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Diffstat (limited to 'java/src/hdf/hdf5lib/H5.java')
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diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java new file mode 100644 index 0000000..fbfc40a --- /dev/null +++ b/java/src/hdf/hdf5lib/H5.java @@ -0,0 +1,9185 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * 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 files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdfgroup.org/HDF5/doc/Copyright.html. 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. + * <p> + * 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. + * <p> + * For details of the HDF5 library, see the HDF5 Documentation at: <a + * href="http://hdfgroup.org/HDF5/">http://hdfgroup.org/HDF5/</a> + * <hr> + * <p> + * <b>Mapping of arguments for Java</b> + * + * <p> + * In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF + * Reference Manual. + * + * <center> + * <table border=2 cellpadding=2> + * <caption><b>HDF-5 C types to Java types</b> </caption> + * <tr> + * <td><b>HDF-5</b></td> + * <td><b>Java</b></td> + * </tr> + * <tr> + * <td>H5T_NATIVE_INT</td> + * <td>int, Integer</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_SHORT</td> + * <td>short, Short</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_FLOAT</td> + * <td>float, Float</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_DOUBLE</td> + * <td>double, Double</td> + * </tr> + * <tr> + * <td>H5T_NATIVE_CHAR</td> + * <td>byte, Byte</td> + * </tr> + * <tr> + * <td>H5T_C_S1</td> + * <td>java.lang.String</td> + * </tr> + * <tr> + * <td>void * <BR> + * (i.e., pointer to `Any')</td> + * <td>Special -- see HDFArray</td> + * </tr> + * </table> + * </center> + * <center> <b>General Rules for Passing Arguments and Results</b> </center> + * <p> + * In general, arguments passed <b>IN</b> to Java are the analogous basic types, as above. The exception is for arrays, + * which are discussed below. + * <p> + * The <i>return value</i> 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 <i>boolean</i> in the Java version, rather than <i>int</i> 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 <a href="#ERRORS">Errors and + * Exceptions</a> below. + * <p> + * Java does not support pass by reference of arguments, so arguments that are returned through <b>OUT</b> parameters + * must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in arrays. + * <p> + * For instance, a function that returns two integers is declared: + * + * <pre> + * h_err_t HDF5dummy( int *a1, int *a2) + * </pre> + * + * For the Java interface, this would be declared: + * + * <pre> + * public synchronized static native int HDF5dummy(int args[]); + * </pre> + * + * where <i>a1</i> is <i>args[0]</i> and <i>a2</i> is <i>args[1]</i>, and would be invoked: + * + * <pre> + * H5.HDF5dummy(a); + * </pre> + * + * <p> + * All the routines where this convention is used will have specific documentation of the details, given below. + * <p> + * <a NAME="ARRAYS"> <b>Arrays</b> </a> + * <p> + * 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, + * + * <pre> + * herr_t H5Dread(int fid, int filetype, int memtype, int memspace, + * void * data); + * </pre> + * + * <p> + * 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). + * <p> + * For Java, this ``ANY'' is a problem, as the type of data must always be declared. Furthermore, multidimensional + * arrays are definitely <i>not</i> 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 <a + * href="./hdf.hdf5lib.HDFArray.html"><b>HDFArray</b></a> 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. + * <p> + * The upshot is that any Java array of numbers (either primitive or sub-classes of type <b>Number</b>) 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: + * + * <pre> + * public synchronized static native int H5Dread(int fid, int filetype, int memtype, int memspace, Object data); + * </pre> + * OPEN_IDS.addElement(id); + + * and the parameter <i>data</i> can be any multi-dimensional array of numbers, such as float[][], or int[][][], or + * Double[][]. + * <p> + * <a NAME="CONSTANTS"> <b>HDF-5 Constants</b></a> + * <p> + * The HDF-5 API defines a set of constants and enumerated values. Most of these values are available to Java programs + * via the class <a href="./hdf.hdf5lib.HDF5Constants.html"> <b>HDF5Constants</b></a>. For example, the parameters for + * the h5open() call include two numeric values, <b><i>HDFConstants.H5F_ACC_RDWR</i></b> and + * <b><i>HDF5Constants.H5P_DEFAULT</i></b>. As would be expected, these numbers correspond to the C constants + * <b><i>H5F_ACC_RDWR</i></b> and <b><i>H5P_DEFAULT</i></b>. + * <p> + * 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 <a + * href="./hdf.hdf5lib.HDF5CDataTypes.html"> <b>HDF5CDataTypes</b></a> looks up the values when initiated. The values + * can be accessed as public variables of the Java class, such as: + * + * <pre> + * int data_type = HDF5CDataTypes.JH5T_NATIVE_INT; + * </pre> + * + * The Java application uses both types of constants the same way, the only difference is that the + * <b><i>HDF5CDataTypes</i></b> may have different values on different platforms. + * <p> + * <a NAME="ERRORS"> <b>Error handling and Exceptions</b></a> + * <p> + * 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. + * <p> + * The exceptions of the JHI5 are organized as sub-classes of the class <a + * href="./hdf.hdf5lib.exceptions.HDF5Exception.html"> <b>HDF5Exception</b></a>. There are two subclasses of + * <b>HDF5Exception</b>, <a href="./hdf.hdf5lib.exceptions.HDF5LibraryException.html"> <b>HDF5LibraryException</b></a> + * and <a href="./hdf.hdf5lib.exceptions.HDF5JavaException.html"> <b>HDF5JavaException</b></a>. 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. + * <p> + * The super-class <b><i>HDF5LibraryException</i></b> implements the method '<b><i>printStackTrace()</i></b>', which + * prints out the HDF-5 error stack, as described in the HDF-5 C API <i><b>H5Eprint()</b>.</i> This may be used by Java + * exception handlers to print out the HDF-5 error stack. + * <hr> + * + * @version HDF5 1.9 <BR> + * <b>See also: <a href ="./hdf.hdf5lib.HDFArray.html"> hdf.hdf5lib.HDFArray</a> </b><BR> + * <a href ="./hdf.hdf5lib.HDF5Constants.html"> hdf.hdf5lib.HDF5Constants</a><BR> + * <a href ="./hdf.hdf5lib.HDF5CDataTypes.html"> hdf.hdf5lib.HDF5CDataTypes</a><BR> + * <a href ="./hdf.hdf5lib.HDF5Exception.html"> hdf.hdf5lib.HDF5Exception</a><BR> + * <a href="http://hdfgroup.org/HDF5/"> http://hdfgroup.org/HDF5"</a> + **/ +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, 9, 9999 }; + + 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<Long> OPEN_IDS = new LinkedHashSet<Long>(); + + 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<Long> 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). + * <P> + * 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(); + + /** + * 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. + * + * <pre> + * libversion[0] = The major version of the library. + * libversion[1] = The minor version of the library. + * libversion[2] = The release number of the library. + * </pre> + * @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; + + /** + * 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; + + // //////////////////////////////////////////////////////////// + // // + // 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 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; + + // /////// unimplemented //////// + // H5_DLL herr_t H5Ddebug(hid_t dset_id); + // 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. + * <p> + * 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: + * <UL> + * <LI> + * H5F_ACC_RDWR Allow read and write access to file.</LI> + * <LI> + * H5F_ACC_RDONLY Allow read-only access to file.</LI> + * <LI> + * H5F_ACC_TRUNC Truncate file, if it already exists, erasing all data previously stored in the file.</LI> + * <LI> + * H5F_ACC_EXCL Fail if file already exists.</LI> + * <LI> + * H5P_DEFAULT Apply default file access and creation properties.</LI> + * </UL> + * + * @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. + * <P> + * 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. <b>object_id</b> 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. + * <P> + * Valid values are: + * <UL> + * <LI> + * H5F_SCOPE_GLOBAL Flushes the entire virtual file.</LI> + * <LI> + * H5F_SCOPE_LOCAL Flushes only the specified file.</LI> + * </UL> + * + * @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 + * <ul> + * <li>metadata_cache[0] = max_size_ptr // current cache maximum size</li> + * <li>metadata_cache[1] = min_clean_size_ptr // current cache minimum clean size</li> + * <li>metadata_cache[2] = cur_size_ptr // current cache size</li> + * </ul> + * + * @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. + * <ul> + * <li>H5F_OBJ_FILE Files only</li> + * <li>H5F_OBJ_DATASET Datasets only</li> + * <li>H5F_OBJ_GROUP Groups only</li> + * <li>H5F_OBJ_DATATYPE Named datatypes only</li> + * <li>H5F_OBJ_ATTR Attributes only</li> + * <li>H5F_OBJ_ALL All of the above</li> + * <li>H5F_OBJ_LOCAL Restrict search to objects opened through current file identifier.</li> + * </ul> + * + * @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; + + // /////// unimplemented //////// + // ssize_t H5Fget_file_image(hid_t file_id, void * buf_ptr, size_t buf_len); + // ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type, size_t nsects, H5F_sect_info_t *sect_info/*out*/); + + // /** + // * 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; + + // //////////////////////////////////////////////////////////// + // // + // 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; + + // //////////////////////////////////////////////////////////// + // // + // H5I: HDF5 1.8 Identifier Interface API Functions // + // // + // //////////////////////////////////////////////////////////// + + public synchronized static native long H5Iget_file_id(long obj_id) throws HDF5LibraryException; + + public synchronized static native long H5Iget_name(long obj_id, String[] name, long size) + throws HDF5LibraryException, NullPointerException; + + 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); + + + // //////////////////////////////////////////////////////////// + // // + // 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; + + // long H5Oget_comment_by_name(int loc_id, String name, String comment, long bufsize, int lapl_id); + + /** + * H5Oset_comment_by_name sets the comment for the specified object. + * + * @param loc_id + * IN: Identifier of a file, group, dataset, or named datatype. + * @param name + * IN: Relative name of the object whose comment is to be set or reset. + * @param comment + * IN: The new comment. + * @param lapl_id + * IN: Link access property list identifier. + * + * @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 synchronized static native H5O_info_t H5Oget_info(long loc_id) throws HDF5LibraryException, + NullPointerException; + + /** + * H5Oget_info_by_idx retrieves the metadata for an object, identifying the object by an index position. + * + * @param loc_id + * IN: File or group identifier + * @param group_name + * IN: Name of group, relative to loc_id, in which object is located + * @param idx_type + * IN: Type of index by which objects are ordered + * @param order + * IN: Order of iteration within index + * @param n + * IN: Object to open + * @param lapl_id + * IN: Access property list identifier for the link pointing to the object (Not currently used; pass as + * H5P_DEFAULT.) + * + * @return object information + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ + public synchronized static native H5O_info_t H5Oget_info_by_idx(long loc_id, String group_name, int idx_type, + int order, long n, 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 synchronized static native H5O_info_t H5Oget_info_by_name(long loc_id, String name, 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 synchronized static native int H5Ovisit(long obj_id, int idx_type, int order, H5O_iterate_cb op, + H5O_iterate_t op_data) throws HDF5LibraryException, NullPointerException; + + /** + * H5Ovisit_by_name recursively visits all objects starting from a specified object. + * + * @param loc_id + * IN: File or group identifier + * @param obj_name + * IN: Relative path to the object + * @param idx_type + * IN: Type of index + * @param order + * IN: Order of iteration within index + * @param op + * IN: Callback function passing data regarding the object to the calling application + * @param op_data + * IN: User-defined pointer to data required by the application for its processing of the object + * @param lapl_id + * IN: Link access property list identifier + * + * @return returns the return value of the first operator that returns a positive value, or zero if all members were + * processed with no operator returning non-zero. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception NullPointerException + * - name is null. + **/ + public synchronized static native int H5Ovisit_by_name(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; + + + /** + * 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; + + // /////// unimplemented //////// + + // //////////////////////////////////////////////////////////// + // // + // 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; + + /** + * 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 positive value if the property exists in the property object; zero if the property does not exist; a + * negative value if failed + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + */ + public synchronized static native int 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; + + /** + * 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; + + /** + * 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. + * + * <pre> + * 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 + * </pre> + * + * @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. + * + * <pre> + * size[0] = sizeof_addr // offset size in bytes + * size[1] = sizeof_size // length size in bytes + * </pre> + * @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. + * + * <pre> + * size[0] = ik // the symbol table's B-tree 1/2 rank + * size[1] = lk // leaf node 1/2 size + * </pre> + * + * @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 + * + * <pre> + * mesg_info[0] = Types of messages that may be stored in this index. + * mesg_info[1] = Minimum message size. + * </pre> + * + * @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. + * + * <pre> + * 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 + * </pre> + * + * @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 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. + * Passing a value of zero (0) indicates that the value of strategy is not to be modified. + * H5F_FILE_SPACE_ALL_PERSIST + * With this strategy, the free-space managers track the free space that results from the + * manipulation of HDF5 objects in the HDF5 file. The free space information is saved when the + * file is closed, and reloaded when the file is reopened. When space is needed for file metadata + * or raw data, the HDF5 library first requests space from the library's free-space managers. + * If the request is not satisfied, the library requests space from the aggregators. If the request + * is still not satisfied, the library requests space from the virtual file driver. That is, the + * library will use all of the mechanisms for allocating space. + * H5F_FILE_SPACE_ALL (Default file space management strategy) + * With this strategy, the free-space managers track the free space that results from the manipulation + * of HDF5 objects in the HDF5 file. The free space information is NOT saved when the file is closed + * and the free space that exists upon file closing becomes unaccounted space in the file. + * Like the previous strategy, the library will try all of the mechanisms for allocating space. When + * space is needed for file metadata or raw data, the library first requests space from the free-space + * managers. If the request is not satisfied, the library requests space from the aggregators. If the + * request is still not satisfied, the library requests space from the virtual file driver. + * H5F_FILE_SPACE_AGGR_VFD + * With this strategy, the library does not track free space that results from the manipulation of HDF5 + * obejcts in the HDF5 file and the free space becomes unaccounted space in the file. + * When space is needed for file metadata or raw data, the library first requests space from the + * aggregators. If the request is not satisfied, the library requests space from the virtual file driver. + * H5F_FILE_SPACE_VFD + * With this strategy, the library does not track free space that results from the manipulation of HDF5 + * obejcts in the HDF5 file and the free space becomes unaccounted space in the file. + * When space is needed for file metadata or raw data, the library requests space from the virtual file driver. + * @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(long fcpl_id, int strategy, long threshold) + throws HDF5LibraryException, IllegalArgumentException; + + /** + * H5Pget_file_space provides the means for applications to manage the HDF5 file's file space for their specific needs. + * + * @param fcpl_id + * IN: File creation property list identifier + * @param strategy + * IN/OUT: The current file space management strategy in use for the file. NULL, strategy not queried. + * @param threshold + * IN/OUT: The current free-space section threshold. NULL, threshold not queried. + * + * @exception HDF5LibraryException + * - Error from the HDF-5 Library. + * @exception IllegalArgumentException + * - Invalid values of max_list and min_btree. + * + **/ + public synchronized static native void H5Pget_file_space(long fcpl_id, int[] strategy, long[] threshold) + 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. + * + * <pre> + * alignment[0] = threshold // threshold value + * alignment[1] = alignment // alignment value + * </pre> + * @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. + * + * <pre> + * 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. + * </pre> + * + * @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; + + // 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; + + /** + * 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. + * + * <pre> + * size[0] = offset // a location to return an offset value + * size[1] = size // a location to return the size of + * // the external file data. + * </pre> + * + * @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 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; + + // 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 + * + * <pre> + * links[0] = The maximum number of links for compact storage + * links[1] = The minimum number of links for dense storage + * </pre> + * + * @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 + * + * <pre> + * link_info[0] = Estimated number of links to be inserted into group + * link_info[1] = Estimated average length of link names + * </pre> + * + * @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. + * + * <pre> + * 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 + * </pre> + * @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 ) + // 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); + + // Dataset creation property list (DCPL) routines // + + // Dataset access property list (DAPL) routines // + + // 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) + + // 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); + + + // Other/Older property list routines // + // herr_t H5Pget_fapl_mpio( int fapl_id, MPI_Comm *comm, MPI_Info *info ) + // herr_t H5Pset_fapl_mpio( int fapl_id, MPI_Comm comm, MPI_Info info ) + + // herr_t H5Pget_fapl_mpiposix( int fapl_id, MPI_Comm *comm, hbool_t *use_gpfs_hints ) + // herr_t H5Pset_fapl_mpiposix( int fapl_id, MPI_Comm comm, hbool_t use_gpfs_hints ) + + // herr_t H5Pget_dxpl_mpio( hid_t dxpl_id, H5FD_mpio_xfer_t *xfer_mode ) + // herr_t H5Pset_dxpl_mpio( hid_t dxpl_id, H5FD_mpio_xfer_t xfer_mode ) + // herr_t H5Pset_dxpl_mpio_chunk_opt (hid_t dxpl_id, H5FD_mpio_chunk_opt_t opt_mode) + // herr_t H5Pset_dxpl_mpio_chunk_opt_num (hid_t dxpl_id, unsigned num_chunk_per_proc) + // herr_t H5Pset_dxpl_mpio_chunk_opt_ratio (hid_t dxpl_id, unsigned percent_proc_per_chunk) + // herr_t H5Pset_dxpl_mpio_collective_opt (hid_t dxpl_id, H5FD_mpio_collective_opt_t opt_mode) + + // //////////////////////////////////////////////////////////// + // // + // 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; + + // //////////////////////////////////////////////////////////// + // // + // 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. + * <P> + * 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 <i>rank</i> 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: + * + * <pre> + * <"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. + * </pre> + * + * @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 <i>rank</i> * 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 //////// + + + + // //////////////////////////////////////////////////////////// + // // + // 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. + * <ul> + * <li>fields[0] = spos OUT: location to return size of in bits.</li> + * <li>fields[1] = epos OUT: location to return exponent bit-position.</li> + * <li>fields[2] = esize OUT: location to return size of exponent in bits.</li> + * <li>fields[3] = mpos OUT: location to return mantissa bit-position.</li> + * <li>fields[4] = msize OUT: location to return size of mantissa in bits.</li> + * </ul> + * + * @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. + * + * <pre> + * 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. + * </pre> + * + * @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. + * + * <pre> + * pad[0] = lsb // least-significant bit padding type + * pad[1] = msb // most-significant bit padding type + * </pre> + * + * @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. + * <P> + * <b>WARNING:</b> 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; + + // /////// 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); + |