier of the group to be flushed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Gflush(long group_id) throws HDF5LibraryException; /** * H5Grefresh causes all buffers associated with a group to be cleared and immediately re-loaded * with updated contents from disk. This function essentially closes the group, evicts all metadata * associated with it from the cache, and then re-opens the group. The reopened group is automatically * re-registered with the same ID. * * @param group_id * IN: Identifier of the group to be refreshed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Grefresh(long group_id) throws HDF5LibraryException; // //////////////////////////////////////////////////////////// // // // H5HF: Fractal Heap Interface Functions // // // // //////////////////////////////////////////////////////////// // No public Functions // //////////////////////////////////////////////////////////// // // // H5HG: Global Heap Interface Functions // // // // //////////////////////////////////////////////////////////// // No public Functions // //////////////////////////////////////////////////////////// // // // H5HL: Local Heap Interface Functions // // // // //////////////////////////////////////////////////////////// // No public Functions // //////////////////////////////////////////////////////////// // // // H5I: HDF5 1.8 Identifier Interface API Functions // // // // //////////////////////////////////////////////////////////// public synchronized static native long H5Iget_file_id(long obj_id) throws HDF5LibraryException; @Deprecated public synchronized static native long H5Iget_name_long(long obj_id, String[] name, long size) throws HDF5LibraryException, NullPointerException; /** * H5Iget_name_str retrieves the name of an object specified by the identifier, obj_id. * * @param obj_id * IN: Identifier of the object. * * @return String for Attribute name. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5Iget_name(long obj_id) throws HDF5LibraryException; public synchronized static native int H5Iget_ref(long obj_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Idec_ref(long obj_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Iinc_ref(long obj_id) throws HDF5LibraryException, NullPointerException; /** * H5Iget_type retrieves the type of the object identified by obj_id. * * @param obj_id * IN: Object identifier whose type is to be determined. * * @return the object type if successful; otherwise H5I_BADID. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Iget_type(long obj_id) throws HDF5LibraryException; /** * H5Iget_type_ref retrieves the reference count on an ID type. The reference count is used by the library to * indicate when an ID type can be destroyed. * * @param type_id * IN: The identifier of the type whose reference count is to be retrieved * * @return The current reference count on success, negative on failure. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Iget_type_ref(long type_id) throws HDF5LibraryException; /** * H5Idec_type_ref decrements the reference count on an identifier type. The reference count is used by the * library to indicate when an identifier type can be destroyed. If the reference count reaches zero, * this function will destroy it. * * @param type_id * IN: The identifier of the type whose reference count is to be decremented * * @return The current reference count on success, negative on failure. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Idec_type_ref(long type_id) throws HDF5LibraryException; /** * H5Iinc_type_ref increments the reference count on an ID type. The reference count is used by the library * to indicate when an ID type can be destroyed. * * @param type_id * IN: The identifier of the type whose reference count is to be incremented * * @return The current reference count on success, negative on failure. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Iinc_type_ref(long type_id) throws HDF5LibraryException; /** * H5Inmembers returns the number of identifiers of the identifier type specified in type. * * @param type_id * IN: Identifier for the identifier type whose member count will be retrieved * * @return Number of identifiers of the specified identifier type * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Inmembers(long type_id) throws HDF5LibraryException; /** * H5Iis_valid indicates if the identifier type specified in obj_id is valid. * * @param obj_id * IN: Identifier to be checked * * @return a boolean, true if the specified identifier id is valid * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Iis_valid(long obj_id) throws HDF5LibraryException; /** * H5Itype_exists indicates if the identifier type specified in type exists. * * @param type_id * IN: the identifier type to be checked * * @return a boolean, true if the specified identifier type exists * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Itype_exists(int type_id) throws HDF5LibraryException; /** * H5Iclear_type deletes all identifiers of the type identified by the argument type. * * @param type_id * IN: Identifier of identifier type which is to be cleared of identifiers * @param force * IN: Whether or not to force deletion of all identifiers * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Iclear_type(int type_id, boolean force) throws HDF5LibraryException; /** * H5Idestroy_type deletes an entire identifier type. All identifiers of this type are destroyed * and no new identifiers of this type can be registered. * * @param type_id * IN: Identifier of identifier type which is to be destroyed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Idestroy_type(int type_id) throws HDF5LibraryException; // /////// unimplemented //////// // void *H5Iobject_verify(hid_t id, H5I_type_t id_type); // hid_t H5Iregister(H5I_type_t type, const void *object); // H5I_type_t H5Iregister_type(size_t hash_size, unsigned reserved, H5I_free_t free_func); // void *H5Iremove_verify(hid_t id, H5I_type_t id_type); // void *H5Isearch(H5I_type_t type, H5I_search_func_t func, void *key); // ////////////////////////////////////////////////////////////////// // H5L: Link Interface Functions // // ////////////////////////////////////////////////////////////////// /** * H5Lcopy copies a link from one location to another. * * @param src_loc * IN: Location identifier of the source link * @param src_name * IN: Name of the link to be copied * @param dst_loc * IN: Location identifier specifying the destination of the copy * @param dst_name * IN: Name to be assigned to the new copy * @param lcpl_id * IN: Link creation property list identifier * @param lapl_id * IN: Link access property list identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native void H5Lcopy(long src_loc, String src_name, long dst_loc, String dst_name, long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lcreate_external creates a new soft link to an external object, which is an object in a different HDF5 file * from the location of the link. * * @param file_name * IN: Name of the target file containing the target object. * @param obj_name * IN: Path within the target file to the target object. * @param link_loc_id * IN: The file or group identifier for the new link. * @param link_name * IN: The name of the new link. * @param lcpl_id * IN: Link creation property list identifier * @param lapl_id * IN: Link access property list identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native void H5Lcreate_external(String file_name, String obj_name, long link_loc_id, String link_name, long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lcreate_hard creates a new hard link to a pre-existing object in an HDF5 file. * * @param cur_loc * IN: The file or group identifier for the target object. * @param cur_name * IN: Name of the target object, which must already exist. * @param dst_loc * IN: The file or group identifier for the new link. * @param dst_name * IN: The name of the new link. * @param lcpl_id * IN: Link creation property list identifier * @param lapl_id * IN: Link access property list identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - cur_name or dst_name is null. **/ public synchronized static native void H5Lcreate_hard(long cur_loc, String cur_name, long dst_loc, String dst_name, long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lcreate_soft creates a new soft link to an object in an HDF5 file. * * @param link_target * IN: Path to the target object, which is not required to exist. * @param link_loc_id * IN: The file or group identifier for the new link. * @param link_name * IN: The name of the new link. * @param lcpl_id * IN: Link creation property list identifier * @param lapl_id * IN: Link access property list identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - link_name is null. **/ public synchronized static native void H5Lcreate_soft(String link_target, long link_loc_id, String link_name, long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Ldelete removes the link specified from a group. * * @param loc_id * IN: Identifier of the file or group containing the object. * @param name * IN: Name of the link to delete. * @param lapl_id * IN: Link access property list identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native void H5Ldelete(long loc_id, String name, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Ldelete_by_idx removes the nth link in a group according to the specified order and in the specified index. * * @param loc_id * IN: File or group identifier specifying location of subject group * @param group_name * IN: Name of subject group * @param idx_type * IN: Index or field which determines the order * @param order * IN: Order within field or index * @param n * IN: Link for which to retrieve information * @param lapl_id * IN: Link access property list identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - group_name is null. **/ public synchronized static native void H5Ldelete_by_idx(long loc_id, String group_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lexists checks if a link with a particular name exists in a group. * * @param loc_id * IN: Identifier of the file or group to query. * @param name * IN: The name of the link to check. * @param lapl_id * IN: Link access property list identifier * * @return a boolean, true if the name exists, otherwise false. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native boolean H5Lexists(long loc_id, String name, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lget_info returns information about the specified link. * * @param loc_id * IN: Identifier of the file or group. * @param name * IN: Name of the link for which information is being sought. * @param lapl_id * IN: Link access property list identifier * * @return a buffer(H5L_info_t) for the link information. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native H5L_info_t H5Lget_info(long loc_id, String name, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lget_info_by_idx opens a named datatype at the location specified by loc_id and return an identifier for the * datatype. * * @param loc_id * IN: File or group identifier specifying location of subject group * @param group_name * IN: Name of subject group * @param idx_type * IN: Type of index * @param order * IN: Order within field or index * @param n * IN: Link for which to retrieve information * @param lapl_id * IN: Link access property list identifier * * @return a buffer(H5L_info_t) for the link information. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - group_name is null. **/ public synchronized static native H5L_info_t H5Lget_info_by_idx(long loc_id, String group_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lget_name_by_idx retrieves name of the nth link in a group, according to the order within a specified field or * index. * * @param loc_id * IN: File or group identifier specifying location of subject group * @param group_name * IN: Name of subject group * @param idx_type * IN: Type of index * @param order * IN: Order within field or index * @param n * IN: Link for which to retrieve information * @param lapl_id * IN: Link access property list identifier * * @return a String for the link name. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - group_name is null. **/ public synchronized static native String H5Lget_name_by_idx(long loc_id, String group_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lget_value returns the link value of a symbolic link. Note that this function is a combination * of H5Lget_info(), H5Lget_val() and for external links, H5Lunpack_elink_val. * * @param loc_id * IN: Identifier of the file or group containing the object. * @param name * IN: Name of the symbolic link. * @param link_value * OUT: Path of the symbolic link, or the file_name and path of an external file. * @param lapl_id * IN: Link access property list identifier * * @return the link type * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Lget_value(long loc_id, String name, String[] link_value, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lget_value_by_idx retrieves value of the nth link in a group, according to the order within an index. * Note that this function is a combination of H5Lget_info(), H5Lget_val() and for external links, * H5Lunpack_elink_val. * * @param loc_id * IN: File or group identifier specifying location of subject group * @param group_name * IN: Name of subject group * @param idx_type * IN: Type of index * @param order * IN: Order within field or index * @param n * IN: Link for which to retrieve information * @param link_value * OUT: Path of the symbolic link, or the file_name and path of an external file. * @param lapl_id * IN: Link access property list identifier * * @return the link type * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - group_name is null. **/ public synchronized static native int H5Lget_value_by_idx(long loc_id, String group_name, int idx_type, int order, long n, String[] link_value, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Literate iterates through links in a group. * * @param grp_id * IN: Identifier specifying subject group * @param idx_type * IN: Type of index * @param order * IN: Order of iteration within index * @param idx * IN: Iteration position at which to start * @param op * IN: Callback function passing data regarding the link to the calling application * @param op_data * IN: User-defined pointer to data required by the application for its processing of the link * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Literate(long grp_id, int idx_type, int order, long idx, H5L_iterate_cb op, H5L_iterate_t op_data) throws HDF5LibraryException; /** * H5Literate_by_name iterates through links in a group. * * @param grp_id * IN: Identifier specifying subject group * @param group_name * IN: Name of subject group * @param idx_type * IN: Type of index * @param order * IN: Order of iteration within index * @param idx * IN: Iteration position at which to start * @param op * IN: Callback function passing data regarding the link to the calling application * @param op_data * IN: User-defined pointer to data required by the application for its processing of the link * @param lapl_id * IN: Link access property list identifier * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - group_name is null. **/ public synchronized static native int H5Literate_by_name(long grp_id, String group_name, int idx_type, int order, long idx, H5L_iterate_cb op, H5L_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lmove renames a link within an HDF5 file. * * @param src_loc * IN: Original file or group identifier. * @param src_name * IN: Original link name. * @param dst_loc * IN: Destination file or group identifier. * @param dst_name * IN: New link name. * @param lcpl_id * IN: Link creation property list identifier to be associated with the new link. * @param lapl_id * IN: Link access property list identifier to be associated with the new link. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native void H5Lmove(long src_loc, String src_name, long dst_loc, String dst_name, long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lvisit recursively visits all links starting from a specified group. * * @param grp_id * IN: Identifier specifying subject group * @param idx_type * IN: Type of index * @param order * IN: Order of iteration within index * @param op * IN: Callback function passing data regarding the link to the calling application * @param op_data * IN: User-defined pointer to data required by the application for its processing of the link * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Lvisit(long grp_id, int idx_type, int order, H5L_iterate_cb op, H5L_iterate_t op_data) throws HDF5LibraryException; /** * H5Lvisit_by_name recursively visits all links starting from a specified group. * * @param loc_id * IN: Identifier specifying subject group * @param group_name * IN: Name of subject group * @param idx_type * IN: Type of index * @param order * IN: Order of iteration within index * @param op * IN: Callback function passing data regarding the link to the calling application * @param op_data * IN: User-defined pointer to data required by the application for its processing of the link * @param lapl_id * IN: link access property * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - group_name is null. **/ public synchronized static native int H5Lvisit_by_name(long loc_id, String group_name, int idx_type, int order, H5L_iterate_cb op, H5L_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Lis_registered tests whether a user-defined link class is currently registered, * either by the HDF5 Library or by the user through the use of H5Lregister. * * @param link_cls_id * IN: User-defined link class identifier * * @return Returns a positive value if the link class has been registered and zero if it is unregistered. * Otherwise returns a negative value; this may mean that the identifier is not a valid user-defined class identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Lis_registered(int link_cls_id) throws HDF5LibraryException; /** * H5Lunregister unregisters a class of user-defined links, preventing them from being traversed, queried, moved, etc. * * @param link_cls_id * IN: User-defined link class identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Lunregister(int link_cls_id) throws HDF5LibraryException; // /////// unimplemented //////// // herr_t H5Lcreate_ud(hid_t link_loc_id, const char *link_name, // H5L_type_t link_type, const void *udata, size_t udata_size, hid_t lcpl_id, // hid_t lapl_id); // herr_t H5Lregister(const H5L_class_t *cls); // herr_t H5Lunpack_elink_val(const void *ext_linkval/*in*/, size_t link_size, // unsigned *flags, const char **filename/*out*/, const char **obj_path /*out*/); // herr_t H5Lget_val(hid_t loc_id, const char *name, void *buf/*out*/, // size_t size, hid_t lapl_id); // herr_t H5Lget_val_by_idx(hid_t loc_id, const char *group_name, // H5_index_t idx_type, H5_iter_order_t order, hsize_t n, // void *buf/*out*/, size_t size, hid_t lapl_id); // //////////////////////////////////////////////////////////// // // // H5MM: Memory Management Interface API Functions // // // // //////////////////////////////////////////////////////////// // /////// unimplemented //////// // typedef void *(*H5MM_allocate_t)(size_t size, void *alloc_info); // typedef void (*H5MM_free_t)(void *mem, void *free_info); // //////////////////////////////////////////////////////////// // // // H5O: HDF5 1.8 Object Interface API Functions // // // // //////////////////////////////////////////////////////////// /** * H5Oclose closes the group, dataset, or named datatype specified. * * @param object_id * IN: Object identifier * * @return non-negative on success * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Oclose(long object_id) throws HDF5LibraryException { if (object_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; log.trace("OPEN_IDS: H5Oclose remove {}", object_id); OPEN_IDS.remove(object_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); return _H5Oclose(object_id); } private synchronized static native int _H5Oclose(long object_id) throws HDF5LibraryException; /** * H5Ocopy copies the group, dataset or named datatype specified from the file or group specified by source location * to the destination location. * * @param src_loc_id * IN: Object identifier indicating the location of the source object to be copied * @param src_name * IN: Name of the source object to be copied * @param dst_loc_id * IN: Location identifier specifying the destination * @param dst_name * IN: Name to be assigned to the new copy * @param ocpypl_id * IN: Object copy property list * @param lcpl_id * IN: Link creation property list for the new hard link * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native void H5Ocopy(long src_loc_id, String src_name, long dst_loc_id, String dst_name, long ocpypl_id, long lcpl_id) throws HDF5LibraryException, NullPointerException; /** * H5Oget_comment retrieves the comment for the specified object. * * @param obj_id * IN: File or group identifier * * @return the comment * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5Oget_comment(long obj_id) throws HDF5LibraryException, IllegalArgumentException; /** * H5Oset_comment sets the comment for the specified object. * * @param obj_id * IN: Identifier of the target object * @param comment * IN: The new comment. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * * @deprecated As of HDF5 1.8 in favor of object attributes. **/ @Deprecated public synchronized static native void H5Oset_comment(long obj_id, String comment) throws HDF5LibraryException; /** * H5Oget_comment_by_name retrieves the comment for an object. * * @param loc_id * IN: Identifier of a file, group, dataset, or named datatype. * @param name * IN: Relative name of the object whose comment is to be set or reset. * @param lapl_id * IN: Link access property list identifier. * * @return the comment * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native String H5Oget_comment_by_name(long loc_id, String name, long lapl_id) throws HDF5LibraryException, IllegalArgumentException, NullPointerException; /** * H5Oset_comment_by_name sets the comment for the specified object. * * @param loc_id * IN: Identifier of a file, group, dataset, or named datatype. * @param name * IN: Relative name of the object whose comment is to be set or reset. * @param comment * IN: The new comment. * @param lapl_id * IN: Link access property list identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. * * @deprecated As of HDF5 1.8 in favor of object attributes. **/ @Deprecated public synchronized static native void H5Oset_comment_by_name(long loc_id, String name, String comment, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Oget_info retrieves the metadata for an object specified by an identifier. * * @param loc_id * IN: Identifier for target object * * @return object information * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static H5O_info_t H5Oget_info(long loc_id) throws HDF5LibraryException, NullPointerException { return H5Oget_info(loc_id, HDF5Constants.H5O_INFO_ALL); } /** * H5Oget_info retrieves the metadata for an object specified by an identifier. * * @param loc_id * IN: Identifier for target object * @param fields * IN: Object fields to select * * @return object information * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native H5O_info_t H5Oget_info(long loc_id, int fields) throws HDF5LibraryException, NullPointerException; /** * H5Oget_info_by_idx retrieves the metadata for an object, identifying the object by an index position. * * @param loc_id * IN: File or group identifier * @param group_name * IN: Name of group, relative to loc_id, in which object is located * @param idx_type * IN: Type of index by which objects are ordered * @param order * IN: Order of iteration within index * @param n * IN: Object to open * @param lapl_id * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as * H5P_DEFAULT.) * * @return object information * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static H5O_info_t H5Oget_info_by_idx(long loc_id, String group_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException { return H5Oget_info_by_idx(loc_id, group_name, idx_type, order, n, HDF5Constants.H5O_INFO_ALL, lapl_id); } /** * H5Oget_info_by_idx retrieves the metadata for an object, identifying the object by an index position. * * @param loc_id * IN: File or group identifier * @param group_name * IN: Name of group, relative to loc_id, in which object is located * @param idx_type * IN: Type of index by which objects are ordered * @param order * IN: Order of iteration within index * @param n * IN: Object to open * @param fields * IN: Object fields to select * @param lapl_id * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as * H5P_DEFAULT.) * * @return object information * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native H5O_info_t H5Oget_info_by_idx(long loc_id, String group_name, int idx_type, int order, long n, int fields, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and relative name. * * @param loc_id * IN: File or group identifier specifying location of group in which object is located * @param name * IN: Relative name of group * @param lapl_id * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as * H5P_DEFAULT.) * * @return object information * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static H5O_info_t H5Oget_info_by_name(long loc_id, String name, long lapl_id) throws HDF5LibraryException, NullPointerException { return H5Oget_info_by_name(loc_id, name, HDF5Constants.H5O_INFO_ALL, lapl_id); } /** * H5Oget_info_by_name retrieves the metadata for an object, identifying the object by location and relative name. * * @param loc_id * IN: File or group identifier specifying location of group in which object is located * @param name * IN: Relative name of group * @param fields * IN: Object fields to select * @param lapl_id * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as * H5P_DEFAULT.) * * @return object information * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native H5O_info_t H5Oget_info_by_name(long loc_id, String name, int fields, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Olink creates a new hard link to an object in an HDF5 file. * * @param obj_id * IN: Object to be linked. * @param new_loc_id * IN: File or group identifier specifying location at which object is to be linked. * @param new_name * IN: Relative name of link to be created. * @param lcpl_id * IN: Link creation property list identifier. * @param lapl_id * IN: Access property list identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native void H5Olink(long obj_id, long new_loc_id, String new_name, long lcpl_id, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Oopen opens a group, dataset, or named datatype specified by a location and a path name. * * @param loc_id * IN: File or group identifier * @param name * IN: Relative path to the object * @param lapl_id * IN: Access property list identifier for the link pointing to the object * * @return an object identifier for the opened object * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static long H5Oopen(long loc_id, String name, long lapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Oopen(loc_id, name, lapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Oopen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Oopen(long loc_id, String name, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Ovisit recursively visits all objects accessible from a specified object. * * @param obj_id * IN: Identifier of the object at which the recursive iteration begins. * @param idx_type * IN: Type of index * @param order * IN: Order of iteration within index * @param op * IN: Callback function passing data regarding the object to the calling application * @param op_data * IN: User-defined pointer to data required by the application for its processing of the object * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static int H5Ovisit(long obj_id, int idx_type, int order, H5O_iterate_cb op, H5O_iterate_t op_data) throws HDF5LibraryException, NullPointerException { return H5Ovisit(obj_id, idx_type, order, op, op_data, HDF5Constants.H5O_INFO_ALL); } /** * H5Ovisit recursively visits all objects accessible from a specified object. * * @param obj_id * IN: Identifier of the object at which the recursive iteration begins. * @param idx_type * IN: Type of index * @param order * IN: Order of iteration within index * @param op * IN: Callback function passing data regarding the object to the calling application * @param op_data * IN: User-defined pointer to data required by the application for its processing of the object * @param fields * IN: Object fields to select * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Ovisit(long obj_id, int idx_type, int order, H5O_iterate_cb op, H5O_iterate_t op_data, int fields) throws HDF5LibraryException, NullPointerException; /** * H5Ovisit_by_name recursively visits all objects starting from a specified object. * * @param loc_id * IN: File or group identifier * @param obj_name * IN: Relative path to the object * @param idx_type * IN: Type of index * @param order * IN: Order of iteration within index * @param op * IN: Callback function passing data regarding the object to the calling application * @param op_data * IN: User-defined pointer to data required by the application for its processing of the object * @param lapl_id * IN: Link access property list identifier * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static int H5Ovisit_by_name(long loc_id, String obj_name, int idx_type, int order, H5O_iterate_cb op, H5O_iterate_t op_data, long lapl_id) throws HDF5LibraryException, NullPointerException { return H5Ovisit_by_name(loc_id, obj_name, idx_type, order, op, op_data, HDF5Constants.H5O_INFO_ALL, lapl_id); } /** * H5Ovisit_by_name recursively visits all objects starting from a specified object. * * @param loc_id * IN: File or group identifier * @param obj_name * IN: Relative path to the object * @param idx_type * IN: Type of index * @param order * IN: Order of iteration within index * @param op * IN: Callback function passing data regarding the object to the calling application * @param op_data * IN: User-defined pointer to data required by the application for its processing of the object * @param fields * IN: Object fields to select * @param lapl_id * IN: Link access property list identifier * * @return returns the return value of the first operator that returns a positive value, or zero if all members were * processed with no operator returning non-zero. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Ovisit_by_name(long loc_id, String obj_name, int idx_type, int order, H5O_iterate_cb op, H5O_iterate_t op_data, int fields, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Oexists_by_name is used by an application to check that an existing link resolves to an object. * Primarily, it is designed to check for dangling soft, external, or user-defined links. * * @param loc_id * IN: File or group identifier * @param obj_name * IN: Relative path to the object * @param lapl_id * IN: Link access property list identifier * * @return Returns TRUE or FALSE if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native boolean H5Oexists_by_name(long loc_id, String obj_name, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Odecr_refcount decrements the hard link reference count for an object. * * @param object_id IN: Object identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native void H5Odecr_refcount(long object_id) throws HDF5LibraryException; /** * H5Oincr_refcount increments the hard link reference count for an object. * * @param object_id IN: Object identifier * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public synchronized static native void H5Oincr_refcount(long object_id) throws HDF5LibraryException; /** * H5Oopen_by_addr opens a group, dataset, or named datatype using its address within an HDF5 file. * * @param loc_id IN: File or group identifier * @param addr IN: Object's address in the file * * @return an object identifier for the opened object * * @exception HDF5LibraryException - Error from the HDF-5 Library. **/ public static long H5Oopen_by_addr(long loc_id, long addr) throws HDF5LibraryException { long id = _H5Oopen_by_addr(loc_id, addr); if (id > 0) { log.trace("OPEN_IDS: H5Oopen_by_addr add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Oopen_by_addr(long loc_id, long addr) throws HDF5LibraryException, NullPointerException; /** * H5Oopen_by_idx opens the nth object in the group specified. * * @param loc_id IN: File or group identifier * @param group_name IN: Name of group, relative to loc_id, in which object is located * @param idx_type IN: Type of index by which objects are ordered * @param order IN: Order of iteration within index * @param n IN: Object to open * @param lapl_id IN: Access property list identifier for the link pointing to the object * * @return an object identifier for the opened object * * @exception HDF5LibraryException - Error from the HDF-5 Library. * @exception NullPointerException - group_name is null. **/ public static long H5Oopen_by_idx(long loc_id, String group_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Oopen_by_idx(loc_id, group_name, idx_type, order, n, lapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Oopen_by_idx add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } public synchronized static native long _H5Oopen_by_idx(long loc_id, String group_name, int idx_type, int order, long n, long lapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Oflush causes all buffers associated with an object to be immediately flushed to disk without removing * the data from the cache. object_id can be any named object associated with an HDF5 file including a * dataset, a group, or a committed datatype. * * @param object_id * IN: Identifier of the object to be flushed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Oflush(long object_id) throws HDF5LibraryException; /** * H5Orefresh causes all buffers associated with an object to be cleared and immediately re-loaded with * updated contents from disk. This function essentially closes the object, evicts all metadata associated * with it from the cache, and then re-opens the object. The reopened object is automatically re-registered * with the same ID. object_id can be any named object associated with an HDF5 file including a * dataset, a group, or a committed datatype. * * @param object_id * IN: Identifier of the object to be refreshed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Orefresh(long object_id) throws HDF5LibraryException; // /////// unimplemented //////// // H5_DLL herr_t H5Odisable_mdc_flushes(hid_t object_id); // H5_DLL herr_t H5Oenable_mdc_flushes(hid_t object_id); // H5_DLL herr_t H5Oare_mdc_flushes_disabled(hid_t object_id, hbool_t *are_disabled); // //////////////////////////////////////////////////////////// // // // H5P: Property List Interface Functions // // // // //////////////////////////////////////////////////////////// // /////// Generic property list routines /////// /** * H5Pget_class_name retrieves the name of a generic property list class * * @param plid * IN: Identifier of property object to query * @return name of a property list if successful; null if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native String H5Pget_class_name(long plid) throws HDF5LibraryException; /** * H5Pcreate creates a new property as an instance of some property list class. * * @param type * IN: The type of property list to create. * * @return a property list identifier (plist) if successful; otherwise Fail (-1). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Pcreate(long type) throws HDF5LibraryException { long id = _H5Pcreate(type); if (id > 0) { log.trace("OPEN_IDS: H5Pcreate add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Pcreate(long type) throws HDF5LibraryException; /** * H5Pget retrieves a copy of the value for a property in a property list (support integer only) * * @param plid * IN: Identifier of property object to query * @param name * IN: Name of property to query * @return value for a property if successful; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native int H5Pget(long plid, String name) throws HDF5LibraryException; /** * Sets a property list value (support integer only) * * @param plid * IN: Property list identifier to modify * @param name * IN: Name of property to modify * @param value * IN: value to set the property to * @return a non-negative value if successful; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native int H5Pset(long plid, String name, int value) throws HDF5LibraryException; /** * H5Pexist determines whether a property exists within a property list or class * * @param plid * IN: Identifier for the property to query * @param name * IN: Name of property to check for * @return a true value if the property exists in the property object; false if the property does not exist; * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native boolean H5Pexist(long plid, String name) throws HDF5LibraryException; /** * H5Pget_size retrieves the size of a property's value in bytes * * @param plid * IN: Identifier of property object to query * @param name * IN: Name of property to query * @return size of a property's value if successful; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native long H5Pget_size(long plid, String name) throws HDF5LibraryException; /** * H5Pget_nprops retrieves the number of properties in a property list or class * * @param plid * IN: Identifier of property object to query * @return number of properties if successful; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native long H5Pget_nprops(long plid) throws HDF5LibraryException; /** * H5Pget_class returns the property list class for the property list identified by the plist parameter. * * @param plist * IN: Identifier of property list to query. * @return a property list class if successful. Otherwise returns H5P_ROOT (-1). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Pget_class(long plist) throws HDF5LibraryException; /** * H5Pget_class_parent retrieves an identifier for the parent class of a property class * * @param plid * IN: Identifier of the property class to query * @return a valid parent class object identifier if successful; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native long H5Pget_class_parent(long plid) throws HDF5LibraryException; /** * H5Pequal determines if two property lists or classes are equal * * @param plid1 * IN: First property object to be compared * @param plid2 * IN: Second property object to be compared * @return positive value if equal; zero if unequal, a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native int H5Pequal(long plid1, long plid2) throws HDF5LibraryException; public static boolean H5P_equal(long plid1, long plid2) throws HDF5LibraryException { if (H5Pequal(plid1, plid2) == 1) return true; return false; } /** * H5Pisa_class checks to determine whether a property list is a member of the specified class * * @param plist * IN: Identifier of the property list * @param pclass * IN: Identifier of the property class * @return a positive value if equal; zero if unequal; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native int H5Pisa_class(long plist, long pclass) throws HDF5LibraryException; /** * H5Pcopy_prop copies a property from one property list or class to another * * @param dst_id * IN: Identifier of the destination property list or class * @param src_id * IN: Identifier of the source property list or class * @param name * IN: Name of the property to copy * @return a non-negative value if successful; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native int H5Pcopy_prop(long dst_id, long src_id, String name) throws HDF5LibraryException; /** * H5Premove removes a property from a property list * * @param plid * IN: Identifier of the property list to modify * @param name * IN: Name of property to remove * @return a non-negative value if successful; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native int H5Premove(long plid, String name) throws HDF5LibraryException; /** * H5Punregister removes a property from a property list class * * @param plid * IN: Property list class from which to remove permanent property * @param name * IN: Name of property to remove * @return a non-negative value if successful; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native int H5Punregister(long plid, String name) throws HDF5LibraryException; /** * Closes an existing property list class * * @param plid * IN: Property list class to close * @return a non-negative value if successful; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public static int H5Pclose_class(long plid) throws HDF5LibraryException { if (plid < 0) return 0; // throw new HDF5LibraryException("Negative ID");; log.trace("OPEN_IDS: H5Pclose_class remove {}", plid); OPEN_IDS.remove(plid); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); return _H5Pclose_class(plid); } public synchronized static native int _H5Pclose_class(long plid) throws HDF5LibraryException; /** * H5Pclose terminates access to a property list. * * @param plist * IN: Identifier of the property list to terminate access to. * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Pclose(long plist) throws HDF5LibraryException { if (plist < 0) return 0; // throw new HDF5LibraryException("Negative ID");; log.trace("OPEN_IDS: H5Pclose remove {}", plist); OPEN_IDS.remove(plist); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); return _H5Pclose(plist); } private synchronized static native int _H5Pclose(long plist) throws HDF5LibraryException; /** * H5Pcopy copies an existing property list to create a new property list. * * @param plist * IN: Identifier of property list to duplicate. * * @return a property list identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Pcopy(long plist) throws HDF5LibraryException { long id = _H5Pcopy(plist); if (id > 0) { log.trace("OPEN_IDS: H5Pcopy add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Pcopy(long plist) throws HDF5LibraryException; public static long H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException { long id = _H5Pcreate_class_nocb(parent_class, name); if (id > 0) { log.trace("OPEN_IDS: H5Pcreate_class_nocb add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException; // public static long H5Pcreate_class(long parent_class, String name, H5P_cls_create_func_cb create_op, H5P_cls_create_func_t create_data, // H5P_cls_copy_func_cb copy_op, H5P_cls_copy_func_t copy_data, H5P_cls_close_func_cb close_op, H5P_cls_close_func_t close_data) throws HDF5LibraryException { // long id = _H5Pcreate_class(parent_class, name, create_op, create_data, copy_op, copy_data, close_op, close_data); // if (id > 0) { // log.trace("OPEN_IDS: H5Pcreate_class add {}", id); // OPEN_IDS.add(id); // log.trace("OPEN_IDS: {}", OPEN_IDS.size()); // } // return id; // } // // private synchronized static native long _H5Pcreate_class(long parent_class, String name, H5P_cls_create_func_cb create_op, H5P_cls_create_func_t create_data, // H5P_cls_copy_func_cb copy_op, H5P_cls_copy_func_t copy_data, H5P_cls_close_func_cb close_op, H5P_cls_close_func_t close_data) throws HDF5LibraryException; public synchronized static native void H5Pregister2_nocb(long plist_class, String name, long size, byte[] def_value) throws HDF5LibraryException; // public synchronized static native void H5Pregister2(long plist_class, String name, long size, byte[] def_value, H5P_prp_create_func_cb prp_create, H5P_prp_set_func_cb prp_set, // H5P_prp_get_func_cb prp_get, H5P_prp_delete_func_cb prp_delete, H5P_prp_copy_func_cb prp_copy, H5P_prp_compare_func_cb prp_cmp, H5P_prp_close_func_cb prp_close) throws HDF5LibraryException; public synchronized static native void H5Pinsert2_nocb(long plist, String name, long size, byte[] value) throws HDF5LibraryException; // public synchronized static native void H5Pinsert2(long plist, String name, long size, byte[] value, H5P_prp_set_func_cb prp_set, H5P_prp_get_func_cb prp_get, // H5P_prp_delete_func_cb prp_delete, H5P_prp_copy_func_cb prp_copy, H5P_prp_compare_func_cb prp_cmp, H5P_prp_close_func_cb prp_close) throws HDF5LibraryException; public synchronized static native int H5Piterate(long plist, int[] idx, H5P_iterate_cb op, H5P_iterate_t op_data) throws HDF5LibraryException; // /////// Object creation property list (OCPL) routines /////// /** * H5Pget_attr_phase_change retrieves attribute storage phase change thresholds. * * @param ocpl_id * IN: : Object (dataset or group) creation property list identifier * @param attributes * The maximun and minimum no. of attributes to be stored. * * 
     *      attributes[0] =  The maximum number of attributes to be stored in compact storage
     *      attributes[1] =  The minimum number of attributes to be stored in dense storage
     *
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. * **/ public synchronized static native int H5Pget_attr_phase_change(long ocpl_id, int[] attributes) throws HDF5LibraryException, NullPointerException; /** * H5Pset_attr_phase_change sets threshold values for attribute storage on an object. These * thresholds determine the point at which attribute storage changes * from compact storage (i.e., storage in the object header) * to dense storage (i.e., storage in a heap and indexed with a B-tree). * * @param ocpl_id * IN: : Object (dataset or group) creation property list identifier * @param max_compact * IN: Maximum number of attributes to be stored in compact storage (Default: 8) * @param min_dense * IN: Minimum number of attributes to be stored in dense storage (Default: 6) * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_attr_phase_change(long ocpl_id, int max_compact, int min_dense) throws HDF5LibraryException; /** * H5Pget_attr_creation_order retrieves the settings for tracking and indexing attribute creation order on an object * * @param ocpl_id * IN: Object (group or dataset) creation property list identifier * * @return Flags specifying whether to track and index attribute creation order * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_attr_creation_order(long ocpl_id) throws HDF5LibraryException; /** * H5Pset_attr_creation_order sets flags specifying whether to track and index attribute creation order on an * object. * * @param ocpl_id * IN: Object creation property list identifier * @param crt_order_flags * IN: Flags specifying whether to track and index attribute creation order * * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_attr_creation_order(long ocpl_id, int crt_order_flags) throws HDF5LibraryException; /** * H5Pget_obj_track_times queries the object creation property list, ocpl_id, to determine whether object times are * being recorded. * * @param ocpl_id * IN: Object creation property list identifier * * @return TRUE or FALSE, specifying whether object times are being recorded * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native boolean H5Pget_obj_track_times(long ocpl_id) throws HDF5LibraryException; /** * H5Pset_obj_track_times sets a property in the object creation property list, ocpl_id, that governs the recording * of times associated with an object. * * @param ocpl_id * IN: Object creation property list identifier * * @param track_times * IN: TRUE or FALSE, specifying whether object times are to be tracked * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_obj_track_times(long ocpl_id, boolean track_times) throws HDF5LibraryException; public synchronized static native int H5Pmodify_filter(long plist, long filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException, NullPointerException; /** * H5Pset_filter adds the specified filter and corresponding properties to the end of an output filter pipeline. * * @param plist * IN: Property list identifier. * @param filter * IN: Filter to be added to the pipeline. * @param flags * IN: Bit vector specifying certain general properties of the filter. * @param cd_nelmts * IN: Number of elements in cd_values * @param cd_values * IN: Auxiliary data for the filter. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_filter(long plist, int filter, int flags, long cd_nelmts, int[] cd_values) throws HDF5LibraryException; /** * H5Pget_nfilters returns the number of filters defined in the filter pipeline associated with the property list * plist. * * @param plist * IN: Property list identifier. * * @return the number of filters in the pipeline if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_nfilters(long plist) throws HDF5LibraryException; /** * H5Pget_filter returns information about a filter, specified by its filter number, in a filter pipeline, specified * by the property list with which it is associated. * * @param plist * IN: Property list identifier. * @param filter_number * IN: Sequence number within the filter pipeline of the filter for which information is sought. * @param flags * OUT: Bit vector specifying certain general properties of the filter. * @param cd_nelmts * IN/OUT: Number of elements in cd_values * @param cd_values * OUT: Auxiliary data for the filter. * @param namelen * IN: Anticipated number of characters in name. * @param name * OUT: Name of the filter. * @param filter_config * OUT:A bit field encoding the returned filter information * * @return the filter identification number if successful. Otherwise returns H5Z_FILTER_ERROR (-1). * * @exception ArrayIndexOutOfBoundsException * Fatal error on Copyback * @exception ArrayStoreException * Fatal error on Copyback * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name or an array is null. * **/ public static int H5Pget_filter(long plist, int filter_number, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException { return H5Pget_filter2(plist, filter_number, flags, cd_nelmts, cd_values, namelen, name, filter_config); } /** * H5Pget_filter2 returns information about a filter, specified by its filter number, in a filter pipeline, * specified by the property list with which it is associated. * * @see public static int H5Pget_filter(int plist, int filter_number, int[] flags, int[] cd_nelmts, int[] cd_values, * int namelen, String[] name, int[] filter_config) * **/ private synchronized static native int H5Pget_filter2(long plist, int filter_number, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException; /** * H5Pget_filter_by_id returns information about the filter specified in filter_id, a filter identifier. plist_id * must be a dataset or group creation property list and filter_id must be in the associated filter pipeline. The * filter_id and flags parameters are used in the same manner as described in the discussion of H5Pset_filter. Aside * from the fact that they are used for output, the parameters cd_nelmts and cd_values[] are used in the same manner * as described in the discussion of H5Pset_filter. On input, the cd_nelmts parameter indicates the number of * entries in the cd_values[] array allocated by the calling program; on exit it contains the number of values * defined by the filter. On input, the namelen parameter indicates the number of characters allocated for the * filter name by the calling program in the array name[]. On exit name[] contains the name of the filter with one * character of the name in each element of the array. If the filter specified in filter_id is not set for the * property list, an error will be returned and H5Pget_filter_by_id1 will fail. * * @param plist_id * IN: Property list identifier. * @param filter_id * IN: Filter identifier. * @param flags * OUT: Bit vector specifying certain general properties of the filter. * @param cd_nelmts * N/OUT: Number of elements in cd_values * @param cd_values * OUT: Auxiliary data for the filter. * @param namelen * IN: Anticipated number of characters in name. * @param name * OUT: Name of the filter. * @param filter_config * OUT: A bit field encoding the returned filter information * * @return the filter identification number if successful. Otherwise returns H5Z_FILTER_ERROR (-1). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception ArrayIndexOutOfBoundsException * Fatal error on Copyback * @exception ArrayStoreException * Fatal error on Copyback * @exception NullPointerException * - name or an array is null. * **/ public static int H5Pget_filter_by_id(long plist_id, long filter_id, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException { return H5Pget_filter_by_id2(plist_id, filter_id, flags, cd_nelmts, cd_values, namelen, name, filter_config); } /** * H5Pget_filter_by_id2 returns information about a filter, specified by its filter id, in a filter pipeline, * specified by the property list with which it is associated. * * @param plist_id * IN: Property list identifier. * @param filter_id * IN: Filter identifier. * @param flags * OUT: Bit vector specifying certain general properties of the filter. * @param cd_nelmts * N/OUT: Number of elements in cd_values * @param cd_values * OUT: Auxiliary data for the filter. * @param namelen * IN: Anticipated number of characters in name. * @param name * OUT: Name of the filter. * @param filter_config * OUT: A bit field encoding the returned filter information * * @return the filter identification number if successful. Otherwise returns H5Z_FILTER_ERROR (-1). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name or an array is null. * **/ public synchronized static native int H5Pget_filter_by_id2(long plist_id, long filter_id, int[] flags, long[] cd_nelmts, int[] cd_values, long namelen, String[] name, int[] filter_config) throws HDF5LibraryException, NullPointerException; public synchronized static native boolean H5Pall_filters_avail(long dcpl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Premove_filter(long obj_id, long filter) throws HDF5LibraryException; /** * H5Pset_deflate sets the compression method for a dataset. * * @param plist * IN: Identifier for the dataset creation property list. * @param level * IN: Compression level. * * @return non-negative if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_deflate(long plist, int level) throws HDF5LibraryException; public synchronized static native int H5Pset_fletcher32(long plist) throws HDF5LibraryException, NullPointerException; // /////// File creation property list (FCPL) routines /////// /** * H5Pget_userblock retrieves the size of a user block in a file creation property list. * * @param plist * IN: Identifier for property list to query. * @param size * OUT: Pointer to location to return user-block size. * * @return a non-negative value and the size of the user block; if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. **/ public synchronized static native int H5Pget_userblock(long plist, long[] size) throws HDF5LibraryException, NullPointerException; /** * H5Pset_userblock sets the user block size of a file creation property list. * * @param plist * IN: Identifier of property list to modify. * @param size * IN: Size of the user-block in bytes. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_userblock(long plist, long size) throws HDF5LibraryException; /** * H5Pget_sizes retrieves the size of the offsets and lengths used in an HDF5 file. This function is only valid for * file creation property lists. * * @param plist * IN: Identifier of property list to query. * @param size * OUT: the size of the offsets and length. * * 
     *      size[0] = sizeof_addr // offset size in bytes
     *      size[1] = sizeof_size // length size in bytes
     *
* @return a non-negative value with the sizes initialized; if successful; * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. * @exception IllegalArgumentException * - size is invalid. **/ public synchronized static native int H5Pget_sizes(long plist, long[] size) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_sizes sets the byte size of the offsets and lengths used to address objects in an HDF5 file. * * @param plist * IN: Identifier of property list to modify. * @param sizeof_addr * IN: Size of an object offset in bytes. * @param sizeof_size * IN: Size of an object length in bytes. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_sizes(long plist, int sizeof_addr, int sizeof_size) throws HDF5LibraryException; /** * H5Pget_sym_k retrieves the size of the symbol table B-tree 1/2 rank and the symbol table leaf node 1/2 size. * * @param plist * IN: Property list to query. * @param size * OUT: the symbol table's B-tree 1/2 rank and leaf node 1/2size. * * 
     *      size[0] = ik // the symbol table's B-tree 1/2 rank
     *      size[1] = lk // leaf node 1/2 size
     *
* * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. * @exception IllegalArgumentException * - size is invalid. **/ public synchronized static native int H5Pget_sym_k(long plist, int[] size) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_sym_k sets the size of parameters used to control the symbol table nodes. * * @param plist * IN: Identifier for property list to query. * @param ik * IN: Symbol table tree rank. * @param lk * IN: Symbol table node size. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_sym_k(long plist, int ik, int lk) throws HDF5LibraryException; /** * H5Pget_istore_k queries the 1/2 rank of an indexed storage B-tree. * * @param plist * IN: Identifier of property list to query. * @param ik * OUT: Pointer to location to return the chunked storage B-tree 1/2 rank. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - ik array is null. **/ public synchronized static native int H5Pget_istore_k(long plist, int[] ik) throws HDF5LibraryException, NullPointerException; /** * H5Pset_istore_k sets the size of the parameter used to control the B-trees for indexing chunked datasets. * * @param plist * IN: Identifier of property list to query. * @param ik * IN: 1/2 rank of chunked storage B-tree. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_istore_k(long plist, int ik) throws HDF5LibraryException; /** * H5Pget_shared_mesg_nindexes retrieves number of shared object header message indexes in file creation property * list. * * @param fcpl_id * IN: : File creation property list identifier * * @return nindexes, the number of shared object header message indexes available in files created with this * property list * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_shared_mesg_nindexes(long fcpl_id) throws HDF5LibraryException; /** * H5Pset_shared_mesg_nindexes sets the number of shared object header message indexes in the specified file * creation property list. * * @param plist_id * IN: File creation property list * @param nindexes * IN: Number of shared object header message indexes to be available in files created with this property * list * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid value of nindexes * **/ public synchronized static native int H5Pset_shared_mesg_nindexes(long plist_id, int nindexes) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_shared_mesg_index Retrieves the configuration settings for a shared message index. * * @param fcpl_id * IN: File creation property list identifier * @param index_num * IN: Index being configured. * @param mesg_info * The message type and minimum message size * * 
     *      mesg_info[0] =  Types of messages that may be stored in this index.
     *      mesg_info[1] =  Minimum message size.
     *
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - mesg_info is null. * @exception IllegalArgumentException * - Invalid value of nindexes * **/ public synchronized static native int H5Pget_shared_mesg_index(long fcpl_id, int index_num, int[] mesg_info) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_shared_mesg_index Configures the specified shared object header message index * * @param fcpl_id * IN: File creation property list identifier. * @param index_num * IN: Index being configured. * @param mesg_type_flags * IN: Types of messages that should be stored in this index. * @param min_mesg_size * IN: Minimum message size. * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid value of nindexes * **/ public synchronized static native int H5Pset_shared_mesg_index(long fcpl_id, int index_num, int mesg_type_flags, int min_mesg_size) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_shared_mesg_phase_change retrieves shared object header message phase change information. * * @param fcpl_id * IN: : File creation property list identifier * @param size * The threshold values for storage of shared object header message indexes in a file. * * 
     *      size[0] =  Threshold above which storage of a shared object header message index shifts from list to B-tree
     *      size[1] =  Threshold below which storage of a shared object header message index reverts to list format
     *
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. * **/ public synchronized static native int H5Pget_shared_mesg_phase_change(long fcpl_id, int[] size) throws HDF5LibraryException, NullPointerException; /** * H5Pset_shared_mesg_phase_change sets shared object header message storage phase change thresholds. * * @param fcpl_id * IN: File creation property list identifier * @param max_list * IN: Threshold above which storage of a shared object header message index shifts from list to B-tree * @param min_btree * IN: Threshold below which storage of a shared object header message index reverts to list format * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid values of max_list and min_btree. * **/ public synchronized static native int H5Pset_shared_mesg_phase_change(long fcpl_id, int max_list, int min_btree) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pset_file_space_strategy sets the file space management strategy for the file associated with fcpl_id to strategy. * There are four strategies that applications can select and they are described in the Parameters section. * * @param fcpl_id * IN: File creation property list identifier * @param strategy * IN: The strategy for file space management. * H5F_FSPACE_STRATEGY_FSM_AGGR * Mechanisms: free-space managers, aggregators, and virtual file drivers * This is the library default when not set. * H5F_FSPACE_STRATEGY_PAGE * Mechanisms: free-space managers with embedded paged aggregation and virtual file drivers * H5F_FSPACE_STRATEGY_AGGR * Mechanisms: aggregators and virtual file drivers * H5F_FSPACE_STRATEGY_NONE * Mechanisms: virtual file drivers * @param persist * IN: True to persist free-space. * @param threshold * IN: The free-space section threshold. The library default is 1, which is to track all free-space sections. * Passing a value of zero (0) indicates that the value of threshold is not to be modified. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid values of max_list and min_btree. * **/ public synchronized static native void H5Pset_file_space_strategy(long fcpl_id, int strategy, boolean persist, long threshold) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_file_space_strategy provides the means for applications to manage the HDF5 file's file space strategy for their specific needs. * * @param fcpl_id * IN: File creation property list identifier * @param persist * IN/OUT: The current free-space persistence. NULL, persist not queried. * @param threshold * IN/OUT: The current free-space section threshold. NULL, threshold not queried. * * @return the current free-space strategy. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid values of max_list and min_btree. * **/ public synchronized static native int H5Pget_file_space_strategy(long fcpl_id, boolean[] persist, long[] threshold) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_file_space_strategy_persist provides the means for applications to manage the HDF5 file's file space strategy for their specific needs. * * @param fcpl_id * IN: File creation property list identifier * * @return the current free-space persistence. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid values of max_list and min_btree. * **/ public synchronized static native boolean H5Pget_file_space_strategy_persist(long fcpl_id) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_file_space_strategy_threshold provides the means for applications to manage the HDF5 file's file space strategy for their specific needs. * * @param fcpl_id * IN: File creation property list identifier * * @return the current free-space section threshold. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid values of max_list and min_btree. * **/ public synchronized static native long H5Pget_file_space_strategy_threshold(long fcpl_id) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pset_file_space_page_size retrieves the file space page size for aggregating small metadata or raw data. * * @param fcpl_id * IN: File creation property list identifier * @param page_size * IN: the file space page size. * * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid values of max_list and min_btree. * **/ public synchronized static native void H5Pset_file_space_page_size(long fcpl_id, long page_size) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_file_space_page_size Sets the file space page size for paged aggregation. * * @param fcpl_id * IN: File creation property list identifier * * @return the current file space page size. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid values of max_list and min_btree. * **/ public synchronized static native long H5Pget_file_space_page_size(long fcpl_id) throws HDF5LibraryException, IllegalArgumentException; // /////// File access property list (FAPL) routines /////// /** * H5Pget_alignment retrieves the current settings for alignment properties from a file access property list. * * @param plist * IN: Identifier of a file access property list. * @param alignment * OUT: threshold value and alignment value. * * 
     *      alignment[0] = threshold // threshold value
     *      alignment[1] = alignment // alignment value
     *
* @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - aligment array is null. * @exception IllegalArgumentException * - aligment array is invalid. **/ public synchronized static native int H5Pget_alignment(long plist, long[] alignment) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_alignment sets the alignment properties of a file access property list so that any file object >= * THRESHOLD bytes will be aligned on an address which is a multiple of ALIGNMENT. * * @param plist * IN: Identifier for a file access property list. * @param threshold * IN: Threshold value. * @param alignment * IN: Alignment value. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_alignment(long plist, long threshold, long alignment) throws HDF5LibraryException; /** * H5Pget_driver returns the identifier of the low-level file driver associated with the file access property list * or data transfer property list plid. * * @param plid * IN: File access or data transfer property list identifier. * @return a valid low-level driver identifier if successful; a negative value if failed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. */ public synchronized static native long H5Pget_driver(long plid) throws HDF5LibraryException; public synchronized static native long H5Pget_family_offset(long fapl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_family_offset(long fapl_id, long offset) throws HDF5LibraryException, NullPointerException; /** * Retrieves the maximum possible number of elements in the meta data cache and the maximum possible number of bytes * and the RDCC_W0 value in the raw data chunk cache. * * @param plist * IN: Identifier of the file access property list. * @param mdc_nelmts * IN/OUT: No longer used, will be ignored. * @param rdcc_nelmts * IN/OUT: Number of elements (objects) in the raw data chunk cache. * @param rdcc_nbytes * IN/OUT: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 * IN/OUT: Preemption policy. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an array is null. **/ public synchronized static native int H5Pget_cache(long plist, int[] mdc_nelmts, long[] rdcc_nelmts, long[] rdcc_nbytes, double[] rdcc_w0) throws HDF5LibraryException, NullPointerException; /** * H5Pset_cache sets the number of elements (objects) in the meta data cache and the total number of bytes in the * raw data chunk cache. * * @param plist * IN: Identifier of the file access property list. * @param mdc_nelmts * IN: No longer used, will be ignored. * @param rdcc_nelmts * IN: Number of elements (objects) in the raw data chunk cache. * @param rdcc_nbytes * IN: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 * IN: Preemption policy. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_cache(long plist, int mdc_nelmts, long rdcc_nelmts, long rdcc_nbytes, double rdcc_w0) throws HDF5LibraryException; /** * H5Pget_mdc_config gets the initial metadata cache configuration contained in a file access property list and * loads it into the instance of H5AC_cache_config_t pointed to by the config_ptr parameter. This configuration is * used when the file is opened. * * @param plist_id * IN: Identifier of the file access property list. * * @return A buffer(H5AC_cache_config_t) for the current metadata cache configuration information * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native H5AC_cache_config_t H5Pget_mdc_config(long plist_id) throws HDF5LibraryException; public synchronized static native void H5Pset_mdc_config(long plist_id, H5AC_cache_config_t config_ptr) throws HDF5LibraryException; /** * H5Pget_gc_references Returns the current setting for the garbage collection refernces property from a file access * property list. * * @param fapl_id * IN File access property list * * @return GC is on (true) or off (false) * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Pget_gc_references(long fapl_id) throws HDF5LibraryException; /** * H5Pset_gc_references Sets the flag for garbage collecting references for the file. Default value for garbage * collecting references is off. * * @param fapl_id * IN File access property list * @param gc_ref * IN set GC on (true) or off (false) * * @return non-negative if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_gc_references(long fapl_id, boolean gc_ref) throws HDF5LibraryException; public synchronized static native int H5Pget_fclose_degree(long plist_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fclose_degree(long plist, int degree) throws HDF5LibraryException, NullPointerException; /** * H5Pget_meta_block_size the current metadata block size setting. * * @param fapl_id * IN: File access property list identifier * * @return the minimum size, in bytes, of metadata block allocations. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native long H5Pget_meta_block_size(long fapl_id) throws HDF5LibraryException; /** * H5Pset_meta_block_size sets the minimum metadata block size. * * @param fapl_id * IN: File access property list identifier * @param size * IN: Minimum size, in bytes, of metadata block allocations. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_meta_block_size(long fapl_id, long size) throws HDF5LibraryException; public synchronized static native long H5Pget_sieve_buf_size(long fapl_id) throws HDF5LibraryException; public synchronized static native void H5Pset_sieve_buf_size(long fapl_id, long size) throws HDF5LibraryException; /** * H5Pget_small_data_block_size retrieves the size of a block of small data in a file creation property list. * * @param plist * IN: Identifier for property list to query. * * @return a non-negative value and the size of the user block; if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Pget_small_data_block_size(long plist) throws HDF5LibraryException; /** * H5Pset_small_data_block_size reserves blocks of size bytes for the contiguous storage of the raw data portion of * small datasets. * * @param plist * IN: Identifier of property list to modify. * @param size * IN: Size of the blocks in bytes. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_small_data_block_size(long plist, long size) throws HDF5LibraryException; /** * H5Pget_libver_bounds retrieves the lower and upper bounds on the HDF5 Library versions that indirectly determine * the object formats versions used when creating objects in the file. * * @param fapl_id * IN: File access property list identifier * @param libver * The earliest/latest version of the library that will be used for writing objects. * * 
     *      libver[0] =  The earliest version of the library that will be used for writing objects
     *      libver[1] =  The latest version of the library that will be used for writing objects.
     *
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. * **/ public synchronized static native int H5Pget_libver_bounds(long fapl_id, int[] libver) throws HDF5LibraryException, NullPointerException; /** * H5Pset_libver_bounds Sets bounds on library versions, and indirectly format versions, to be used when creating * objects * * @param fapl_id * IN: File access property list identifier * @param low * IN: The earliest version of the library that will be used for writing objects * @param high * IN: The latest version of the library that will be used for writing objects. * * * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Argument is Illegal * **/ public synchronized static native int H5Pset_libver_bounds(long fapl_id, int low, int high) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_elink_file_cache_size retrieves the size of the external link open file cache. * * @param fapl_id * IN: File access property list identifier * * @return External link open file cache size in number of files. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_elink_file_cache_size(long fapl_id) throws HDF5LibraryException; /** * H5Pset_elink_file_cache_size sets the number of files that can be held open in an external link open file cache. * * @param fapl_id * IN: File access property list identifier * @param efc_size * IN: External link open file cache size in number of files. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_elink_file_cache_size(long fapl_id, int efc_size) throws HDF5LibraryException; /** * H5Pset_mdc_log_options sets metadata cache logging options. * * @param fapl_id * IN: File access property list identifier * @param is_enabled * IN: Whether logging is enabled. * @param location * IN: Location of log in UTF-8/ASCII (file path/name) (On Windows, this must be ASCII). * @param start_on_access * IN: Whether the logging begins as soon as the file is opened or created. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - location is null. * **/ public synchronized static native void H5Pset_mdc_log_options(long fapl_id, boolean is_enabled, String location, boolean start_on_access) throws HDF5LibraryException, NullPointerException; /** * H5Pget_mdc_log_options gets metadata cache logging options. * * @param fapl_id * IN: File access property list identifier * @param mdc_log_options * the options * mdc_logging_options[0] = is_enabled, whether logging is enabled * mdc_logging_options[1] = start_on_access, whether the logging begins as soon as the file is opened or created * * @return the location of log in UTF-8/ASCII (file path/name) (On Windows, this must be ASCII). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native String H5Pget_mdc_log_options(long fapl_id, boolean[] mdc_log_options) throws HDF5LibraryException; /** * H5Pget_metadata_read_attempts retrieves the number of read attempts that is set in the file access property list plist_id. * * @param plist_id * IN: File access property list identifier * * @return The number of read attempts. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native long H5Pget_metadata_read_attempts(long plist_id) throws HDF5LibraryException; /** * H5Pset_metadata_read_attempts sets the number of reads that the library will try when reading checksummed * metadata in an HDF5 file opened with SWMR access. When reading such metadata, the library will compare the * checksum computed for the metadata just read with the checksum stored within the piece of checksum. When * performing SWMR operations on a file, the checksum check might fail when the library reads data on a system * that is not atomic. To remedy such situations, the library will repeatedly read the piece of metadata until * the check passes or finally fails the read when the allowed number of attempts is reached. * * @param plist_id * IN: File access property list identifier * @param attempts * IN: The number of read attempts which is a value greater than 0. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_metadata_read_attempts(long plist_id, long attempts) throws HDF5LibraryException; /** * H5Pget_evict_on_close retrieves the file access property list setting that determines whether an HDF5 object * will be evicted from the library's metadata cache when it is closed. * * @param fapl_id * IN: File access property list identifier * * @return indication if the object will be evicted on close. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native boolean H5Pget_evict_on_close(long fapl_id) throws HDF5LibraryException; /** * H5Pset_evict_on_close controls the library's behavior of evicting metadata associated with a closed object. * * @param fapl_id * IN: File access property list identifier * @param evict_on_close * IN: Whether the HDF5 object should be evicted on close. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close) throws HDF5LibraryException; // Dataset creation property list (DCPL) routines // /** * H5Pget_layout returns the layout of the raw data for a dataset. * * @param plist * IN: Identifier for property list to query. * * @return the layout type of a dataset creation property list if successful. Otherwise returns H5D_LAYOUT_ERROR * (-1). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_layout(long plist) throws HDF5LibraryException; /** * H5Pset_layout sets the type of storage used store the raw data for a dataset. * * @param plist * IN: Identifier of property list to query. * @param layout * IN: Type of storage layout for raw data. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_layout(long plist, int layout) throws HDF5LibraryException; /** * H5Pget_chunk retrieves the size of chunks for the raw data of a chunked layout dataset. * * @param plist * IN: Identifier of property list to query. * @param max_ndims * IN: Size of the dims array. * @param dims * OUT: Array to store the chunk dimensions. * * @return chunk dimensionality successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - dims array is null. * @exception IllegalArgumentException * - max_ndims <=0 **/ public synchronized static native int H5Pget_chunk(long plist, int max_ndims, long[] dims) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_chunk sets the size of the chunks used to store a chunked layout dataset. * * @param plist * IN: Identifier for property list to query. * @param ndims * IN: The number of dimensions of each chunk. * @param dim * IN: An array containing the size of each chunk. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - dims array is null. * @exception IllegalArgumentException * - dims <=0 **/ public synchronized static native int H5Pset_chunk(long plist, int ndims, byte[] dim) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; public synchronized static int H5Pset_chunk(long plist, int ndims, long[] dim) throws HDF5Exception, NullPointerException, IllegalArgumentException { if (dim == null) { return -1; } HDFArray theArray = new HDFArray(dim); byte[] thedims = theArray.byteify(); int retVal = H5Pset_chunk(plist, ndims, thedims); thedims = null; theArray = null; return retVal; } /** * H5Pset_virtual maps elements of the virtual dataset (VDS) described by the * virtual dataspace identifier vspace_id to the elements of the source dataset * described by the source dataset dataspace identifier src_space_id. The source * dataset is identified by the name of the file where it is located, src_file_name, * and the name of the dataset, src_dset_name. * * @param dcpl_id * IN: The identifier of the dataset creation property list that will be used when creating the virtual dataset. * @param vspace_id * IN: The dataspace identifier with the selection within the virtual dataset applied, possibly an unlimited selection. * @param src_file_name * IN: The name of the HDF5 file where the source dataset is located. The file might not exist yet. The name can be specified using a C-style printf statement. * @param src_dset_name * IN: The path to the HDF5 dataset in the file specified by src_file_name. The dataset might not exist yet. The dataset name can be specified using a C-style printf statement. * @param src_space_id * IN: The source dataset dataspace identifier with a selection applied, possibly an unlimited selection. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an name string is null. * @exception IllegalArgumentException * - An id is <=0 **/ public synchronized static native void H5Pset_virtual(long dcpl_id, long vspace_id, String src_file_name, String src_dset_name, long src_space_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pget_virtual_count gets the number of mappings for a virtual dataset that has the creation property list specified by dcpl_id. * * @param dcpl_id * IN: The identifier of the virtual dataset creation property list. * * @return a non-negative number of mappings if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - An id is <=0 **/ public synchronized static native long H5Pget_virtual_count(long dcpl_id) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_virtual_vspace takes the dataset creation property list for the virtual dataset, dcpl_id, and the mapping index, index, * and returns a dataspace identifier for the selection within the virtual dataset used in the mapping. * * @param dcpl_id * IN: The identifier of the virtual dataset creation property list. * @param index * IN: Mapping index. * * @return a valid dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - An id is <=0 **/ public synchronized static native long H5Pget_virtual_vspace(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_virtual_srcspace takes the dataset creation property list for the virtual dataset, dcpl_id, and the mapping index, index, * and returns a dataspace identifier for the selection within the source dataset used in the mapping. * * @param dcpl_id * IN: The identifier of the virtual dataset creation property list. * @param index * IN: Mapping index. * * @return a valid dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - An id is <=0 **/ public synchronized static native long H5Pget_virtual_srcspace(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_virtual_filename takes the dataset creation property list for the virtual dataset, dcpl_id, the mapping index, index, * the size of the filename for a source dataset, size, and retrieves the name of the file for a source dataset used in the mapping. * * @param dcpl_id * IN: The identifier of the virtual dataset creation property list. * @param index * IN: Mapping index. * * @return the name of the file containing the source dataset if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - An id is <=0 **/ public synchronized static native String H5Pget_virtual_filename(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_virtual_dsetname takes the dataset creation property list for the virtual dataset, dcpl_id, the mapping index, index, the * size of the dataset name for a source dataset, size, and retrieves the name of the source dataset used in the mapping. * * @param dcpl_id * IN: The identifier of the virtual dataset creation property list. * @param index * IN: Mapping index. * * @return the name of the source dataset if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - An id is <=0 **/ public synchronized static native String H5Pget_virtual_dsetname(long dcpl_id, long index) throws HDF5LibraryException, IllegalArgumentException; // ///// unimplemented ///// // /** // * H5Pget_vds_file_cache_size retrieves the size of the vds link open file cache. // * // * @param fapl_id // * IN: File access property list identifier // * // * @return VDS link open file cache size in number of files. // * // * @exception HDF5LibraryException // * - Error from the HDF-5 Library. // * // **/ // public synchronized static native int H5Pget_vds_file_cache_size(long fapl_id) throws HDF5LibraryException; // // /** // * H5Pset_vds_file_cache_size sets the number of files that can be held open in an vds link open file cache. // * // * @param fapl_id // * IN: File access property list identifier // * @param efc_size // * IN: VDS link open file cache size in number of files. // * // * @exception HDF5LibraryException // * - Error from the HDF-5 Library. // * // **/ // public synchronized static native void H5Pset_vds_file_cache_size(long fapl_id, int efc_size) // throws HDF5LibraryException; /** * H5Pget_external returns information about an external file. * * @param plist * IN: Identifier of a dataset creation property list. * @param idx * IN: External file index. * @param name_size * IN: Maximum length of name array. * @param name * OUT: Name of the external file. * @param size * OUT: the offset value and the size of the external file data. * * 
     *      size[0] = offset // a location to return an offset value
     *      size[1] = size // a location to return the size of
     *                // the external file data.
     *
* * @return a non-negative value if successful * * @exception ArrayIndexOutOfBoundsException * Fatal error on Copyback * @exception ArrayStoreException * Fatal error on Copyback * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name or size is null. * @exception IllegalArgumentException * - name_size <= 0 . * **/ public synchronized static native int H5Pget_external(long plist, int idx, long name_size, String[] name, long[] size) throws ArrayIndexOutOfBoundsException, ArrayStoreException, HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Pset_external adds an external file to the list of external files. * * @param plist * IN: Identifier of a dataset creation property list. * @param name * IN: Name of an external file. * @param offset * IN: Offset, in bytes, from the beginning of the file to the location in the file where the data * starts. * @param size * IN: Number of bytes reserved in the file for the data. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Pset_external(long plist, String name, long offset, long size) throws HDF5LibraryException, NullPointerException; /** * H5Pget_external_count returns the number of external files for the specified dataset. * * @param plist * IN: Identifier of a dataset creation property list. * * @return the number of external files if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pget_external_count(long plist) throws HDF5LibraryException; public synchronized static native int H5Pset_szip(long plist, int options_mask, int pixels_per_block) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_shuffle(long plist_id) throws HDF5LibraryException, NullPointerException; /** * H5Pset_nbit Sets up the use of the N-Bit filter. * * @param plist_id * IN: Dataset creation property list identifier. * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_nbit(long plist_id) throws HDF5LibraryException; /** * H5Pset_scaleoffset sets the Scale-Offset filter for a dataset. * * @param plist_id * IN: Dataset creation property list identifier. * @param scale_type * IN: Flag indicating compression method. * @param scale_factor * IN: Parameter related to scale. * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid arguments * **/ public synchronized static native int H5Pset_scaleoffset(long plist_id, int scale_type, int scale_factor) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_fill_value queries the fill value property of a dataset creation property list. * * @param plist_id * IN: Property list identifier. * @param type_id * IN: The datatype identifier of value. * @param value * IN: The fill value. * * @return a non-negative value if successful * * @exception HDF5Exception * - Error converting data array. **/ public synchronized static native int H5Pget_fill_value(long plist_id, long type_id, byte[] value) throws HDF5Exception; /** * H5Pget_fill_value queries the fill value property of a dataset creation property list. * * @param plist_id * IN: Property list identifier. * @param type_id * IN: The datatype identifier of value. * @param obj * IN: The fill value. * * @return a non-negative value if successful * * @exception HDF5Exception * - Error converting data array. **/ public synchronized static int H5Pget_fill_value(long plist_id, long type_id, Object obj) throws HDF5Exception { HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.emptyBytes(); int status = H5Pget_fill_value(plist_id, type_id, buf); if (status >= 0) { obj = theArray.arrayify(buf); } return status; } /** * H5Pset_fill_value sets the fill value for a dataset creation property list. * * @param plist_id * IN: Property list identifier. * @param type_id * IN: The datatype identifier of value. * @param value * IN: The fill value. * * @return a non-negative value if successful * * @exception HDF5Exception * - Error converting data array **/ public synchronized static native int H5Pset_fill_value(long plist_id, long type_id, byte[] value) throws HDF5Exception; /** * H5Pset_fill_value sets the fill value for a dataset creation property list. * * @param plist_id * IN: Property list identifier. * @param type_id * IN: The datatype identifier of value. * @param obj * IN: The fill value. * * @return a non-negative value if successful * * @exception HDF5Exception * - Error converting data array **/ public synchronized static int H5Pset_fill_value(long plist_id, long type_id, Object obj) throws HDF5Exception { HDFArray theArray = new HDFArray(obj); byte[] buf = theArray.byteify(); int retVal = H5Pset_fill_value(plist_id, type_id, buf); buf = null; theArray = null; return retVal; } public synchronized static native int H5Pfill_value_defined(long plist_id, int[] status) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pget_alloc_time(long plist_id, int[] alloc_time) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_alloc_time(long plist_id, int alloc_time) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pget_fill_time(long plist_id, int[] fill_time) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fill_time(long plist_id, int fill_time) throws HDF5LibraryException, NullPointerException; // /////// Dataset creation property list (DCPL) routines /////// /** * H5Pset_chunk_opts Sets the edge chunk option in a dataset creation property list. * * @param dcpl_id * IN: Dataset creation property list identifier * @param opts * IN: Edge chunk option flag. Valid values are: * H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS - filters are not applied to partial edge chunks. * 0 - Disables option; partial edge chunks will be compressed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library **/ public synchronized static native void H5Pset_chunk_opts(long dcpl_id, int opts) throws HDF5LibraryException; /** * H5Pget_chunk_opts retrieves the edge chunk option setting stored in the dataset creation property list . * * @param dcpl_id * IN: Dataset creation property list * @return The edge chunk option setting. * * @exception HDF5LibraryException * - Error from the HDF-5 Library **/ public synchronized static native int H5Pget_chunk_opts(long dcpl_id) throws HDF5LibraryException; // /////// Dataset access property list (DAPL) routines /////// /** * Retrieves the maximum possible number of elements in the meta data cache and the maximum possible number of bytes * and the RDCC_W0 value in the raw data chunk cache on a per-datset basis. * * @param dapl_id * IN: Identifier of the dataset access property list. * @param rdcc_nslots * IN/OUT: Number of elements (objects) in the raw data chunk cache. * @param rdcc_nbytes * IN/OUT: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 * IN/OUT: Preemption policy. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an array is null. **/ public synchronized static native void H5Pget_chunk_cache(long dapl_id, long[] rdcc_nslots, long[] rdcc_nbytes, double[] rdcc_w0) throws HDF5LibraryException, NullPointerException; /** * H5Pset_chunk_cache sets the number of elements (objects) in the meta data cache and the total number of bytes in * the raw data chunk cache on a per-datset basis. * * @param dapl_id * IN: Identifier of the datset access property list. * @param rdcc_nslots * IN: Number of elements (objects) in the raw data chunk cache. * @param rdcc_nbytes * IN: Total size of the raw data chunk cache, in bytes. * @param rdcc_w0 * IN: Preemption policy. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Pset_chunk_cache(long dapl_id, long rdcc_nslots, long rdcc_nbytes, double rdcc_w0) throws HDF5LibraryException; /** * H5Pset_virtual_view takes the access property list for the virtual dataset, dapl_id, and the flag, * view, and sets the VDS view according to the flag value. * * @param dapl_id * IN: Dataset access property list identifier for the virtual dataset * @param view * IN: Flag specifying the extent of the data to be included in the view. * * @exception HDF5LibraryException * - Error from the HDF-5 Library **/ public synchronized static native void H5Pset_virtual_view(long dapl_id, int view) throws HDF5LibraryException; /** * H5Pget_virtual_view takes the virtual dataset access property list, dapl_id, and retrieves the flag, * view, set by the H5Pset_virtual_view call. * * @param dapl_id * IN: Dataset access property list identifier for the virtual dataset * @return The flag specifying the view of the virtual dataset. * * @exception HDF5LibraryException * - Error from the HDF-5 Library **/ public synchronized static native int H5Pget_virtual_view(long dapl_id) throws HDF5LibraryException; /** * H5Pset_virtual_printf_gap sets the access property list for the virtual dataset, dapl_id, to instruct the * library to stop looking for the mapped data stored in the files and/or datasets with the printf-style names * after not finding gap_size files and/or datasets. The found source files and datasets will determine the * extent of the unlimited virtual dataset with the printf-style mappings. * * @param dapl_id * IN: Dataset access property list identifier for the virtual dataset * @param gap_size * IN: Maximum number of files and/or datasets allowed to be missing for determining * the extent of an unlimited virtual dataset with printf-style mappings. * * @exception HDF5LibraryException * - Error from the HDF-5 Library **/ public synchronized static native void H5Pset_virtual_printf_gap(long dapl_id, long gap_size) throws HDF5LibraryException; /** * H5Pget_virtual_printf_gap returns the maximum number of missing printf-style files and/or datasets for * determining the extent of an unlimited virtual dataaset, gap_size, using the access property list for * the virtual dataset, dapl_id. * * @param dapl_id * IN: Dataset access property list identifier for the virtual dataset * @return Maximum number of files and/or datasets allowed to be missing for determining * the extent of an unlimited virtual dataset with printf-style mappings. * * @exception HDF5LibraryException * - Error from the HDF-5 Library **/ public synchronized static native long H5Pget_virtual_printf_gap(long dapl_id) throws HDF5LibraryException; /** * H5Pget_virtual_prefix Retrieves prefix applied to virtual file paths. * * @param dapl_id * IN: Link access property list identifier * * @return the prefix to be applied to virtual file paths. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native String H5Pget_virtual_prefix(long dapl_id) throws HDF5LibraryException; /** * H5Pset_virtual_prefix Sets prefix to be applied to virtual file paths. * * @param dapl_id * IN: Dataset access property list identifier * @param prefix * IN: Prefix to be applied to virtual file paths * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - prefix is null. * **/ public synchronized static native void H5Pset_virtual_prefix(long dapl_id, String prefix) throws HDF5LibraryException, NullPointerException; /** * H5Pget_efile_prefix Retrieves prefix applied to external file paths. * * @param dapl_id * IN: Link access property list identifier * * @return the prefix to be applied to external file paths. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native String H5Pget_efile_prefix(long dapl_id) throws HDF5LibraryException; /** * H5Pset_efile_prefix Sets prefix to be applied to external file paths. * * @param dapl_id * IN: Dataset access property list identifier * @param prefix * IN: Prefix to be applied to external file paths * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - prefix is null. * **/ public synchronized static native void H5Pset_efile_prefix(long dapl_id, String prefix) throws HDF5LibraryException, NullPointerException; // public synchronized static native void H5Pset_append_flush(long plist_id, int ndims, long[] boundary, H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException; // public synchronized static native void H5Pget_append_flush(long plist_id, int dims, long[] boundary, H5D_append_cb func, H5D_append_t udata) throws HDF5LibraryException; // /////// Dataset xfer property list (DXPL) routines /////// /** * H5Pget_data_transform retrieves the data transform expression previously set in the dataset transfer property * list plist_id by H5Pset_data_transform. * * @param plist_id * IN: Identifier of the property list or class * @param size * IN: Number of bytes of the transform expression to copy to * @param expression * OUT: A data transform expression * * @return The size of the transform expression if successful; 0(zero) if no transform expression exists. Otherwise * returns a negative value. * * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Size is <= 0. * **/ public synchronized static native long H5Pget_data_transform(long plist_id, String[] expression, long size) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pset_data_transform sets a data transform expression * * @param plist_id * IN: Identifier of the property list or class * @param expression * IN: Pointer to the null-terminated data transform expression * * @return a non-negative valule if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - expression is null. * **/ public synchronized static native int H5Pset_data_transform(long plist_id, String expression) throws HDF5LibraryException, NullPointerException; /** * HH5Pget_buffer gets type conversion and background buffers. Returns buffer size, in bytes, if successful; * otherwise 0 on failure. * * @param plist * Identifier for the dataset transfer property list. * @param tconv * byte array of application-allocated type conversion buffer. * @param bkg * byte array of application-allocated background buffer. * * @return buffer size, in bytes, if successful; otherwise 0 on failure * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - plist is invalid. **/ public synchronized static native int H5Pget_buffer(long plist, byte[] tconv, byte[] bkg) throws HDF5LibraryException, IllegalArgumentException; public synchronized static native long H5Pget_buffer_size(long plist) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pset_buffer sets type conversion and background buffers. status to TRUE or FALSE. * * Given a dataset transfer property list, H5Pset_buffer sets the maximum size for the type conversion buffer and * background buffer and optionally supplies pointers to application-allocated buffers. If the buffer size is * smaller than the entire amount of data being transferred between the application and the file, and a type * conversion buffer or background buffer is required, then strip mining will be used. * * Note that there are minimum size requirements for the buffer. Strip mining can only break the data up along the * first dimension, so the buffer must be large enough to accommodate a complete slice that encompasses all of the * remaining dimensions. For example, when strip mining a 100x200x300 hyperslab of a simple data space, the buffer * must be large enough to hold 1x200x300 data elements. When strip mining a 100x200x300x150 hyperslab of a simple * data space, the buffer must be large enough to hold 1x200x300x150 data elements. * * @param plist * Identifier for the dataset transfer property list. * @param size * Size, in bytes, of the type conversion and background buffers. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - plist is invalid. **/ public synchronized static native void H5Pset_buffer_size(long plist, long size) throws HDF5LibraryException, IllegalArgumentException; public synchronized static native int H5Pget_edc_check(long plist) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_edc_check(long plist, int check) throws HDF5LibraryException, NullPointerException; /** * H5Pget_btree_ratio Get the B-tree split ratios for a dataset transfer property list. * * @param plist_id * IN Dataset transfer property list * @param left * OUT split ratio for leftmost nodes * @param right * OUT split ratio for righttmost nodes * @param middle * OUT split ratio for all other nodes * * @return non-negative if succeed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an input array is null. **/ public synchronized static native int H5Pget_btree_ratios(long plist_id, double[] left, double[] middle, double[] right) throws HDF5LibraryException, NullPointerException; /** * H5Pset_btree_ratio Sets B-tree split ratios for a dataset transfer property list. The split ratios determine what * percent of children go in the first node when a node splits. * * @param plist_id * IN Dataset transfer property list * @param left * IN split ratio for leftmost nodes * @param right * IN split ratio for righttmost nodes * @param middle * IN split ratio for all other nodes * * @return non-negative if succeed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Pset_btree_ratios(long plist_id, double left, double middle, double right) throws HDF5LibraryException; public synchronized static native int H5Pget_hyper_vector_size(long dxpl_id, long[] vector_size) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_hyper_vector_size(long dxpl_id, long vector_size) throws HDF5LibraryException, NullPointerException; // /////// Link creation property list (LCPL) routines /////// /** * H5Pget_create_intermediate_group determines whether property is set to enable creating missing intermediate * groups. * * @param lcpl_id * IN: Link creation property list identifier * * @return Boolean true or false * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native boolean H5Pget_create_intermediate_group(long lcpl_id) throws HDF5LibraryException; /** * H5Pset_create_intermediate_group specifies in property list whether to create missing intermediate groups * * @param lcpl_id * IN: Link creation property list identifier * @param crt_intermed_group * IN: Flag specifying whether to create intermediate groups upon the creation of an object * * @return a non-negative valule if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_create_intermediate_group(long lcpl_id, boolean crt_intermed_group) throws HDF5LibraryException; // /////// Group creation property list (GCPL) routines /////// /** * H5Pget_local_heap_size_hint Retrieves the anticipated size of the local heap for original-style groups. * * @param gcpl_id * IN: Group creation property list identifier * * @return size_hint, the anticipated size of local heap * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native long H5Pget_local_heap_size_hint(long gcpl_id) throws HDF5LibraryException; /** * H5Pset_local_heap_size_hint Specifies the anticipated maximum size of a local heap. * * @param gcpl_id * IN: Group creation property list identifier * @param size_hint * IN: Anticipated maximum size in bytes of local heap * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_local_heap_size_hint(long gcpl_id, long size_hint) throws HDF5LibraryException; /** * H5Pget_link_phase_change Queries the settings for conversion between compact and dense groups. * * @param gcpl_id * IN: Group creation property list identifier * @param links * The max. no. of compact links & the min. no. of dense links, which are used for storing groups * * 
     *      links[0] =  The maximum number of links for compact storage
     *      links[1] =  The minimum number of links for dense storage
     *
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. * **/ public synchronized static native int H5Pget_link_phase_change(long gcpl_id, int[] links) throws HDF5LibraryException, NullPointerException; /** * H5Pset_link_phase_change Sets the parameters for conversion between compact and dense groups. * * @param gcpl_id * IN: Group creation property list identifier * @param max_compact * IN: Maximum number of links for compact storage(Default: 8) * @param min_dense * IN: Minimum number of links for dense storage(Default: 6) * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid values of max_compact and min_dense. * **/ public synchronized static native int H5Pset_link_phase_change(long gcpl_id, int max_compact, int min_dense) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_est_link_info Queries data required to estimate required local heap or object header size. * * @param gcpl_id * IN: Group creation property list identifier * @param link_info * Estimated number of links to be inserted into group And the estimated average length of link names * * 
     *      link_info[0] =  Estimated number of links to be inserted into group
     *      link_info[1] =  Estimated average length of link names
     *
* * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - link_info is null. * **/ public synchronized static native int H5Pget_est_link_info(long gcpl_id, int[] link_info) throws HDF5LibraryException, NullPointerException; /** * H5Pset_est_link_info Sets estimated number of links and length of link names in a group. * * @param gcpl_id * IN: Group creation property list identifier * @param est_num_entries * IN: Estimated number of links to be inserted into group * @param est_name_len * IN: Estimated average length of link names * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid values to est_num_entries and est_name_len. * **/ public synchronized static native int H5Pset_est_link_info(long gcpl_id, int est_num_entries, int est_name_len) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_link_creation_order queries the group creation property list, gcpl_id, and returns a flag indicating * whether link creation order is tracked and/or indexed in a group. * * @param gcpl_id * IN: Group creation property list identifier * * @return crt_order_flags -Creation order flag(s) * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_link_creation_order(long gcpl_id) throws HDF5LibraryException; /** * H5Pset_link_creation_order Sets flags in a group creation property list, gcpl_id, for tracking and/or indexing * links on creation order. * * @param gcpl_id * IN: Group creation property list identifier * @param crt_order_flags * IN: Creation order flag(s) * * * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_link_creation_order(long gcpl_id, int crt_order_flags) throws HDF5LibraryException; // /////// String creation property list (STRCPL) routines /////// public synchronized static native int H5Pget_char_encoding(long plist_id) throws HDF5LibraryException; public synchronized static native void H5Pset_char_encoding(long plist_id, int encoding) throws HDF5LibraryException; // /////// Link access property list (LAPL) routines /////// /** * H5Pget_nlinks retrieves the maximum number of soft or user-defined link traversals allowed, nlinks, before the * library assumes it has found a cycle and aborts the traversal. This value is retrieved from the link access * property list lapl_id. * * @param lapl_id * IN: File access property list identifier * * @return Returns a Maximum number of links to traverse. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native long H5Pget_nlinks(long lapl_id) throws HDF5LibraryException; /** * H5Pset_nlinks sets the maximum number of soft or user-defined link traversals allowed, nlinks, before the library * assumes it has found a cycle and aborts the traversal. This value is set in the link access property list * lapl_id. * * @param lapl_id * IN: File access property list identifier * @param nlinks * IN: Maximum number of links to traverse * * @return Returns a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Argument is Illegal * **/ public synchronized static native int H5Pset_nlinks(long lapl_id, long nlinks) throws HDF5LibraryException, IllegalArgumentException; /** * H5Pget_elink_prefix Retrieves prefix applied to external link paths. * * @param lapl_id * IN: Link access property list identifier * @param prefix * OUT: Prefix applied to external link paths * * @return If successful, returns a non-negative value specifying the size in bytes of the prefix without the NULL * terminator; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - prefix is null. * **/ public synchronized static native long H5Pget_elink_prefix(long lapl_id, String[] prefix) throws HDF5LibraryException, NullPointerException; /** * H5Pset_elink_prefix Sets prefix to be applied to external link paths. * * @param lapl_id * IN: Link access property list identifier * @param prefix * IN: Prefix to be applied to external link paths * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - prefix is null. * **/ public synchronized static native int H5Pset_elink_prefix(long lapl_id, String prefix) throws HDF5LibraryException, NullPointerException; /** * H5Pget_elink_fapl Retrieves the file access property list identifier associated with the link access property * list. * * @param lapl_id * IN: Link access property list identifier * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public static long H5Pget_elink_fapl(long lapl_id) throws HDF5LibraryException { long id = _H5Pget_elink_fapl(lapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Pget_elink_fapl add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Pget_elink_fapl(long lapl_id) throws HDF5LibraryException; /** * H5Pset_elink_fapl sets a file access property list for use in accessing a file pointed to by an external link. * * @param lapl_id * IN: Link access property list identifier * @param fapl_id * IN: File access property list identifier * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_elink_fapl(long lapl_id, long fapl_id) throws HDF5LibraryException; /** * H5Pget_elink_acc_flags retrieves the external link traversal file access flag from the specified link access * property list. * * @param lapl_id * IN: Link access property list identifier * * @return File access flag for link traversal. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_elink_acc_flags(long lapl_id) throws HDF5LibraryException; /** * H5Pset_elink_acc_flags Sets the external link traversal file access flag in a link access property list. * * @param lapl_id * IN: Link access property list identifier * @param flags * IN: The access flag for external link traversal. * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception IllegalArgumentException * - Invalid Flag values. * **/ public synchronized static native int H5Pset_elink_acc_flags(long lapl_id, int flags) throws HDF5LibraryException, IllegalArgumentException; // /////// Object copy property list (OCPYPL) routines /////// /** * H5Pget_copy_object retrieves the properties to be used when an object is copied. * * @param ocp_plist_id * IN: Object copy property list identifier * * @return Copy option(s) set in the object copy property list * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_copy_object(long ocp_plist_id) throws HDF5LibraryException; /** * H5Pset_copy_object Sets properties to be used when an object is copied. * * @param ocp_plist_id * IN: Object copy property list identifier * @param copy_options * IN: Copy option(s) to be set * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native void H5Pset_copy_object(long ocp_plist_id, int copy_options) throws HDF5LibraryException; // /////// Other/Older property list routines /////// /** * H5Pget_version retrieves the version information of various objects for a file creation property list. * * @param plist * IN: Identifier of the file creation property list. * @param version_info * OUT: version information. * * 
     *      version_info[0] = boot  // boot block version number
     *      version_info[1] = freelist  // global freelist version
     *      version_info[2] = stab  // symbol tabl version number
     *      version_info[3] = shhdr  // shared object header version
     *
* @return a non-negative value, with the values of version_info initialized, if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - version_info is null. * @exception IllegalArgumentException * - version_info is illegal. **/ public synchronized static native int H5Pget_version(long plist, int[] version_info) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // /////// file drivers property list routines /////// public synchronized static native void H5Pget_fapl_core(long fapl_id, long[] increment, boolean[] backing_store) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fapl_core(long fapl_id, long increment, boolean backing_store) throws HDF5LibraryException, NullPointerException; /** * H5Pget_fapl_direct Retrieve direct I/O settings. * * @param fapl_id * IN: File access property list identifier * @param info * OUT: Returned property list information info[0] = alignment Required memory alignment boundary info[1] * = block_size File system block size info[2] = cbuf_size Copy buffer size * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pget_fapl_direct(long fapl_id, long[] info) throws HDF5LibraryException; /** * H5Pset_fapl_direct Sets up use of the direct I/O driver. * * @param fapl_id * IN: File access property list identifier * @param alignment * IN: Required memory alignment boundary * @param block_size * IN: File system block size * @param cbuf_size * IN: Copy buffer size * * @return a non-negative value if successful; otherwise returns a negative value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * **/ public synchronized static native int H5Pset_fapl_direct(long fapl_id, long alignment, long block_size, long cbuf_size) throws HDF5LibraryException; public synchronized static native int H5Pget_fapl_family(long fapl_id, long[] memb_size, long[] memb_fapl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fapl_family(long fapl_id, long memb_size, long memb_fapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Pget_fapl_multi Sets up use of the multi I/O driver. * * @param fapl_id * IN: File access property list identifier * @param memb_map * IN: Maps memory usage types to other memory usage types. * @param memb_fapl * IN: Property list for each memory usage type. * @param memb_name * IN: Name generator for names of member files. * @param memb_addr * IN: The offsets within the virtual address space, from 0 (zero) to HADDR_MAX, at which each type of * data storage begins. * * @return a boolean value; Allows read-only access to incomplete file sets when TRUE. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an array is null. * **/ public synchronized static native boolean H5Pget_fapl_multi(long fapl_id, int[] memb_map, long[] memb_fapl, String[] memb_name, long[] memb_addr) throws HDF5LibraryException, NullPointerException; /** * H5Pset_fapl_multi Sets up use of the multi I/O driver. * * @param fapl_id * IN: File access property list identifier * @param memb_map * IN: Maps memory usage types to other memory usage types. * @param memb_fapl * IN: Property list for each memory usage type. * @param memb_name * IN: Name generator for names of member files. * @param memb_addr * IN: The offsets within the virtual address space, from 0 (zero) to HADDR_MAX, at which each type of * data storage begins. * @param relax * IN: Allows read-only access to incomplete file sets when TRUE. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an array is null. * **/ public synchronized static native void H5Pset_fapl_multi(long fapl_id, int[] memb_map, long[] memb_fapl, String[] memb_name, long[] memb_addr, boolean relax) throws HDF5LibraryException, NullPointerException; /** * H5Pset_fapl_log Sets up the logging virtual file driver (H5FD_LOG) for use. H5Pset_fapl_log modifies the file * access property list to use the logging driver, H5FD_LOG. The logging virtual file driver (VFD) is a clone of the * standard SEC2 (H5FD_SEC2) driver with additional facilities for logging VFD metrics and activity to a file. * * @param fapl_id * IN: File access property list identifier. * @param logfile * IN: logfile is the name of the file in which the logging entries are to be recorded. * @param flags * IN: Flags specifying the types of logging activity. * @param buf_size * IN: The size of the logging buffers, in bytes. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - logfile is null. **/ public synchronized static native void H5Pset_fapl_log(long fapl_id, String logfile, long flags, long buf_size) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fapl_sec2(long fapl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native void H5Pset_fapl_split(long fapl_id, String meta_ext, long meta_plist_id, String raw_ext, long raw_plist_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fapl_stdio(long fapl_id) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Pset_fapl_windows(long fapl_id) throws HDF5LibraryException, NullPointerException; // /////// unimplemented //////// // Generic property list routines // // herr_t H5Pencode(hid_t plist_id, void *buf, size_t *nalloc); // hid_t H5Pdecode(const void *buf); // Object creation property list (OCPL) routines // // File creation property list (FCPL) routines // // File access property list (FAPL) routines // // herr_t H5Pset_driver(hid_t plist_id, hid_t new_driver_id, const void *new_driver_info) // const void *H5Pget_driver_info(hid_t plist_id) // herr_t H5Pget_multi_type(hid_t fapl_id, H5FD_mem_t *type) // herr_t H5Pset_multi_type(hid_t fapl_id, H5FD_mem_t type) // herr_t H5Pget_file_image(hid_t fapl_id, void **buf_ptr_ptr, size_t *buf_len_ptr); // herr_t H5Pset_file_image(hid_t fapl_id, void *buf_ptr, size_t buf_len); // herr_t H5Pget_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callbacks_ptr); // herr_t H5Pset_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callbacks_ptr); // herr_t H5Pset_core_write_tracking(hid_t fapl_id, hbool_t is_enabled, size_t page_size); // herr_t H5Pget_core_write_tracking(hid_t fapl_id, hbool_t *is_enabled, size_t *page_size); // #ifdef H5_HAVE_PARALLEL // herr_t H5Pset_all_coll_metadata_ops(hid_t accpl_id, hbool_t is_collective); // H5_DLL 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 */ // H5_DLL herr_t H5Pset_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr); // H5_DLL herr_t H5Pget_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr /*out*/); // H5_DLL 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 // H5_DLL herr_t H5Pget_mpio_actual_chunk_opt_mode(hid_t plist_id, H5D_mpio_actual_chunk_opt_mode_t *actual_chunk_opt_mode); // H5_DLL herr_t H5Pget_mpio_actual_io_mode(hid_t plist_id, H5D_mpio_actual_io_mode_t *actual_io_mode); // H5_DLL herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_cause, uint32_t *global_no_collective_cause); // #endif /* H5_HAVE_PARALLEL */ // Link creation property list (LCPL) routines // // Group creation property list (GCPL) routines // // String creation property list (STRCPL) routines // // Link access property list (LAPL) routines // // herr_t H5Pget_elink_cb( hid_t lapl_id, H5L_elink_traverse_t *func, void **op_data ) // herr_t H5Pset_elink_cb( hid_t lapl_id, H5L_elink_traverse_t func, void *op_data ) // Object copy property list (OCPYPL) routines // // herr_t H5Padd_merge_committed_dtype_path(hid_t plist_id, const char *path); // herr_t H5Pfree_merge_committed_dtype_paths(hid_t plist_id); // herr_t H5Pget_mcdt_search_cb(hid_t plist_id, H5O_mcdt_search_cb_t *func, void **op_data); // herr_t H5Pset_mcdt_search_cb(hid_t plist_id, H5O_mcdt_search_cb_t func, void *op_data); // //////////////////////////////////////////////////////////// // // // H5PL: HDF5 1.8 Plugin API Functions // // // // //////////////////////////////////////////////////////////// /** * H5PLset_loading_state uses one argument to enable or disable individual plugins. * The plugin_flags parameter is an encoded integer in which each bit controls a specific * plugin or class of plugins. * A plugin bit set to 0 (zero) prevents the use of the dynamic plugin corresponding * to that bit position. A plugin bit set to 1 (one) allows the use of that dynamic plugin. * All dynamic plugins can be enabled by setting plugin_flags to a negative value. * A value of 0 (zero) will disable all dynamic plugins. * * H5PLset_loading_state inspects the HDF5_PLUGIN_PRELOAD environment variable every * time it is called. If the environment variable is set to the special :: string, * all dynamic plugins will be disabled. * * @param plugin_flags * IN: The list of dynamic plugin types to enable or disable. * A plugin bit set to 0 (zero) prevents use of that dynamic plugin. * A plugin bit set to 1 (one) enables use of that dynamic plugin. * Setting plugin_flags to a negative value enables all dynamic plugins. * Setting plugin_flags to 0 (zero) disables all dynamic plugins. * * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5PLset_loading_state(int plugin_flags) throws HDF5LibraryException; /** * H5PLget_loading_state retrieves the state of the dynamic plugins flag, plugin_flags.. * * @return the list of dynamic plugin types that are enabled or disabled. * A plugin bit set to 0 (zero) indicates that that dynamic plugin is disabled. * A plugin bit set to 1 (one) indicates that that dynamic plugin is enabled. * If the value of plugin_flags is negative, all dynamic plugins are enabled. * If the value of plugin_flags is 0 (zero), all dynamic plugins are disabled. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5PLget_loading_state() throws HDF5LibraryException; /** * H5PLappend inserts the plugin path at the end of the table. * * @param plugin_path * IN: Path for location of filter plugin libraries. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5PLappend(String plugin_path) throws HDF5LibraryException; /** * H5PLprepend inserts the plugin path at the beginning of the table. * * @param plugin_path * IN: Path for location of filter plugin libraries. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5PLprepend(String plugin_path) throws HDF5LibraryException; /** * H5PLreplace replaces the plugin path at the specified index. * * @param plugin_path * IN: Path for location of filter plugin libraries. * @param index * IN: The table index (0-based). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5PLreplace(String plugin_path, int index) throws HDF5LibraryException; /** * H5PLinsert inserts the plugin path at the specified index. * * @param plugin_path * IN: Path for location of filter plugin libraries. * @param index * IN: The table index (0-based). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5PLinsert(String plugin_path, int index) throws HDF5LibraryException; /** * H5PLremove removes the plugin path at the specified index. * * @param index * IN: The table index (0-based). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5PLremove(int index) throws HDF5LibraryException; /** * H5PLget retrieves the plugin path at the specified index. * * @param index * IN: The table index (0-based). * * @return the current path at the index in plugin path table * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5PLget(int index) throws HDF5LibraryException; /** * H5PLsize retrieves the size of the current list of plugin paths. * * @return the current number of paths in the plugin path table * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5PLsize() throws HDF5LibraryException; // //////////////////////////////////////////////////////////// // // // H5R: HDF5 1.8 Reference API Functions // // // // //////////////////////////////////////////////////////////// private synchronized static native int H5Rcreate(byte[] ref, long loc_id, String name, int ref_type, long space_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rcreate creates the reference, ref, of the type specified in ref_type, pointing to the object name located at * loc_id. * * @param loc_id * IN: Location identifier used to locate the object being pointed to. * @param name * IN: Name of object at location loc_id. * @param ref_type * IN: Type of reference. * @param space_id * IN: Dataspace identifier with selection. * * @return the reference (byte[]) if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an input array is null. * @exception IllegalArgumentException * - an input array is invalid. **/ public synchronized static byte[] H5Rcreate(long loc_id, String name, int ref_type, long space_id) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { /* These sizes are correct for HDF5.1.2 */ int ref_size = 8; if (ref_type == HDF5Constants.H5R_DATASET_REGION) { ref_size = 12; } byte rbuf[] = new byte[ref_size]; /* will raise an exception if fails */ H5Rcreate(rbuf, loc_id, name, ref_type, space_id); return rbuf; } /** * Given a reference to some object, H5Rdereference opens that object and return an identifier. * * @param dataset * IN: Dataset containing reference object. * @param access_list * IN: Property list of the object being referenced. * @param ref_type * IN: The reference type of ref. * @param ref * IN: reference to an object * * @return valid identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - output array is null. * @exception IllegalArgumentException * - output array is invalid. **/ public static long H5Rdereference(long dataset, long access_list, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { long id = _H5Rdereference(dataset, access_list, ref_type, ref); if (id > 0) { log.trace("OPEN_IDS: H5Rdereference add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Rdereference(long dataset, long access_list, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rget_name retrieves a name for the object identified by ref. * * @param loc_id * IN: Identifier for the dataset containing the reference or for the group that dataset is in. * @param ref_type * IN: Type of reference. * @param ref * IN: An object or dataset region reference. * @param name * OUT: A name associated with the referenced object or dataset region. * @param size * IN: The size of the name buffer. * * @return Returns the length of the name if successful, returning 0 (zero) if no name is associated with the * identifier. Otherwise returns a negative value. * * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - size is null. * @exception IllegalArgumentException * - Argument is illegal. * **/ public synchronized static native long H5Rget_name(long loc_id, int ref_type, byte[] ref, String[] name, long size) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rget_obj_type Given a reference to an object ref, H5Rget_obj_type returns the type of the object pointed to. * * @param loc_id * IN: loc_id of the reference object. * @param ref_type * IN: Type of reference to query. * @param ref * IN: the reference * * @return Returns the object type * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - array is null. * @exception IllegalArgumentException * - array is invalid. **/ public synchronized static native int H5Rget_obj_type(long loc_id, int ref_type, byte ref[]) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Rget_obj_type2 Retrieves the type of object that an object reference points to. * * @see public static int H5Rget_obj_type(int loc_id, int ref_type, byte ref[]) **/ private synchronized static native int H5Rget_obj_type2(long loc_id, int ref_type, byte ref[], int[] obj_type) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * Given a reference to an object ref, H5Rget_region creates a copy of the dataspace of the dataset pointed to and * defines a selection in the copy which is the region pointed to. * * @param loc_id * IN: loc_id of the reference object. * @param ref_type * IN: The reference type of ref. * @param ref * OUT: the reference to the object and region * * @return a valid identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - output array is null. * @exception IllegalArgumentException * - output array is invalid. **/ public static long H5Rget_region(long loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { long id = _H5Rget_region(loc_id, ref_type, ref); if (id > 0) { log.trace("OPEN_IDS: H5Rget_region add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Rget_region(long loc_id, int ref_type, byte[] ref) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; // //////////////////////////////////////////////////////////// // // // H5S: Dataspace Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Sclose releases a dataspace. * * @param space_id * Identifier of dataspace to release. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Sclose(long space_id) throws HDF5LibraryException { if (space_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; log.trace("OPEN_IDS: H5Sclose remove {}", space_id); OPEN_IDS.remove(space_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); return _H5Sclose(space_id); } private synchronized static native int _H5Sclose(long space_id) throws HDF5LibraryException; /** * H5Scopy creates a new dataspace which is an exact copy of the dataspace identified by space_id. * * @param space_id * Identifier of dataspace to copy. * @return a dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Scopy(long space_id) throws HDF5LibraryException { long id = _H5Scopy(space_id); if (id > 0) { log.trace("OPEN_IDS: H5Scopy add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Scopy(long space_id) throws HDF5LibraryException; /** * H5Screate creates a new dataspace of a particular type. * * @param type * IN: The type of dataspace to be created. * * @return a dataspace identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Screate(int type) throws HDF5LibraryException { long id = _H5Screate(type); if (id > 0) { log.trace("OPEN_IDS: H5Screate add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Screate(int type) throws HDF5LibraryException; /** * H5Screate_simple creates a new simple data space and opens it for access. * * @param rank * IN: Number of dimensions of dataspace. * @param dims * IN: An array of the size of each dimension. * @param maxdims * IN: An array of the maximum size of each dimension. * * @return a dataspace identifier * * @exception HDF5Exception * - Error from the HDF-5 Library. * @exception NullPointerException * - dims or maxdims is null. **/ public static long H5Screate_simple(int rank, long[] dims, long[] maxdims) throws HDF5Exception, NullPointerException { long id = _H5Screate_simple(rank, dims, maxdims); if (id > 0) { log.trace("OPEN_IDS: H5Screate_simple add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Screate_simple(int rank, long[] dims, long[] maxdims) throws HDF5Exception, NullPointerException; /** * H5Sdecode reconstructs the HDF5 data space object and returns a new object handle for it. * * @param buf * IN: Buffer for the data space object to be decoded. * * @return a new object handle * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native long H5Sdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Sencode converts a data space description into binary form in a buffer. * * @param obj_id * IN: Identifier of the object to be encoded. * * @return the buffer for the object to be encoded into. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native byte[] H5Sencode(long obj_id) throws HDF5LibraryException, NullPointerException; /** * H5Sextent_copy copies the extent from source_space_id to dest_space_id. This action may change the type of the * dataspace. * * @param dest_space_id * IN: The identifier for the dataspace from which the extent is copied. * @param source_space_id * IN: The identifier for the dataspace to which the extent is copied. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sextent_copy(long dest_space_id, long source_space_id) throws HDF5LibraryException; /** * H5Sextent_equal determines whether the dataspace extents of two dataspaces, space1_id and space2_id, are equal. * * @param first_space_id * IN: The identifier for the first dataspace. * @param second_space_id * IN: The identifier for the seconddataspace. * * @return true if successful, else false * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sextent_equal(long first_space_id, long second_space_id) throws HDF5LibraryException; /** * 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 spaceid * Identifier of dataspace to release. * @param start * coordinates of lowest corner of bounding box. * @param end * coordinates of highest corner of bounding box. * * @return a non-negative value if successful,with start and end initialized. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - start or end is null. **/ public synchronized static native int H5Sget_select_bounds(long spaceid, long[] start, long[] end) throws HDF5LibraryException, NullPointerException; /** * H5Sget_select_elem_npoints returns the number of element points in the current dataspace selection. * * @param spaceid * Identifier of dataspace to release. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Sget_select_elem_npoints(long spaceid) throws HDF5LibraryException; /** * H5Sget_select_elem_pointlist returns an array of of element points in the current dataspace selection. The point * coordinates have the same dimensionality (rank) as the dataspace they are located within, one coordinate per * point. * * @param spaceid * Identifier of dataspace to release. * @param startpoint * first point to retrieve * @param numpoints * number of points to retrieve * @param buf * returns points startblock to startblock+num-1, each points is rank longs. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native int H5Sget_select_elem_pointlist(long spaceid, long startpoint, long numpoints, long[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Sget_select_hyper_blocklist returns an array of hyperslab blocks. The block coordinates have the same * dimensionality (rank) as the dataspace they are located within. The list of blocks is formatted as follows: * * 

     *    <"start" coordinate>, immediately followed by
     *    <"opposite" corner coordinate>, followed by
     *   the next "start" and "opposite" coordinates,
     *   etc.
     *   until all of the selected blocks have been listed.
     *
* * @param spaceid * Identifier of dataspace to release. * @param startblock * first block to retrieve * @param numblocks * number of blocks to retrieve * @param buf * returns blocks startblock to startblock+num-1, each block is rank * 2 (corners) longs. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid, long startblock, long numblocks, long[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Sget_select_hyper_nblocks returns the number of hyperslab blocks in the current dataspace selection. * * @param spaceid * Identifier of dataspace to release. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Sget_select_hyper_nblocks(long spaceid) throws HDF5LibraryException; /** * H5Sget_select_npoints determines the number of elements in the current selection of a dataspace. * * @param space_id * IN: Identifier of the dataspace object to query * * @return the number of elements in the selection if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Sget_select_npoints(long space_id) throws HDF5LibraryException; /** * H5Sget_select_type retrieves the type of selection currently defined for the dataspace space_id. * * @param space_id * IN: Identifier of the dataspace object to query * * @return the dataspace selection type if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sget_select_type(long space_id) throws HDF5LibraryException; /** * H5Sget_simple_extent_dims returns the size and maximum sizes of each dimension of a dataspace through the dims * and maxdims parameters. * * @param space_id * IN: Identifier of the dataspace object to query * @param dims * OUT: Pointer to array to store the size of each dimension. * @param maxdims * OUT: Pointer to array to store the maximum size of each dimension. * * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - dims or maxdims is null. **/ public synchronized static native int H5Sget_simple_extent_dims(long space_id, long[] dims, long[] maxdims) throws HDF5LibraryException, NullPointerException; /** * H5Sget_simple_extent_ndims determines the dimensionality (or rank) of a dataspace. * * @param space_id * IN: Identifier of the dataspace * * @return the number of dimensions in the dataspace if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sget_simple_extent_ndims(long space_id) throws HDF5LibraryException; /** * H5Sget_simple_extent_npoints determines the number of elements in a dataspace. * * @param space_id * ID of the dataspace object to query * @return the number of elements in the dataspace if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Sget_simple_extent_npoints(long space_id) throws HDF5LibraryException; /** * H5Sget_simple_extent_type queries a dataspace to determine the current class of a dataspace. * * @param space_id * Dataspace identifier. * * @return a dataspace class name if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sget_simple_extent_type(long space_id) throws HDF5LibraryException; /** * H5Sis_simple determines whether a dataspace is a simple dataspace. * * @param space_id * Identifier of the dataspace to query * * @return true if is a simple dataspace * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sis_simple(long space_id) throws HDF5LibraryException; /** * H5Soffset_simple sets the offset of a simple dataspace space_id. * * @param space_id * IN: The identifier for the dataspace object to reset. * @param offset * IN: The offset at which to position the selection. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - offset array is null. **/ public synchronized static native int H5Soffset_simple(long space_id, byte[] offset) throws HDF5LibraryException, NullPointerException; public synchronized static int H5Soffset_simple(long space_id, long[] offset) throws HDF5Exception, NullPointerException { if (offset == null) { return -1; } HDFArray theArray = new HDFArray(offset); byte[] theArr = theArray.byteify(); int retVal = H5Soffset_simple(space_id, theArr); theArr = null; theArray = null; return retVal; } /** * H5Sselect_all selects the entire extent of the dataspace space_id. * * @param space_id * IN: The identifier of the dataspace to be selected. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sselect_all(long space_id) throws HDF5LibraryException; /** * H5Sselect_elements selects array elements to be included in the selection for the space_id dataspace. * * @param space_id * Identifier of the dataspace. * @param op * operator specifying how the new selection is combined. * @param num_elements * Number of elements to be selected. * @param coord * A 2-dimensional array specifying the coordinates of the elements. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ private synchronized static native int H5Sselect_elements(long space_id, int op, int num_elements, byte[] coord) throws HDF5LibraryException, NullPointerException; /** * H5Sselect_elements selects array elements to be included in the selection for the space_id dataspace. * * @param space_id * Identifier of the dataspace. * @param op * operator specifying how the new selection is combined. * @param num_elements * Number of elements to be selected. * @param coord2D * A 2-dimensional array specifying the coordinates of the elements. * * @return a non-negative value if successful * * @exception HDF5Exception * - Error in the data conversion * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - cord array is **/ public synchronized static int H5Sselect_elements(long space_id, int op, int num_elements, long[][] coord2D) throws HDF5Exception, HDF5LibraryException, NullPointerException { if (coord2D == null) { return -1; } HDFArray theArray = new HDFArray(coord2D); byte[] coord = theArray.byteify(); int retVal = H5Sselect_elements(space_id, op, num_elements, coord); coord = null; theArray = null; return retVal; } /** * H5Sselect_hyperslab selects a hyperslab region to add to the current selected region for the dataspace specified * by space_id. The start, stride, count, and block arrays must be the same size as the rank of the dataspace. * * @param space_id * IN: Identifier of dataspace selection to modify * @param op * IN: Operation to perform on current selection. * @param start * IN: Offset of start of hyperslab * @param stride * IN: Hyperslab stride. * @param count * IN: Number of blocks included in hyperslab. * @param block * IN: Size of block in hyperslab. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an input array is null. * @exception IllegalArgumentException * - an input array is invalid. **/ public synchronized static int H5Sselect_hyperslab(long space_id, int op, byte[] start, byte[] stride, byte[] count, byte[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { ByteBuffer startbb = ByteBuffer.wrap(start); long[] lastart = (startbb.asLongBuffer()).array(); ByteBuffer stridebb = ByteBuffer.wrap(stride); long[] lastride = (stridebb.asLongBuffer()).array(); ByteBuffer countbb = ByteBuffer.wrap(count); long[] lacount = (countbb.asLongBuffer()).array(); ByteBuffer blockbb = ByteBuffer.wrap(block); long[] lablock = (blockbb.asLongBuffer()).array(); return H5Sselect_hyperslab(space_id, op, lastart, lastride, lacount, lablock); } public synchronized static native int H5Sselect_hyperslab(long space_id, int op, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Sselect_none resets the selection region for the dataspace space_id to include no elements. * * @param space_id * IN: The identifier of the dataspace to be reset. * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sselect_none(long space_id) throws HDF5LibraryException; /** * H5Sselect_valid verifies that the selection for the dataspace. * * @param space_id * The identifier for the dataspace in which the selection is being reset. * * @return true if the selection is contained within the extent and FALSE if it is not or is an error. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sselect_valid(long space_id) throws HDF5LibraryException; /** * H5Sset_extent_none removes the extent from a dataspace and sets the type to H5S_NONE. * * @param space_id * The identifier for the dataspace from which the extent is to be removed. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Sset_extent_none(long space_id) throws HDF5LibraryException; /** * H5Sset_extent_simple sets or resets the size of an existing dataspace. * * @param space_id * Dataspace identifier. * @param rank * Rank, or dimensionality, of the dataspace. * @param current_size * Array containing current size of dataspace. * @param maximum_size * Array containing maximum size of dataspace. * * @return a dataspace identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Sset_extent_simple(long space_id, int rank, long[] current_size, long[] maximum_size) throws HDF5LibraryException, NullPointerException; public synchronized static long H5Sset_extent_simple(long space_id, int rank, byte[] current_size, byte[] maximum_size) throws HDF5LibraryException, NullPointerException { ByteBuffer csbb = ByteBuffer.wrap(current_size); long[] lacs = (csbb.asLongBuffer()).array(); ByteBuffer maxsbb = ByteBuffer.wrap(maximum_size); long[] lamaxs = (maxsbb.asLongBuffer()).array(); return H5Sset_extent_simple(space_id, rank, lacs, lamaxs); } /** * H5Sget_regular_hyperslab determines if a hyperslab selection is regular for the dataspace specified * by space_id. The start, stride, count, and block arrays must be the same size as the rank of the dataspace. * * @param space_id * IN: Identifier of dataspace selection to modify * @param start * OUT: Offset of start of hyperslab * @param stride * OUT: Hyperslab stride. * @param count * OUT: Number of blocks included in hyperslab. * @param block * OUT: Size of block in hyperslab. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - an output array is null. * @exception IllegalArgumentException * - an output array is invalid. **/ public synchronized static native void H5Sget_regular_hyperslab(long space_id, long[] start, long[] stride, long[] count, long[] block) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Sis_regular_hyperslab retrieves a regular hyperslab selection for the dataspace specified * by space_id. * * @param space_id * IN: Identifier of dataspace selection to query * * @return a TRUE/FALSE for hyperslab selection if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException; // /////// unimplemented //////// // #ifdef NEW_HYPERSLAB_API // H5_DLL hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op, // const hsize_t start[], // const hsize_t _stride[], // const hsize_t count[], // const hsize_t _block[]); // H5_DLL herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op, // hid_t space2_id); // H5_DLL hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op, // hid_t space2_id); // #endif /* NEW_HYPERSLAB_API */ // //////////////////////////////////////////////////////////// // // // H5T: Datatype Interface Functions // // // // //////////////////////////////////////////////////////////// /** * H5Tarray_create creates a new array datatype object. * * @param base_id * IN: Datatype identifier for the array base datatype. * @param ndims * IN: Rank of the array. * @param dim * IN: Size of each array dimension. * * @return a valid datatype identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - dim is null. **/ public static long H5Tarray_create(long base_id, int ndims, long[] dim) throws HDF5LibraryException, NullPointerException { long id = _H5Tarray_create2(base_id, ndims, dim); if (id > 0) { log.trace("OPEN_IDS: H5Tarray_create add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tarray_create2(long base_id, int ndims, long[] dim) throws HDF5LibraryException, NullPointerException; /** * H5Tclose releases a datatype. * * @param type_id * IN: Identifier of datatype to release. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Tclose(long type_id) throws HDF5LibraryException { if (type_id < 0) return 0; // throw new HDF5LibraryException("Negative ID");; log.trace("OPEN_IDS: H5Tclose remove {}", type_id); OPEN_IDS.remove(type_id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); return _H5Tclose(type_id); } private synchronized static native int _H5Tclose(long type_id) throws HDF5LibraryException; /** * H5Tcommit saves a transient datatype as an immutable named datatype in a file. * * @param loc_id * IN: Location identifier. * @param name * IN: Name given to committed datatype. * @param type_id * IN: Identifier of datatype to be committed. * @param lcpl_id * IN: Link creation property list. * @param tcpl_id * IN: Datatype creation property list. * @param tapl_id * IN: Datatype access property list. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native void H5Tcommit(long loc_id, String name, long type_id, long lcpl_id, long tcpl_id, long tapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Tcommit_anon commits a transient datatype (not immutable) to a file, turning it into a named datatype with the * specified creation and property lists. * * @param loc_id * IN: Location identifier. * @param type_id * IN: Identifier of datatype to be committed. * @param tcpl_id * IN: Datatype creation property list. * @param tapl_id * IN: Datatype access property list. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Tcommit_anon(long loc_id, long type_id, long tcpl_id, long tapl_id) throws HDF5LibraryException; /** * H5Tcommitted queries a type to determine whether the type specified by the type identifier is a named type or a * transient type. * * @param type_id * IN: Identifier of datatype. * * @return true the datatype has been committed * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Tcommitted(long type_id) throws HDF5LibraryException; /** * H5Tcompiler_conv finds out whether the library's conversion function from type src_id to type dst_id is a * compiler (hard) conversion. * * @param src_id * IN: Identifier of source datatype. * @param dst_id * IN: Identifier of destination datatype. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Tcompiler_conv(long src_id, long dst_id) throws HDF5LibraryException; /** ** H5Tconvert converts nelmts elements from the type specified by the src_id identifier to type dst_id. * * @param src_id * IN: Identifier of source datatype. * @param dst_id * IN: Identifier of destination datatype. * @param nelmts * IN: Size of array buf. * @param buf * IN: Array containing pre- and post-conversion values. * @param background * IN: Optional background buffer. * @param plist_id * IN: Dataset transfer property list identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native void H5Tconvert(long src_id, long dst_id, long nelmts, byte[] buf, byte[] background, long plist_id) throws HDF5LibraryException, NullPointerException; // int H5Tconvert(int src_id, int dst_id, long nelmts, Pointer buf, Pointer background, int plist_id); /** * H5Tcopy copies an existing datatype. The returned type is always transient and unlocked. * * @param type_id * IN: Identifier of datatype to copy. Can be a datatype identifier, a predefined datatype (defined in * H5Tpublic.h), or a dataset Identifier. * * @return a datatype identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Tcopy(long type_id) throws HDF5LibraryException { long id = _H5Tcopy(type_id); if (id > 0) { log.trace("OPEN_IDS: H5Tcopy add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tcopy(long type_id) throws HDF5LibraryException; /** * H5Tcreate creates a new dataype of the specified class with the specified number of bytes. * * @param tclass * IN: Class of datatype to create. * @param size * IN: The number of bytes in the datatype to create. * * @return datatype identifier * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Tcreate(int tclass, long size) throws HDF5LibraryException { long id = _H5Tcreate(tclass, size); if (id > 0) { log.trace("OPEN_IDS: H5Tcreate add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tcreate(int type, long size) throws HDF5LibraryException; /** * H5Tdecode reconstructs the HDF5 data type object and returns a new object handle for it. * * @param buf * IN: Buffer for the data type object to be decoded. * * @return a new object handle * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public static long H5Tdecode(byte[] buf) throws HDF5LibraryException, NullPointerException { long id = _H5Tdecode(buf); if (id > 0) { log.trace("OPEN_IDS: H5Tdecode add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tdecode(byte[] buf) throws HDF5LibraryException, NullPointerException; /** * H5Tdetect_class determines whether the datatype specified in dtype_id contains any datatypes of the datatype * class specified in dtype_class. * * @param type_id * IN: Identifier of datatype to query. * @param cls * IN: Identifier of datatype cls. * * @return true if the datatype specified in dtype_id contains any datatypes of the datatype class * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Tdetect_class(long type_id, int cls) throws HDF5LibraryException; /** * H5Tencode converts a data type description into binary form in a buffer. * * @param obj_id * IN: Identifier of the object to be encoded. * @param buf * OUT: Buffer for the object to be encoded into. If the provided buffer is NULL, only the size of buffer * needed is returned. * @param nalloc * IN: The size of the allocated buffer. * * @return the size needed for the allocated buffer. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - buf is null. **/ public synchronized static native int H5Tencode(long obj_id, byte[] buf, long nalloc) throws HDF5LibraryException, NullPointerException; // /** // * H5Tencode converts a data type description into binary form in a buffer. // * // * @param obj_id IN: Identifier of the object to be encoded. // * // * @return the buffer for the object to be encoded into. // * // * @exception HDF5LibraryException - Error from the HDF-5 Library. // **/ // public synchronized static native byte[] H5Tencode(int obj_id) // throws HDF5LibraryException; /** * H5Tenum_create creates a new enumeration datatype based on the specified base datatype, parent_id, which must be * an integer type. * * @param base_id * IN: Identifier of the parent datatype to release. * * @return the datatype identifier for the new enumeration datatype * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Tenum_create(long base_id) throws HDF5LibraryException { long id = _H5Tenum_create(base_id); if (id > 0) { log.trace("OPEN_IDS: H5Tenum_create add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tenum_create(long base_id) throws HDF5LibraryException; /** * H5Tenum_insert inserts a new enumeration datatype member into an enumeration datatype. * * @param type * IN: Identifier of datatype. * @param name * IN: The name of the member * @param value * IN: The value of the member, data of the correct type * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native void H5Tenum_insert(long type, String name, byte[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_insert inserts a new enumeration datatype member into an enumeration datatype. * * @param type * IN: Identifier of datatype. * @param name * IN: The name of the member * @param value * IN: The value of the member, data of the correct type * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static int H5Tenum_insert(long type, String name, int[] value) throws HDF5LibraryException, NullPointerException { return H5Tenum_insert_int(type, name, value); } public static int H5Tenum_insert(long type, String name, int value) throws HDF5LibraryException, NullPointerException { int[] val = { value }; return H5Tenum_insert_int(type, name, val); } private synchronized static native int H5Tenum_insert_int(long type, String name, int[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_nameof finds the symbol name that corresponds to the specified value of the enumeration datatype type. * * @param type * IN: Identifier of datatype. * @param value * IN: The value of the member, data of the correct * @param size * IN: The probable length of the name * * @return the symbol name. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - value is null. **/ public synchronized static native String H5Tenum_nameof(long type, byte[] value, long size) throws HDF5LibraryException, NullPointerException; // int H5Tenum_nameof(int type, Pointer value, Buffer name/* out */, long size); /** * H5Tenum_nameof finds the symbol name that corresponds to the specified value of the enumeration datatype type. * * @param type * IN: Identifier of datatype. * @param value * IN: The value of the member, data of the correct * @param name * OUT: The name of the member * @param size * IN: The max length of the name * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static int H5Tenum_nameof(long type, int[] value, String[] name, int size) throws HDF5LibraryException, NullPointerException { return H5Tenum_nameof_int(type, value, name, size); } private synchronized static native int H5Tenum_nameof_int(long type, int[] value, String[] name, int size) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_valueof finds the value that corresponds to the specified name of the enumeration datatype type. * * @param type * IN: Identifier of datatype. * @param name * IN: The name of the member * @param value * OUT: The value of the member * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Tenum_valueof(long type, String name, byte[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tenum_valueof finds the value that corresponds to the specified name of the enumeration datatype type. * * @param type * IN: Identifier of datatype. * @param name * IN: The name of the member * @param value * OUT: The value of the member * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static int H5Tenum_valueof(long type, String name, int[] value) throws HDF5LibraryException, NullPointerException { return H5Tenum_valueof_int(type, name, value); } private synchronized static native int H5Tenum_valueof_int(long type, String name, int[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tequal determines whether two datatype identifiers refer to the same datatype. * * @param type_id1 * IN: Identifier of datatype to compare. * @param type_id2 * IN: Identifier of datatype to compare. * * @return true if the datatype identifiers refer to the same datatype, else false. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Tequal(long type_id1, long type_id2) throws HDF5LibraryException; /** * H5Tget_array_dims returns the sizes of the dimensions of the specified array datatype object. * * @param type_id * IN: Datatype identifier of array object. * @param dims * OUT: Sizes of array dimensions. * * @return the non-negative number of dimensions of the array type * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - dims is null. **/ public static int H5Tget_array_dims(long type_id, long[] dims) throws HDF5LibraryException, NullPointerException { return H5Tget_array_dims2(type_id, dims); } /** * H5Tget_array_dims2 returns the sizes of the dimensions of the specified array datatype object. * * @param type_id * IN: Datatype identifier of array object. * @param dims * OUT: Sizes of array dimensions. * * @return the non-negative number of dimensions of the array type * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - dims is null. **/ public synchronized static native int H5Tget_array_dims2(long type_id, long[] dims) throws HDF5LibraryException, NullPointerException; /** * H5Tget_array_ndims returns the rank, the number of dimensions, of an array datatype object. * * @param type_id * IN: Datatype identifier of array object. * * @return the rank of the array * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_array_ndims(long type_id) throws HDF5LibraryException; /** * H5Tget_class returns the datatype class identifier. * * @param type_id * IN: Identifier of datatype to query. * * @return datatype class identifier if successful; otherwise H5T_NO_CLASS(-1). * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_class(long type_id) throws HDF5LibraryException; /** * H5Tget_class_name returns the datatype class identifier. * * @param class_id * IN: Identifier of class from H5Tget_class. * * @return class name if successful; otherwise H5T_NO_CLASS. * **/ public static String H5Tget_class_name(long class_id) { String retValue = null; if (HDF5Constants.H5T_INTEGER == class_id) /* integer types */ retValue = "H5T_INTEGER"; else if (HDF5Constants.H5T_FLOAT == class_id) /* floating-point types */ retValue = "H5T_FLOAT"; else if (HDF5Constants.H5T_TIME == class_id) /* date and time types */ retValue = "H5T_TIME"; else if (HDF5Constants.H5T_STRING == class_id) /* character string types */ retValue = "H5T_STRING"; else if (HDF5Constants.H5T_BITFIELD == class_id) /* bit field types */ retValue = "H5T_BITFIELD"; else if (HDF5Constants.H5T_OPAQUE == class_id) /* opaque types */ retValue = "H5T_OPAQUE"; else if (HDF5Constants.H5T_COMPOUND == class_id) /* compound types */ retValue = "H5T_COMPOUND"; else if (HDF5Constants.H5T_REFERENCE == class_id)/* reference types */ retValue = "H5T_REFERENCE"; else if (HDF5Constants.H5T_ENUM == class_id) /* enumeration types */ retValue = "H5T_ENUM"; else if (HDF5Constants.H5T_VLEN == class_id) /* Variable-Length types */ retValue = "H5T_VLEN"; else if (HDF5Constants.H5T_ARRAY == class_id) /* Array types */ retValue = "H5T_ARRAY"; else retValue = "H5T_NO_CLASS"; return retValue; } /** * H5Tget_create_plist returns a property list identifier for the datatype creation property list associated with * the datatype specified by type_id. * * @param type_id * IN: Identifier of datatype. * * @return a datatype property list identifier. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Tget_create_plist(long type_id) throws HDF5LibraryException { long id = _H5Tget_create_plist(type_id); if (id > 0) { log.trace("OPEN_IDS: _H5Tget_create_plist add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tget_create_plist(long type_id) throws HDF5LibraryException; /** * H5Tget_cset retrieves the character set type of a string datatype. * * @param type_id * IN: Identifier of datatype to query. * * @return a valid character set type if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_cset(long type_id) throws HDF5LibraryException; /** * H5Tset_cset the character set to be used. * * @param type_id * IN: Identifier of datatype to modify. * @param cset * IN: Character set type. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_cset(long type_id, int cset) throws HDF5LibraryException; /** * H5Tget_ebias retrieves the exponent bias of a floating-point type. * * @param type_id * Identifier of datatype to query. * * @return the bias if successful; otherwise 0. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_ebias(long type_id) throws HDF5LibraryException; /** * H5Tset_ebias sets the exponent bias of a floating-point type. * * @param type_id * Identifier of datatype to set. * @param ebias * Exponent bias value. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Tset_ebias(long type_id, int ebias) throws HDF5LibraryException { H5Tset_ebias(type_id, (long) ebias); return 0; } /** * H5Tget_ebias retrieves the exponent bias of a floating-point type. * * @param type_id * IN: Identifier of datatype to query. * * @return the bias * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_ebias_long(long type_id) throws HDF5LibraryException; /** * H5Tset_ebias sets the exponent bias of a floating-point type. * * @param type_id * IN: Identifier of datatype to set. * @param ebias * IN: Exponent bias value. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Tset_ebias(long type_id, long ebias) throws HDF5LibraryException; /** * H5Tget_fields retrieves information about the locations of the various bit fields of a floating point datatype. * * @param type_id * IN: Identifier of datatype to query. * @param fields * OUT: location of size and bit-position. *
    *
  • fields[0] = spos OUT: location to return size of in bits.
    • *
  • fields[1] = epos OUT: location to return exponent bit-position.
    • *
  • fields[2] = esize OUT: location to return size of exponent in bits.
    • *
  • fields[3] = mpos OUT: location to return mantissa bit-position.
    • *
  • fields[4] = msize OUT: location to return size of mantissa in bits.
    • *
* * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - fields is null. * @exception IllegalArgumentException * - fields array is invalid. **/ public synchronized static native void H5Tget_fields(long type_id, long[] fields) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Tget_fields retrieves information about the locations of the various bit fields of a floating point datatype. * * @param type_id * IN: Identifier of datatype to query. * @param fields * OUT: location of size and bit-position. * * 
     *      fields[0] = spos  OUT: location to return size of in bits.
     *      fields[1] = epos  OUT: location to return exponent bit-position.
     *      fields[2] = esize OUT: location to return size of exponent in bits.
     *      fields[3] = mpos  OUT: location to return mantissa bit-position.
     *      fields[4] = msize OUT: location to return size of mantissa in bits.
     *
* * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - fields is null. * @exception IllegalArgumentException * - fields array is invalid. **/ public static int H5Tget_fields(long type_id, int[] fields) throws HDF5LibraryException, NullPointerException, IllegalArgumentException { return H5Tget_fields_int(type_id, fields); } private synchronized static native int H5Tget_fields_int(long type_id, int[] fields) throws HDF5LibraryException, NullPointerException, IllegalArgumentException; /** * H5Tset_fields sets the locations and sizes of the various floating point bit fields. * * @param type_id * IN: Identifier of datatype to set. * @param spos * IN: Size position. * @param epos * IN: Exponent bit position. * @param esize * IN: Size of exponent in bits. * @param mpos * IN: Mantissa bit position. * @param msize * IN: Size of mantissa in bits. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Tset_fields(long type_id, long spos, long epos, long esize, long mpos, long msize) throws HDF5LibraryException; /** * H5Tset_fields sets the locations and sizes of the various floating point bit fields. * * @param type_id * Identifier of datatype to set. * @param spos * Size position. * @param epos * Exponent bit position. * @param esize * Size of exponent in bits. * @param mpos * Mantissa bit position. * @param msize * Size of mantissa in bits. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Tset_fields(long type_id, int spos, int epos, int esize, int mpos, int msize) throws HDF5LibraryException { H5Tset_fields(type_id, (long) spos, (long) epos, (long) esize, (long) mpos, (long) msize); return 0; } /** * H5Tget_inpad retrieves the internal padding type for unused bits in floating-point datatypes. * * @param type_id * IN: Identifier of datatype to query. * * @return a valid padding type if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_inpad(long type_id) throws HDF5LibraryException; /** * If any internal bits of a floating point type are unused (that is, those significant bits which are not part of * the sign, exponent, or mantissa), then H5Tset_inpad will be filled according to the value of the padding value * property inpad. * * @param type_id * IN: Identifier of datatype to modify. * @param inpad * IN: Padding type. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_inpad(long type_id, int inpad) throws HDF5LibraryException; /** * H5Tget_member_class returns the class of datatype of the specified member. * * @param type_id * IN: Datatype identifier of compound object. * @param membno * IN: Compound object member number. * * @return the class of the datatype of the field if successful; * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_member_class(long type_id, int membno) throws HDF5LibraryException; /** * H5Tget_member_index retrieves the index of a field of a compound datatype. * * @param type_id * IN: Identifier of datatype to query. * @param field_name * IN: Field name of the field index to retrieve. * * @return if field is defined, the index; else negative. **/ public synchronized static native int H5Tget_member_index(long type_id, String field_name); /** * H5Tget_member_name retrieves the name of a field of a compound datatype or an element of an enumeration datatype. * * @param type_id * IN: Identifier of datatype to query. * @param field_idx * IN: Field index (0-based) of the field name to retrieve. * * @return a valid pointer to the name if successful; otherwise null. **/ public synchronized static native String H5Tget_member_name(long type_id, int field_idx); /** * H5Tget_member_offset returns the byte offset of the specified member of the compound datatype. This is the byte * offset in the HDF-5 file/library, NOT the offset of any Java object which might be mapped to this data item. * * @param type_id * IN: Identifier of datatype to query. * @param membno * IN: Field index (0-based) of the field type to retrieve. * * @return the offset of the member. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_member_offset(long type_id, int membno) throws HDF5LibraryException; /** * H5Tget_member_type returns the datatype of the specified member. * * @param type_id * IN: Identifier of datatype to query. * @param field_idx * IN: Field index (0-based) of the field type to retrieve. * * @return the identifier of a copy of the datatype of the field if successful; * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Tget_member_type(long type_id, int field_idx) throws HDF5LibraryException { long id = _H5Tget_member_type(type_id, field_idx); if (id > 0) { log.trace("OPEN_IDS: H5Tget_member_type add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tget_member_type(long type_id, int field_idx) throws HDF5LibraryException; /** * H5Tget_member_value returns the value of the enumeration datatype member memb_no. * * @param type_id * IN: Datatype identifier for the enumeration datatype. * @param membno * IN: Number of the enumeration datatype member. * @param value * OUT: The value of the member * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - value is null. **/ public synchronized static native void H5Tget_member_value(long type_id, int membno, byte[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tget_member_value returns the value of the enumeration datatype member memb_no. * * @param type_id * IN: Identifier of datatype. * @param membno * IN: The name of the member * @param value * OUT: The value of the member * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - value is null. **/ public static int H5Tget_member_value(long type_id, int membno, int[] value) throws HDF5LibraryException, NullPointerException { return H5Tget_member_value_int(type_id, membno, value); } private synchronized static native int H5Tget_member_value_int(long type_id, int membno, int[] value) throws HDF5LibraryException, NullPointerException; /** * H5Tget_native_type returns the equivalent native datatype for the datatype specified in type_id. * * @param type_id * IN: Identifier of datatype to query. Direction of search is assumed to be in ascending order. * * @return the native datatype identifier for the specified dataset datatype. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static long H5Tget_native_type(long type_id) throws HDF5LibraryException { return H5Tget_native_type(type_id, HDF5Constants.H5T_DIR_ASCEND); } /** * H5Tget_native_type returns the equivalent native datatype for the datatype specified in type_id. * * @param type_id * IN: Identifier of datatype to query. * @param direction * IN: Direction of search. * * @return the native datatype identifier for the specified dataset datatype. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Tget_native_type(long type_id, int direction) throws HDF5LibraryException { long id = _H5Tget_native_type(type_id, direction); if (id > 0) { log.trace("OPEN_IDS: H5Tget_native_type add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tget_native_type(long tid, int direction) throws HDF5LibraryException; /** * H5Tget_nmembers retrieves the number of fields a compound datatype has. * * @param type_id * IN: Identifier of datatype to query. * * @return number of members datatype has if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_nmembers(long type_id) throws HDF5LibraryException; /** * H5Tget_norm retrieves the mantissa normalization of a floating-point datatype. * * @param type_id * IN: Identifier of datatype to query. * * @return a valid normalization type if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_norm(long type_id) throws HDF5LibraryException; /** * H5Tset_norm sets the mantissa normalization of a floating-point datatype. * * @param type_id * IN: Identifier of datatype to set. * @param norm * IN: Mantissa normalization type. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_norm(long type_id, int norm) throws HDF5LibraryException; /** * H5Tget_offset retrieves the bit offset of the first significant bit. * * @param type_id * IN: Identifier of datatype to query. * * @return a positive offset value if successful; otherwise 0. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_offset(long type_id) throws HDF5LibraryException; /** * H5Tset_offset sets the bit offset of the first significant bit. * * @param type_id * Identifier of datatype to set. * @param offset * Offset of first significant bit. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Tset_offset(long type_id, int offset) throws HDF5LibraryException { H5Tset_offset(type_id, (long) offset); return 0; } /** * H5Tset_offset sets the bit offset of the first significant bit. * * @param type_id * IN: Identifier of datatype to set. * @param offset * IN: Offset of first significant bit. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Tset_offset(long type_id, long offset) throws HDF5LibraryException; /** * H5Tget_order returns the byte order of an atomic datatype. * * @param type_id * IN: Identifier of datatype to query. * * @return a byte order constant if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_order(long type_id) throws HDF5LibraryException; /** * H5Tset_order sets the byte ordering of an atomic datatype. * * @param type_id * IN: Identifier of datatype to set. * @param order * IN: Byte ordering constant. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_order(long type_id, int order) throws HDF5LibraryException; /** * H5Tget_pad retrieves the padding type of the least and most-significant bit padding. * * @param type_id * IN: Identifier of datatype to query. * @param pad * OUT: locations to return least-significant and most-significant bit padding type. * * 
     *      pad[0] = lsb // least-significant bit padding type
     *      pad[1] = msb // most-significant bit padding type
     *
* * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - pad is null. **/ public synchronized static native int H5Tget_pad(long type_id, int[] pad) throws HDF5LibraryException, NullPointerException; /** * H5Tset_pad sets the least and most-significant bits padding types. * * @param type_id * IN: Identifier of datatype to set. * @param lsb * IN: Padding type for least-significant bits. * @param msb * IN: Padding type for most-significant bits. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_pad(long type_id, int lsb, int msb) throws HDF5LibraryException; /** * H5Tget_precision returns the precision of an atomic datatype. * * @param type_id * Identifier of datatype to query. * * @return the number of significant bits if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_precision(long type_id) throws HDF5LibraryException; /** * H5Tset_precision sets the precision of an atomic datatype. * * @param type_id * Identifier of datatype to set. * @param precision * Number of bits of precision for datatype. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static int H5Tset_precision(long type_id, int precision) throws HDF5LibraryException { H5Tset_precision(type_id, (long) precision); return 0; } /** * H5Tget_precision returns the precision of an atomic datatype. * * @param type_id * IN: Identifier of datatype to query. * * @return the number of significant bits if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_precision_long(long type_id) throws HDF5LibraryException; /** * H5Tset_precision sets the precision of an atomic datatype. * * @param type_id * IN: Identifier of datatype to set. * @param precision * IN: Number of bits of precision for datatype. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Tset_precision(long type_id, long precision) throws HDF5LibraryException; /** * H5Tget_sign retrieves the sign type for an integer type. * * @param type_id * IN: Identifier of datatype to query. * * @return a valid sign type if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_sign(long type_id) throws HDF5LibraryException; /** * H5Tset_sign sets the sign proprety for an integer type. * * @param type_id * IN: Identifier of datatype to set. * @param sign * IN: Sign type. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_sign(long type_id, int sign) throws HDF5LibraryException; /** * H5Tget_size returns the size of a datatype in bytes. * * @param type_id * IN: Identifier of datatype to query. * * @return the size of the datatype in bytes * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native long H5Tget_size(long type_id) throws HDF5LibraryException; /** * H5Tset_size sets the total size in bytes, size, for an atomic datatype (this operation is not permitted on * compound datatypes). * * @param type_id * IN: Identifier of datatype to change size. * @param size * IN: Size in bytes to modify datatype. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_size(long type_id, long size) throws HDF5LibraryException; /** * H5Tget_strpad retrieves the string padding method for a string datatype. * * @param type_id * IN: Identifier of datatype to query. * * @return a valid string padding type if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tget_strpad(long type_id) throws HDF5LibraryException; /** * H5Tset_strpad defines the storage mechanism for the string. * * @param type_id * IN: Identifier of datatype to modify. * @param strpad * IN: String padding type. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_strpad(long type_id, int strpad) throws HDF5LibraryException; /** * H5Tget_super returns the type from which TYPE is derived. * * @param type * IN: Identifier of datatype. * * @return the parent type * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Tget_super(long type) throws HDF5LibraryException { long id = _H5Tget_super(type); if (id > 0) { log.trace("OPEN_IDS: H5Tget_super add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tget_super(long type) throws HDF5LibraryException; /** * H5Tget_tag returns the tag associated with datatype type_id. * * @param type * IN: Identifier of datatype. * * @return the tag * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native String H5Tget_tag(long type) throws HDF5LibraryException; /** * H5Tset_tag tags an opaque datatype type_id with a unique ASCII identifier tag. * * @param type * IN: Datatype identifier for the opaque datatype to be tagged. * @param tag * IN: Descriptive ASCII string with which the opaque datatype is to be tagged. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tset_tag(long type, String tag) throws HDF5LibraryException; /** * H5Tinsert adds another member to the compound datatype type_id. * * @param type_id * IN: Identifier of compound datatype to modify. * @param name * IN: Name of the field to insert. * @param offset * IN: Offset in memory structure of the field to insert. * @param field_id * IN: Datatype identifier of the field to insert. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public synchronized static native int H5Tinsert(long type_id, String name, long offset, long field_id) throws HDF5LibraryException, NullPointerException; /** * H5Tis_variable_str determines whether the datatype identified in type_id is a variable-length string. * * @param type_id * IN: Identifier of datatype to query. * * @return true if type_id is a variable-length string. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native boolean H5Tis_variable_str(long type_id) throws HDF5LibraryException; /** * H5Tlock locks the datatype specified by the type_id identifier, making it read-only and non-destrucible. * * @param type_id * IN: Identifier of datatype to lock. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tlock(long type_id) throws HDF5LibraryException; /** * H5Topen opens a named datatype at the location specified by loc_id and return an identifier for the datatype. * * @param loc_id * IN: A file, group, or datatype identifier. * @param name * IN: A datatype name, defined within the file or group identified by loc_id. * @param tapl_id * IN: Datatype access property list. * * @return a named datatype identifier if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. * @exception NullPointerException * - name is null. **/ public static long H5Topen(long loc_id, String name, long tapl_id) throws HDF5LibraryException, NullPointerException { long id = _H5Topen2(loc_id, name, tapl_id); if (id > 0) { log.trace("OPEN_IDS: H5Topen add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Topen2(long loc_id, String name, long tapl_id) throws HDF5LibraryException, NullPointerException; /** * H5Tpack recursively removes padding from within a compound datatype to make it more efficient (space-wise) to * store that data. *

* WARNING: This call only affects the C-data, even if it succeeds, there may be no visible effect on Java * objects. * * @param type_id * IN: Identifier of datatype to modify. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native int H5Tpack(long type_id) throws HDF5LibraryException; /** * H5Tvlen_create creates a new variable-length (VL) dataype. * * @param base_id * IN: Identifier of parent datatype. * * @return a non-negative value if successful * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public static long H5Tvlen_create(long base_id) throws HDF5LibraryException { long id = _H5Tvlen_create(base_id); if (id > 0) { log.trace("OPEN_IDS: H5Tvlen_create add {}", id); OPEN_IDS.add(id); log.trace("OPEN_IDS: {}", OPEN_IDS.size()); } return id; } private synchronized static native long _H5Tvlen_create(long base_id) throws HDF5LibraryException; /** * H5Tflush causes all buffers associated with a committed datatype to be immediately flushed to disk * without removing the data from the cache. * * @param dtype_id * IN: Identifier of the committed datatype to be flushed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Tflush(long dtype_id) throws HDF5LibraryException; /** * H5Trefresh causes all buffers associated with a committed datatype to be cleared and immediately * re-loaded with updated contents from disk. This function essentially closes the datatype, evicts * all metadata associated with it from the cache, and then re-opens the datatype. The reopened datatype * is automatically re-registered with the same ID. * * @param dtype_id * IN: Identifier of the committed datatype to be refreshed. * * @exception HDF5LibraryException * - Error from the HDF-5 Library. **/ public synchronized static native void H5Trefresh(long dtype_id) throws HDF5LibraryException; // /////// unimplemented //////// // H5T_conv_t H5Tfind(int src_id, int dst_id, H5T_cdata_t *pcdata); // public synchronized static native int H5Tregister(H5T_pers_t pers, String name, int src_id, int dst_id, // H5T_conv_t func) // throws HDF5LibraryException, NullPointerException; // public synchronized static native int H5Tunregister(H5T_pers_t pers, String name, int src_id, int dst_id, // H5T_conv_t func) // throws HDF5LibraryException, NullPointerException; // //////////////////////////////////////////////////////////// // // // H5Z: Filter Interface Functions // // // // //////////////////////////////////////////////////////////// public synchronized static native int H5Zfilter_avail(int filter) throws HDF5LibraryException, NullPointerException; public synchronized static native int H5Zget_filter_info(int filter) throws HDF5LibraryException; public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException, NullPointerException; } // /////// unimplemented //////// // herr_t H5Zregister(const void *cls);