diff options
36 files changed, 9790 insertions, 632 deletions
@@ -197,6 +197,7 @@ ./doxygen/aliases ./doxygen/Doxyfile.in ./doxygen/dox/api-compat-macros.dox +./doxygen/dox/H5AC_cache_config_t.dox ./doxygen/dox/H5Acreate.dox ./doxygen/dox/H5Aiterate.dox ./doxygen/dox/H5Fget_info.dox @@ -563,6 +564,7 @@ ./src/H5err.txt ./src/H5detect.c ./src/H5make_libsettings.c +./src/H5module.h ./src/H5mpi.c ./src/H5overflow.txt ./src/H5private.h diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in index 711fa7a..24fc4ba 100644 --- a/doxygen/Doxyfile.in +++ b/doxygen/Doxyfile.in @@ -854,6 +854,7 @@ INPUT_ENCODING = UTF-8 FILE_PATTERNS = H5*public.h \ H5*module.h \ + H5FDmpio.h \ H5VLconnector.h \ H5VLconnector_passthru.h \ H5VLnative.h \ diff --git a/doxygen/aliases b/doxygen/aliases index aa22bd4..c10c3e8 100644 --- a/doxygen/aliases +++ b/doxygen/aliases @@ -60,8 +60,8 @@ ALIASES += space_id{1}="\param[in] \1 Dataspace identifier" # Dataypes ################################################################################ -ALIASES += dtype_id="\param[in] dtype_id Datatype identifier" -ALIASES += dtype_id{1}="\param[in] \1 Datatype identifier" +ALIASES += type_id="\param[in] type_id Datatype identifier" +ALIASES += type_id{1}="\param[in] \1 Datatype identifier" ALIASES += file_type_id{1}="\param[in] \1 Datatype (in-file) identifier" ALIASES += mem_type_id{1}="\param[in] \1 Datatype (in-memory) identifier" @@ -133,15 +133,21 @@ ALIASES += lapl_id{1}="\param[in] \1 Link access property list identifier" ALIASES += lcpl_id="\param[in] lcpl_id Link creation property list identifier" ALIASES += lcpl_id{1}="\param[in] \1 Link creation property list identifier" -ALIASES += vipl_id="\param[in] vipl_id VOL initialization property list identifier" -ALIASES += vipl_id{1}="\param[in] \1 vipl_id VOL initialization property list identifier" - ALIASES += plist_id="\param[in] plist_id Property list identifier" ALIASES += plist_id{1}="\param[in] \1 Property list identifier" ALIASES += plistcls_id="\param[in] plistcls_id Property list class identifier" ALIASES += plistcls_id{1}="\param[in] \1 Property list class identifier" +ALIASES += tapl_id="\param[in] tapl_id Datatype access property list identifier" +ALIASES += tapl_id{1}="\param[in] \1 Datatype access property list identifier" + +ALIASES += tcpl_id="\param[in] tcpl_id Datatype creation property list identifier" +ALIASES += tcpl_id{1}="\param[in] \1 Datatype creation property list identifier" + +ALIASES += vipl_id="\param[in] vipl_id VOL initialization property list identifier" +ALIASES += vipl_id{1}="\param[in] \1 vipl_id VOL initialization property list identifier" + ################################################################################ # Objects ################################################################################ diff --git a/doxygen/dox/H5AC_cache_config_t.dox b/doxygen/dox/H5AC_cache_config_t.dox new file mode 100644 index 0000000..9b9862b --- /dev/null +++ b/doxygen/dox/H5AC_cache_config_t.dox @@ -0,0 +1,415 @@ +/** + * \page H5AC-cache-config-t Metadata Cache Configuration + * \tableofcontents + * + * \section gcf General configuration fields + * + * \par version + * Integer field containing the version number of this version + * of the H5AC_cache_config_t structure. Any instance of + * H5AC_cache_config_t passed to the cache must have a known + * version number, or an error will be flagged. + * + * \par rpt_fcn_enabled + * \parblock + * Boolean field used to enable and disable the default + * reporting function. This function is invoked every time the + * automatic cache resize code is run, and reports on its activities. + * + * This is a debugging function, and should normally be turned off. + * \endparblock + * + * \par open_trace_file + * \parblock + * Boolean field indicating whether the trace_file_name + * field should be used to open a trace file for the cache. + * + * \Emph{*** DEPRECATED ***} Use \Code{H5Fstart/stop} logging functions instead + * + * The trace file is a debuging feature that allow the capture of + * top level metadata cache requests for purposes of debugging and/or + * optimization. This field should normally be set to \c FALSE, as + * trace file collection imposes considerable overhead. + * + * This field should only be set to \c TRUE when the trace_file_name + * contains the full path of the desired trace file, and either + * there is no open trace file on the cache, or the \c close_trace_file + * field is also \c TRUE. + * \endparblock + * + * \par close_trace_file + * \parblock + * Boolean field indicating whether the current trace + * file (if any) should be closed. + * + * \Emph{*** DEPRECATED ***} Use \Code{H5Fstart/stop} logging functions instead + * + * See the above comments on the open_trace_file field. This field + * should be set to \c FALSE unless there is an open trace file on the + * cache that you wish to close. + * \endparblock + * + * \par trace_file_name + * \parblock + * Full path of the trace file to be opened if the + * open_trace_file field is \c TRUE. + * + * \Emph{*** DEPRECATED ***} Use \Code{H5Fstart/stop} logging functions instead + * + * In the parallel case, an ascii representation of the mpi rank of + * the process will be appended to the file name to yield a unique + * trace file name for each process. + * + * The length of the path must not exceed #H5AC__MAX_TRACE_FILE_NAME_LEN + * characters. + * \endparblock + * + * \par evictions_enabled + * \parblock + * Boolean field used to either report the current + * evictions enabled status of the cache, or to set the cache's + * evictions enabled status. + * + * In general, the metadata cache should always be allowed to + * evict entries. However, in some cases it is advantageous to + * disable evictions briefly, and thereby postpone metadata + * writes. However, this must be done with care, as the cache + * can grow quickly. If you do this, re-enable evictions as + * soon as possible and monitor cache size. + * + * At present, evictions can only be disabled if automatic + * cache resizing is also disabled (that is, \Code{(incr_mode == + * H5C_incr__off ) && ( decr_mode == H5C_decr__off )}). There + * is no logical reason why this should be so, but it simplifies + * implementation and testing, and I can't think of any reason + * why it would be desireable. If you can think of one, I'll + * revisit the issue. (JM) + * \endparblock + * + * \par set_initial_size + * Boolean flag indicating whether the size of the + * initial size of the cache is to be set to the value given in + * the initial_size field. If set_initial_size is \c FALSE, the + * initial_size field is ignored. + * + * \par initial_size + * If enabled, this field contain the size the cache is + * to be set to upon receipt of this structure. Needless to say, + * initial_size must lie in the closed interval \Code{[min_size, max_size]}. + * + * \par min_clean_fraction + * \c double in the range 0 to 1 indicating the fraction + * of the cache that is to be kept clean. This field is only used + * in parallel mode. Typical values are 0.1 to 0.5. + * + * \par max_size + * Maximum size to which the cache can be adjusted. The + * supplied value must fall in the closed interval + * \Code{[MIN_MAX_CACHE_SIZE, MAX_MAX_CACHE_SIZE]}. Also, \c max_size must + * be greater than or equal to \c min_size. + * + * \par min_size + * Minimum size to which the cache can be adjusted. The + * supplied value must fall in the closed interval + * \Code{[H5C__MIN_MAX_CACHE_SIZE, H5C__MAX_MAX_CACHE_SIZE]}. Also, \c min_size + * must be less than or equal to \c max_size. + * + * \par epoch_length + * \parblock + * Number of accesses on the cache over which to collect + * hit rate stats before running the automatic cache resize code, + * if it is enabled. + * + * At the end of an epoch, we discard prior hit rate data and start + * collecting afresh. The epoch_length must lie in the closed + * interval \Code{[H5C__MIN_AR_EPOCH_LENGTH, H5C__MAX_AR_EPOCH_LENGTH]}. + * \endparblock + * + * + * \section csicf Cache size increase control fields + * + * \par incr_mode + * Instance of the \c H5C_cache_incr_mode enumerated type whose + * value indicates how we determine whether the cache size should be + * increased. At present there are two possible values: + * \li \c H5C_incr__off: Don't attempt to increase the size of the cache + * automatically.\n + * When this increment mode is selected, the remaining fields + * in the cache size increase section ar ignored. + * \li \c H5C_incr__threshold: Attempt to increase the size of the cache + * whenever the average hit rate over the last epoch drops + * below the value supplied in the \c lower_hr_threshold + * field.\n + * Note that this attempt will fail if the cache is already + * at its maximum size, or if the cache is not already using + * all available space. + * + * Note that you must set \c decr_mode to \c H5C_incr__off if you + * disable metadata cache entry evictions. + * + * \par lower_hr_threshold + * \parblock + * Lower hit rate threshold. If the increment mode + * (\c incr_mode) is \c H5C_incr__threshold and the hit rate drops below the + * value supplied in this field in an epoch, increment the cache size by + * \c size_increment. Note that cache size may not be incremented above + * \c max_size, and that the increment may be further restricted by the + * \c max_increment field if it is enabled. + * + * When enabled, this field must contain a value in the range [0.0, 1.0]. + * Depending on the \c incr_mode selected, it may also have to be less than + * \c upper_hr_threshold. + * \endparblock + * + * \par increment + * \parblock + * Double containing the multiplier used to derive the new + * cache size from the old if a cache size increment is triggered. + * The increment must be greater than 1.0, and should not exceed 2.0. + * + * The new cache size is obtained my multiplying the current max cache + * size by the increment, and then clamping to \c max_size and to stay + * within the \c max_increment as necessary. + * \endparblock + * + * \par apply_max_increment + * Boolean flag indicating whether the \c max_increment + * field should be used to limit the maximum cache size increment. + * + * \par max_increment + * If enabled by the \c apply_max_increment field described + * above, this field contains the maximum number of bytes by which the + * cache size can be increased in a single re-size. + * + * \par flash_incr_mode + * \parblock + * Instance of the \c H5C_cache_flash_incr_mode enumerated + * type whose value indicates whether and by which algorithm we should + * make flash increases in the size of the cache to accommodate insertion + * of large entries and large increases in the size of a single entry. + * + * The addition of the flash increment mode was occasioned by performance + * problems that appear when a local heap is increased to a size in excess + * of the current cache size. While the existing re-size code dealt with + * this eventually, performance was very bad for the remainder of the + * epoch. + * + * At present, there are two possible values for the \c flash_incr_mode: + * + * \li \c H5C_flash_incr__off: Don't perform flash increases in the size of the cache. + * + * \li \c H5C_flash_incr__add_space: Let \c x be either the size of a newly + * newly inserted entry, or the number of bytes by which the + * size of an existing entry has been increased.\n + * If \Code{x > flash_threshold * current max cache size}, + * increase the current maximum cache size by \Code{x * flash_multiple} + * less any free space in the cache, and star a new epoch. For + * now at least, pay no attention to the maximum increment. + * + * In both of the above cases, the flash increment pays no attention to + * the maximum increment (at least in this first incarnation), but DOES + * stay within max_size. + * + * With a little thought, it should be obvious that the above flash + * cache size increase algorithm is not sufficient for all circumstances + * -- for example, suppose the user round robins through + * \Code{(1/flash_threshold) +1} groups, adding one data set to each on each + * pass. Then all will increase in size at about the same time, requiring + * the max cache size to at least double to maintain acceptable + * performance, however the above flash increment algorithm will not be + * triggered. + * + * Hopefully, the add space algorithms detailed above will be sufficient + * for the performance problems encountered to date. However, we should + * expect to revisit the issue. + * \endparblock + * + * \par flash_multiple + * Double containing the multiple described above in the + * \c H5C_flash_incr__add_space section of the discussion of the + * \c flash_incr_mode section. This field is ignored unless \c flash_incr_mode + * is \c H5C_flash_incr__add_space. + * + * \par flash_threshold + * Double containing the factor by which current max cache + * size is multiplied to obtain the size threshold for the add_space flash + * increment algorithm. The field is ignored unless \c flash_incr_mode is + * \c H5C_flash_incr__add_space. + * + * + * \section csdcf Cache size decrease control fields + * + * \par decr_mode + * \parblock + * Instance of the \c H5C_cache_decr_mode enumerated type whose + * value indicates how we determine whether the cache size should be + * decreased. At present there are four possibilities. + * + * \li \c H5C_decr__off: Don't attempt to decrease the size of the cache + * automatically.\n + * When this increment mode is selected, the remaining fields + * in the cache size decrease section are ignored. + * \li \c H5C_decr__threshold: Attempt to decrease the size of the cache + * whenever the average hit rate over the last epoch rises + * above the value supplied in the \c upper_hr_threshold + * field. + * \li \c H5C_decr__age_out: At the end of each epoch, search the cache for + * entries that have not been accessed for at least the number + * of epochs specified in the epochs_before_eviction field, and + * evict these entries. Conceptually, the maximum cache size + * is then decreased to match the new actual cache size. However, + * this reduction may be modified by the \c min_size, the + * \c max_decrement, and/or the \c empty_reserve. + * \li \c H5C_decr__age_out_with_threshold: Same as age_out, but we only + * attempt to reduce the cache size when the hit rate observed + * over the last epoch exceeds the value provided in the + * \c upper_hr_threshold field. + * + * Note that you must set \c decr_mode to \c H5C_decr__off if you + * disable metadata cache entry evictions. + * \endparblock + * + * \par upper_hr_threshold + * \parblock + * Upper hit rate threshold. The use of this field + * varies according to the current \c decr_mode : + * + * \c H5C_decr__off or \c H5C_decr__age_out: The value of this field is + * ignored. + * + * \li \c H5C_decr__threshold: If the hit rate exceeds this threshold in any + * epoch, attempt to decrement the cache size by size_decrement.\n + * Note that cache size may not be decremented below \c min_size.\n + * Note also that if the \c upper_threshold is 1.0, the cache size\n + * will never be reduced. + * + * \li \c H5C_decr__age_out_with_threshold: If the hit rate exceeds this + * threshold in any epoch, attempt to reduce the cache size + * by evicting entries that have not been accessed for more + * than the specified number of epochs. + * \endparblock + * + * \par decrement + * \parblock + * This field is only used when the decr_mode is + * \c H5C_decr__threshold. + * + * The field is a double containing the multiplier used to derive the + * new cache size from the old if a cache size decrement is triggered. + * The decrement must be in the range 0.0 (in which case the cache will + * try to contract to its minimum size) to 1.0 (in which case the + * cache will never shrink). + * \endparblock + * + * \par apply_max_decrement + * Boolean flag used to determine whether decrements + * in cache size are to be limited by the \c max_decrement field. + * + * \par max_decrement + * Maximum number of bytes by which the cache size can be + * decreased in a single re-size. Note that decrements may also be + * restricted by the \c min_size of the cache, and (in age out modes) by + * the \c empty_reserve field. + * + * \par epochs_before_eviction + * \parblock + * Integer field used in \c H5C_decr__age_out and + * \c H5C_decr__age_out_with_threshold decrement modes. + * + * This field contains the number of epochs an entry must remain + * unaccessed before it is evicted in an attempt to reduce the + * cache size. If applicable, this field must lie in the range + * \Code{[1, H5C__MAX_EPOCH_MARKERS]}. + * \endparblock + * + * \par apply_empty_reserve + * Boolean field controlling whether the empty_reserve + * field is to be used in computing the new cache size when the + * decr_mode is H5C_decr__age_out or H5C_decr__age_out_with_threshold. + * + * \par empty_reserve + * \parblock + * To avoid a constant racheting down of cache size by small + * amounts in the \c H5C_decr__age_out and \c H5C_decr__age_out_with_threshold + * modes, this field allows one to require that any cache size + * reductions leave the specified fraction of unused space in the cache. + * + * The value of this field must be in the range [0.0, 1.0]. I would + * expect typical values to be in the range of 0.01 to 0.1. + * \endparblock + * + * + * \section pcf Parallel Configuration Fields + * + * In PHDF5, all operations that modify metadata must be executed collectively. + * + * We used to think that this was enough to ensure consistency across the + * metadata caches, but since we allow processes to read metadata individually, + * the order of dirty entries in the LRU list can vary across processes, + * which can result in inconsistencies between the caches. + * + * PHDF5 uses several strategies to prevent such inconsistencies in metadata, + * all of which use the fact that the same stream of dirty metadata is seen + * by all processes for purposes of synchronization. This is done by + * having each process count the number of bytes of dirty metadata generated, + * and then running a "sync point" whenever this count exceeds a user + * specified threshold (see \c dirty_bytes_threshold below). + * + * The current metadata write strategy is indicated by the + * \c metadata_write_strategy field. The possible values of this field, along + * with the associated metadata write strategies are discussed below. + * + * \par dirty_bytes_threshold + * \parblock + * Threshold of dirty byte creation used to + * synchronize updates between caches. (See above for outline and + * motivation.) + * + * This value MUST be consistent across all processes accessing the + * file. This field is ignored unless HDF5 has been compiled for + * parallel. + * \endparblock + * + * \par metadata_write_strategy + * Integer field containing a code indicating the + * desired metadata write strategy. The valid values of this field + * are enumerated and discussed below: + * + * \li #H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY\n + * When metadata_write_strategy is set to this value, only process + * zero is allowed to write dirty metadata to disk. All other + * processes must retain dirty metadata until they are informed at + * a sync point that the dirty metadata in question has been written + * to disk.\n + * When the sync point is reached (or when there is a user generated + * flush), process zero flushes sufficient entries to bring it into + * complience with its min clean size (or flushes all dirty entries in + * the case of a user generated flush), broad casts the list of + * entries just cleaned to all the other processes, and then exits + * the sync point.\n + * Upon receipt of the broadcast, the other processes mark the indicated + * entries as clean, and leave the sync point as well. + * + * \li #H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED\n + * In the distributed metadata write strategy, process zero still makes + * the decisions as to what entries should be flushed, but the actual + * flushes are distributed across the processes in the computation to + * the extent possible.\n + * In this strategy, when a sync point is triggered (either by dirty + * metadata creation or manual flush), all processes enter a barrier.\n + * On the other side of the barrier, process 0 constructs an ordered + * list of the entries to be flushed, and then broadcasts this list + * to the caches in all the processes.\n + * All processes then scan the list of entries to be flushed, flushing + * some, and marking the rest as clean. The algorithm for this purpose + * ensures that each entry in the list is flushed exactly once, and + * all are marked clean in each cache.\n + * Note that in the case of a flush of the cache, no message passing + * is necessary, as all processes have the same list of dirty entries, + * and all of these entries must be flushed. Thus in this case it is + * sufficient for each process to sort its list of dirty entries after + * leaving the initial barrier, and use this list as if it had been + * received from process zero.\n + * To avoid possible messages from the past/future, all caches must + * wait until all caches are done before leaving the sync point. + */
\ No newline at end of file diff --git a/doxygen/dox/mainpage.dox b/doxygen/dox/mainpage.dox index 83fc323..eda967b 100644 --- a/doxygen/dox/mainpage.dox +++ b/doxygen/dox/mainpage.dox @@ -1,36 +1,44 @@ -/*! \mainpage API Documentation for HDF5 Version 1.13 (Draft) +/*! \mainpage HDF5 C-API Reference + * + * The HDF5 C-API provides applications with fine-grained control over all + * aspects HDF5 functionality. This functionality is grouped into the following + * \Emph{modules}: + * \li \ref H5A "Attributes" — Management of HDF5 attributes (\ref H5A) + * \li \ref H5D "Datasets" — Management of HDF5 datasets (\ref H5D) + * \li \ref H5S "Dataspaces" — Management of HDF5 dataspaces which describe the shape of datasets and attributes (\ref H5S) + * \li \ref H5T "Datatypes" — Management of datatypes which describe elements of datasets and attributes (\ref H5T) + * \li \ref H5E "Error Handling" — Functions for handling errors that occur within HDF5 (\ref H5E) + * \li \ref H5F "Files" — Management of HDF5 files (\ref H5F) + * \li \ref H5Z "Filters" — Configuration of filters that process data during I/O operation (\ref H5Z) + * \li \ref H5G "Groups" — Management of groups in HDF5 files (\ref H5G) + * \li \ref H5I "Identifiers" — Management of object identifiers and object names (\ref H5I) + * \li \ref H5 "Library" — General purpose library functions (\ref H5) + * \li \ref H5L "Links" — Management of links in HDF5 groups (\ref H5L) + * \li \ref H5O "Objects" — Management of objects in HDF5 files (\ref H5O) + * \li \ref H5PL "Plugins" — Programmatic control over dynamically loaded plugins (\ref H5PL) + * \li \ref H5P "Property Lists" — Management of property lists to control HDF5 library behavior (\ref H5P) + * \li \ref H5R "References" — Management of references to specific objects and data regions in an HDF5 file (\ref H5R) + * \li \ref H5VL "Virtual Object Layer" — Management of the Virtual Object Layer (\ref H5VL) + * + * Here are a few simple rules to follow: + * + * \li \Bold{Handle discipline:} If you acquire a handle (by creation or coopy), \Emph{you own it!} (..., i.e., you have to close it.) + * \li \Bold{Dynamic memory allocation:} ... + * \li \Bold{Use of locations:} Identifier + name combo + * + * \attention \Bold{C++ Developers using HDF5 C-API functions beware:}\n + * If a C routine that takes a function pointer as an argument is called from + * within C++ code, the C routine should be returned from normally. + * Examples of this kind of routine include callbacks such as H5Pset_elink_cb() + * and H5Pset_type_conv_cb() and functions such as H5Tconvert() and H5Ewalk2().\n + * Exiting the routine in its normal fashion allows the HDF5 C library to clean + * up its work properly. In other words, if the C++ application jumps out of + * the routine back to the C++ \c catch statement, the library is not given the + * opportunity to close any temporary data structures that were set up when the + * routine was called. The C++ application should save some state as the + * routine is started so that any problem that occurs might be diagnosed. * * \todo Fix the search form for server deployments. * \todo Make it mobile-friendly * - * \section intro_sec Introduction - * - * \todo Write an introduction. - * - * \section quick_links Quick Links - * - * <ul> - * <li>\ref PDT "Predefined Datatypes"</li> - * <li>\ref api-compat-macros "API Compatibility Macros"</li> - * <li><a href="https://hdf5.wiki/">HDF5 Wiki</a></li> - * </ul> - * - * \section using_locations The Use of Locations (Identifier + Name) in the HDF5 API - * - * \todo Make this crystal clear! - * - * \section cpp_note Programming Note for C++ Developers Using C Functions - * - * If a C routine that takes a function pointer as an argument is called from - * within C++ code, the C routine should be returned from normally. - * - * Examples of this kind of routine include callbacks such as H5Pset_elink_cb() - * and H5Pset_type_conv_cb() and functions such as H5Tconvert() and H5Ewalk2(). - * - * Exiting the routine in its normal fashion allows the HDF5 C library to clean - * up its work properly. In other words, if the C++ application jumps out of - * the routine back to the C++ \c catch statement, the library is not given the - * opportunity to close any temporary data structures that were set up when the - * routine was called. The C++ application should save some state as the - * routine is started so that any problem that occurs might be diagnosed. */
\ No newline at end of file @@ -14,6 +14,7 @@ /****************/ /* Module Setup */ /****************/ +#include "H5module.h" /* This source code file is part of the H5 module */ /***********/ /* Headers */ @@ -55,6 +56,9 @@ static int H5__mpi_delete_cb(MPI_Comm comm, int keyval, void *attr_val, int *fla /* Package Variables */ /*********************/ +/* Package initialization variable */ +hbool_t H5_PKG_INIT_VAR = FALSE; + /*****************************/ /* Library Private Variables */ /*****************************/ @@ -85,6 +89,33 @@ H5_debug_t H5_debug_g; /* debugging info */ /*******************/ /*-------------------------------------------------------------------------- +NAME + H5__init_package -- Initialize interface-specific information +USAGE + herr_t H5__init_package() +RETURNS + Non-negative on success/Negative on failure +DESCRIPTION + Initializes any interface-specific data or routines. +--------------------------------------------------------------------------*/ +herr_t +H5__init_package(void) +{ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT + + /* Run the library initialization routine, if it hasn't already ran */ + if (!H5_INIT_GLOBAL && !H5_TERM_GLOBAL) { \ + if (H5_init_library() < 0) + HGOTO_ERROR(H5E_LIB, H5E_CANTINIT, FAIL, "unable to initialize library") + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5__init_package() */ + +/*-------------------------------------------------------------------------- * NAME * H5_init_library -- Initialize library-global information * USAGE @@ -103,6 +134,11 @@ H5_init_library(void) { herr_t ret_value = SUCCEED; + /* Set the 'library initialized' flag as early as possible, to avoid + * possible re-entrancy. + */ + H5_INIT_GLOBAL = TRUE; \ + FUNC_ENTER_NOAPI(FAIL) #ifdef H5_HAVE_PARALLEL diff --git a/src/H5Amodule.h b/src/H5Amodule.h index 707fc54..09e6c4a 100644 --- a/src/H5Amodule.h +++ b/src/H5Amodule.h @@ -29,4 +29,21 @@ #define H5_MY_PKG_ERR H5E_ATTR #define H5_MY_PKG_INIT YES +/**\defgroup H5A H5A + * \brief Attribute Interface + * + * \details The Attribute Interface, H5A, provides a mechanism for attaching + * additional information to a dataset, group, or named datatype. + * + * Attributes are accessed by opening the object that they are + * attached to and are not independent objects. Typically an + * attribute is small in size and contains user metadata about the + * object that it is attached to. + * + * Attributes look similar to HDF5 datasets in that they have a + * datatype and dataspace. However, they do not support partial + * I/O operations and cannot be compressed or extended. + * + */ + #endif /* _H5Amodule_H */ diff --git a/src/H5Apublic.h b/src/H5Apublic.h index 89a3b04..3b836e7 100644 --- a/src/H5Apublic.h +++ b/src/H5Apublic.h @@ -45,18 +45,306 @@ typedef herr_t (*H5A_operator2_t)(hid_t location_id /*in*/, const char *attr_nam extern "C" { #endif +/*-------------------------------------------------------------------------*/ +/** + * \ingroup H5A + * + * \brief Closes the specified attribute + * + * \attr_id + * + * \return \herr_t + * + * \details H5Aclose() terminates access to the attribute specified by + * \p attr_id by releasing the identifier. + * + * \attention Further use of a released attribute identifier is illegal; a + * function using such an identifier will generate an error. + * + * \since 1.0.0 + * + * \see H5Acreate(), H5Aopen() + */ +H5_DLL herr_t H5Aclose(hid_t attr_id); +/* --------------------------------------------------------------------------*/ +/** + * \ingroup H5A + * + * \brief Creates an attribute attached to a specified object + * + * \fgdt_loc_id + * \param[in] attr_name Name of attribute + * \param[in] type_id Attribute datatype identifier + * \space_id + * \acpl_id + * \aapl_id + * + * \return \hid_tv{attribute} + * + * \details H5Acreate2() creates an attribute, \p attr_name, which is attached + * to the object specified by the identifier \p loc_id. + * + * The attribute name, \p attr_name, must be unique for the object. + * + * The attribute is created with the specified datatype and dataspace, + * \p type_id and \p space_id, which are created with the H5T and + * H5S interfaces, respectively. + * + * If \p type_id is either a fixed-length or variable-length string, + * it is important to set the string length when defining the + * datatype. String datatypes are derived from #H5T_C_S1 (or + * #H5T_FORTRAN_S1 for Fortran), which defaults to 1 character in + * size. See H5Tset_size() and Creating variable-length string + * datatypes. + * + * The access property list is currently unused, but will be used in + * the future. This property list should currently be #H5P_DEFAULT. + * + * The attribute identifier returned by this function must be released + * with H5Aclose() resource leaks will develop. + * + * \note The \p acpl and \p aapl parameters are currently not used; specify + * #H5P_DEFAULT. + * \note If \p loc_id is a file identifier, the attribute will be attached + * that file’s root group. + * + * \since 1.8.0 + * + * \see H5Aclose() + * + */ H5_DLL hid_t H5Acreate2(hid_t loc_id, const char *attr_name, hid_t type_id, hid_t space_id, hid_t acpl_id, hid_t aapl_id); +/*--------------------------------------------------------------------------*/ +/** + * \ingroup H5A + * + * \brief Creates an attribute attached to a specified object + * + * \fgdt_loc_id + * \param[in] obj_name Name, relative to \p loc_id, of object that + * attribute is to be attached to + * \param[in] attr_name Attribute name + * \param[in] type_id Attribute datatype identifier + * \space_id + * \acpl_id + * \aapl_id + * \lapl_id + * + * \return \hid_tv{attribute} + * + * \details H5Acreate_by_name() creates an attribute, \p attr_name, which is + * attached to the object specified by \p loc_id and \p obj_name. + * + * \p loc_id is a location identifier; \p obj_name is the object + * name relative to \p loc_id. If \p loc_id fully specifies the + * object to which the attribute is to be attached, \p obj_name + * should be '.' (a dot). + * + * The attribute name, \p attr_name, must be unique for the object. + * + * The attribute is created with the specified datatype and + * dataspace, \p type_id and \p space_id, which are created with + * the H5T and H5S interfaces respectively. + * + * The attribute creation and access property lists are currently + * unused, but will be used in the future for optional attribute + * creation and access properties. These property lists should + * currently be #H5P_DEFAULT. + * + * The link access property list, \p lapl_id, may provide + * information regarding the properties of links required to access + * the object, \p obj_name. + * + * The attribute identifier returned by this function must be + * released with H5close() or resource leaks will develop. + * + * \since 1.8.0 + * + */ H5_DLL hid_t H5Acreate_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, hid_t type_id, hid_t space_id, hid_t acpl_id, hid_t aapl_id, hid_t lapl_id); +/*--------------------------------------------------------------------------*/ +/** + * \ingroup H5A + * + * \brief Opens an attribute for an object specified by object identifier and + * attribute name + * + * \fgdt_loc_id{obj_id} + * \param[in] attr_name Name of attribute to open + * \aapl_id + * + * \return \hid_tv{attribute} + * + * \details H5Aopen() opens an existing attribute, \p attr_name, that is + * attached to object specified by an object identifier, \p obj_id. + * + * The attribute access property list, \p aapl_id, is currently unused + * and should be #H5P_DEFAULT. + * + * This function, H5Aopen_by_idx() or H5Aopen_by_name() must be called + * before the attribute can be accessed for any further purpose, + * including reading, writing, or any modification. + * + * The attribute identifier returned by this function must be released + * with H5Aclose() or resource leaks will develop. + * + * \since 1.8.0 + * + * \see H5Aclose(), H5Acreate() + */ H5_DLL hid_t H5Aopen(hid_t obj_id, const char *attr_name, hid_t aapl_id); -H5_DLL hid_t H5Aopen_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, hid_t aapl_id, - hid_t lapl_id); +/*--------------------------------------------------------------------------*/ +/** + * \ingroup H5A + * + * \brief Opens the nth attribute attached to an object + * + * \loc_id + * \param[in] obj_name Name of object to which attribute is attached, + * relative to location + * \param[in] idx_type Type of index + * \param[in] order Index traversal order + * \param[in] n Attribute’s position in index + * \aapl_id + * \lapl_id + * + * \return \hid_tv{attribute} + * + * \details H5Aopen_by_idx() opens an existing attribute that is attached + * to an object specified by location and name, \p loc_id and + * \p obj_name, respectively. If \p loc_id fully specifies the + * object to which the attribute is attached, \p obj_name, should + * be '.' (a dot). + * + * The attribute is identified by an index type, an index traversal + * order, and a position in the index, \p idx_type, \p order and + * \p n, respectively. These parameters and their valid values are + * discussed in the description of H5Aiterate2(). + * + * The attribute access property list, \p aapl_id, is currently + * unused and should currently be #H5P_DEFAULT. + * + * The link access property list, \p lapl_id, may provide + * information regarding the properties of links required to access + * the object, \p obj_name. + * + * This function, H5Aopen(), or H5Aopen_by_name() must be called + * before an attribute can be accessed for any further purpose, + * including reading, writing, or any modification. + * + * The attribute identifier returned by this function must be + * released with H5Aclose() or resource leaks will develop. + * + * \since 1.8.0 + * + */ H5_DLL hid_t H5Aopen_by_idx(hid_t loc_id, const char *obj_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, hid_t aapl_id, hid_t lapl_id); -H5_DLL herr_t H5Awrite(hid_t attr_id, hid_t type_id, const void *buf); +/*--------------------------------------------------------------------------*/ +/** + * \ingroup H5A + * + * \brief Opens an attribute for an object by object name and attribute name + * + * \fgdt_loc_id + * \param[in] obj_name Name of object to which attribute is attached, + * relative to \p loc_id + * \param[in] attr_name Name of attribute to open + * \aapl_id + * \lapl_id + * + * \return \hid_tv{attribute} + * + * \details H5Aopen_by_name() opens an existing attribute, \p attr_name, + * that is attached to an object specified by location and name, + * \p loc_id and \p obj_name, respectively. + * + * \p loc_id specifies a location from which the target object can + * be located and \p obj_name is an object name relative to + * \p loc_id. If \p loc_id fully specifies the object to which the + * attribute is attached, \p obj_name should be '.' (a dot). + * + * The attribute access property list, \p aapl_id, is currently + * unused and should currently be #H5P_DEFAULT. + * + * The link access property list, \p lapl_id, may provide + * information regarding the properties of links required to access + * the object, \p obj_name. + * + * This function, H5Aopen(), or H5Aopen_by_idx() must be called + * before an attribute can be accessed for any further purpose, + * including reading, writing, or any modification. + * + * The attribute identifier returned by this function must be + * released with H5Aclose() or resource leaks will develop. + * + * \since 1.8.0 + * + */ +H5_DLL hid_t H5Aopen_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, hid_t aapl_id, + hid_t lapl_id); +/*-------------------------------------------------------------------------- */ +/** + * \ingroup H5A + * + * \brief Reads the value of an attribute + * + * \attr_id + * \mem_type_id{type_id} + * \param[out] buf Buffer for data to be read + * + * \return \herr_t + * + * \details H5Aread() reads an attribute, specified with \p attr_id. The + * attribute's in-memory datatype is specified with \p type_id. The + * entire attribute is read into \p buf from the file. + * + * Datatype conversion takes place at the time of a read or write and + * is automatic. + * + * \version 1.8.8 Fortran updated to Fortran2003. + * \version 1.4.2 The \p dims parameter was added to the Fortran API in this + * release. + * \since 1.0.0 + * + * \see H5Awrite() + * +*/ H5_DLL herr_t H5Aread(hid_t attr_id, hid_t type_id, void *buf); -H5_DLL herr_t H5Aclose(hid_t attr_id); +/*--------------------------------------------------------------------------*/ +/** + * \ingroup H5A + * + * \brief Writes data to an attribute + * + * \attr_id + * \mem_type_id{type_id} + * \param[out] buf Data to be written + * + * \return \herr_t + * + * \details H5Awrite() writes an attribute, specified with \p attr_id. The + * attribute's in-memory datatype is specified with \p type_id. + * The entire attribute is written from \p buf to the file. + * + * If \p type_id is either a fixed-length or variable-length string, + * it is important to set the string length when defining the datatype. + * String datatypes are derived from #H5T_C_S1 (or #H5T_FORTRAN_S1 for + * Fortran codes), which defaults to 1 character in size. + * See H5Tset_size() and Creating variable-length string datatypes. + * + * Datatype conversion takes place at the time of a read or write and + * is automatic. + * + * \version 1.8.8 Fortran updated to Fortran2003. + * \version 1.4.2 Fortran \p dims parameter added in this release + * \since 1.0.0 + * \see H5Aread() + * + */ +H5_DLL herr_t H5Awrite(hid_t attr_id, hid_t type_id, const void *buf); H5_DLL hid_t H5Aget_space(hid_t attr_id); H5_DLL hid_t H5Aget_type(hid_t attr_id); H5_DLL hid_t H5Aget_create_plist(hid_t attr_id); @@ -100,6 +388,51 @@ typedef herr_t (*H5A_operator1_t)(hid_t location_id /*in*/, const char *attr_nam void *operator_data /*in,out*/); /* Function prototypes */ +/* --------------------------------------------------------------------------*/ +/** + * \ingroup H5A + * + * \brief Creates an attribute attached to a specified object + * + * \fgdt_loc_id + * \param[in] name Name of attribute to locate and open + * \param[in] type_id Identifier of attribute datatype + * \space_id + * \acpl_id + * + * \return \hid_tv{attribute} + * + * \note The \p acpl parameters is currently not used; specify #H5P_DEFAULT. + * + * \deprecated Deprecated in favor of H5Acreate2() + * + * \details H5Acreate1() creates an attribute, \p name, which is attached + * to the object specified by the identifier \p loc_id. + * + * The attribute name, \p name, must be unique for the object. + * + * The attribute is created with the specified datatype and dataspace, + * \p type_id and \p space_id, which are created with the H5T and + * H5S interfaces, respectively. + * + * If \p type_id is either a fixed-length or variable-length string, + * it is important to set the string length when defining the + * datatype. String datatypes are derived from #H5T_C_S1 (or + * #H5T_FORTRAN_S1 for Fortran), which defaults to 1 character in + * size. See H5Tset_size() and Creating variable-length string + * datatypes. + * + * The attribute identifier returned by this function must be released + * with H5Aclose() resource leaks will develop. + * + * \since 1.8.0 + * + * \version 1.8.0 The function H5Acreate() was renamed to H5Acreate1() and + * deprecated in this release. + * + * \see H5Aclose() + * + */ H5_DLL hid_t H5Acreate1(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t acpl_id); H5_DLL hid_t H5Aopen_name(hid_t loc_id, const char *name); H5_DLL hid_t H5Aopen_idx(hid_t loc_id, unsigned idx); diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h index fbee9c5..10cfbbe 100644 --- a/src/H5Fpublic.h +++ b/src/H5Fpublic.h @@ -225,6 +225,7 @@ typedef enum H5F_file_space_type_t { H5F_FILE_SPACE_NTYPES /**< Sentinel */ } H5F_file_space_type_t; +//! [H5F_retry_info_t_snip] #define H5F_NUM_METADATA_READ_RETRY_TYPES 21 /** @@ -235,6 +236,7 @@ typedef struct H5F_retry_info_t { unsigned nbins; uint32_t *retries[H5F_NUM_METADATA_READ_RETRY_TYPES]; } H5F_retry_info_t; +//! [H5F_retry_info_t_snip] /** * Callback for H5Pset_object_flush_cb() in a file access property list @@ -952,32 +954,542 @@ H5_DLL ssize_t H5Fget_file_image(hid_t file_id, void *buf_ptr, size_t buf_len); /** * \ingroup MDC * - * \todo Finish this! + * \brief Obtains current metadata cache configuration for target file + * + * \file_id + * \param[in,out] config_ptr Pointer to the H5AC_cache_config_t instance in which + * the current metadata cache configuration is to be + * reported. The fields of this structure are discussed + * \ref H5AC-cache-config-t "here". + * \return \herr_t + * + * \details H5Fget_mdc_config() loads the current metadata cache configuration + * into the instance of H5AC_cache_config_t pointed to by the \p config_ptr + * parameter. + * + * Note that the \c version field of \p config_ptr must be initialized + * --this allows the library to support old versions of the H5AC_cache_config_t + * structure. + * + * \par General configuration section + * <table> + * <tr> + * <td><em>int</em> <code>version</code> </td> + * <td>IN: Integer field indicating the the version of the H5AC_cache_config_t in use. This field should + * be set to #H5AC__CURR_CACHE_CONFIG_VERSION (defined in H5ACpublic.h).</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>rpt_fcn_enabled</code> </td> + * <td><p>OUT: Boolean flag indicating whether the adaptive cache resize report function is enabled. This + * field should almost always be set to disabled (<code>0</code>). Since resize algorithm activity is + * reported via stdout, it MUST be set to disabled (<code>0</code>) on Windows machines.</p><p>The + * report function is not supported code, and can be expected to change between versions of the + * library. Use it at your own risk.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>open_trace_file</code> </td> + * <td>OUT: Boolean field indicating whether the <code>trace_file_name</code> field should be used to open + * a trace file for the cache. This field will always be set to <code>0</code> in this context.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>close_trace_file</code> </td> + * <td>OUT: Boolean field indicating whether the current trace file (if any) should be closed. This field + * will always be set to <code>0</code> in this context.</td></tr> + * <tr> + * <td><em>char*</em><code>trace_file_name</code> </td> + * <td>OUT: Full path name of the trace file to be opened if the <code>open_trace_file</code> field is set + * to <code>1</code>. This field will always be set to the empty string in this context.</td></tr> + * <tr> + * <td><em>hbool_t</em> <code>evictions_enabled</code> </td> + * <td>OUT: Boolean flag indicating whether metadata cache entry evictions are + * enabled.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>set_initial_size</code> </td> + * <td>OUT: Boolean flag indicating whether the cache should be created with a user specified initial + * maximum size.<p>If the configuration is loaded from the cache, this flag will always be set + * to <code>0</code>.</p></td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>initial_size</code> </td> + * <td>OUT: Initial maximum size of the cache in bytes, if applicable.<p>If the configuration is loaded + * from the cache, this field will contain the cache maximum size as of the time of the + * call.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>min_clean_fraction</code> </td> + * <td>OUT: Float value specifying the minimum fraction of the cache that must be kept either clean or + * empty when possible.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>max_size</code> </td> + * <td>OUT: Upper bound (in bytes) on the range of values that the adaptive cache resize code can select + * as the maximum cache size.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>min_size</code> </td> + * <td>OUT: Lower bound (in bytes) on the range of values that the adaptive cache resize code can select + * as the maximum cache size.</td> + * </tr> + * <tr> + * <td><em>long int</em> <code>epoch_length</code> </td> + * <td>OUT: Number of cache accesses between runs of the adaptive cache resize + * code.</td> + * </tr> + * </table> + * + * \par Increment configuration section + * <table> + * <tr> + * <td><em>enum H5C_cache_incr_mode</em> <code>incr_mode</code> </td> + * <td>OUT: Enumerated value indicating the operational mode of the automatic cache size increase code. At + * present, only the following values are legal:<p>\c H5C_incr__off: Automatic cache size increase is + * disabled.</p><p>\c H5C_incr__threshold: Automatic cache size increase is enabled using the hit rate + * threshold algorithm.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>lower_hr_threshold</code> </td> + * <td>OUT: Hit rate threshold used in the hit rate threshold cache size increase algorithm.</td> + * </tr> + * <tr> + * <td><em>double</em> <code>increment</code> </td> + * <td>OUT: The factor by which the current maximum cache size is multiplied to obtain an initial new + * maximum cache size if a size increase is triggered in the hit rate threshold cache size increase + * algorithm.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_max_increment</code> </td> + * <td>OUT: Boolean flag indicating whether an upper limit will be applied to the size of cache size + * increases.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>max_increment</code> </td> + * <td>OUT: The maximum number of bytes by which the maximum cache size can be increased in a single step + * -- if applicable.</td> + * </tr> + * <tr> + * <td><em>enum H5C_cache_flash_incr_mode</em> <code>flash_incr_mode</code> </td> + * <td>OUT: Enumerated value indicating the operational mode of the flash cache size increase code. At + * present, only the following values are legal:<p>\c H5C_flash_incr__off: Flash cache size increase is + * disabled.</p><p>\c H5C_flash_incr__add_space: Flash cache size increase is enabled using the add space + * algorithm.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>flash_threshold</code> </td> + * <td>OUT: The factor by which the current maximum cache size is multiplied to obtain the minimum size + * entry / entry size increase which may trigger a flash cache size + * increase.</td> + * </tr> + * <tr> + * <td><em>double</em> <code>flash_multiple</code> </td> + * <td>OUT: The factor by which the size of the triggering entry / entry size increase is multiplied to + * obtain the initial cache size increment. This increment may be reduced to reflect existing free space + * in the cache and the <code>max_size</code> field above.</td> + * </tr> + * </table> + * + * \par Decrement configuration section + * <table> + * <tr><td colspan="2"><strong>Decrement configuration + * section:</strong></td> + * </tr> + * <tr> + * <td><em>enum H5C_cache_decr_mode</em> <code>decr_mode</code> </td> + * <td>OUT: Enumerated value indicating the operational mode of the automatic cache size decrease code. At + * present, the following values are legal:<p>H5C_decr__off: Automatic cache size decrease is disabled, + * and the remaining decrement fields are ignored.</p><p>H5C_decr__threshold: Automatic cache size + * decrease is enabled using the hit rate threshold algorithm.</p><p>H5C_decr__age_out: Automatic cache + * size decrease is enabled using the ageout algorithm.</p><p>H5C_decr__age_out_with_threshold: + * Automatic cache size decrease is enabled using the ageout with hit rate threshold + * algorithm</p></td> + * </tr> + * <tr><td><em>double</em> <code>upper_hr_threshold</code> </td> + * <td>OUT: Upper hit rate threshold. This value is only used if the decr_mode is either + * H5C_decr__threshold or H5C_decr__age_out_with_threshold.</td> + * </tr> + * <tr> + * <td><em>double</em> <code>decrement</code> </td> + * <td>OUT: Factor by which the current max cache size is multiplied to obtain an initial value for the + * new cache size when cache size reduction is triggered in the hit rate threshold cache size reduction + * algorithm.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_max_decrement</code> </td> + * <td>OUT: Boolean flag indicating whether an upper limit should be applied to the size of cache size + * decreases.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>max_decrement</code> </td> + * <td>OUT: The maximum number of bytes by which cache size can be decreased if any single step, if + * applicable.</td> + * </tr> + * <tr> + * <td><em>int</em> <code>epochs_before_eviction</code> </td> + * <td>OUT: The minimum number of epochs that an entry must reside unaccessed in cache before being + * evicted under either of the ageout cache size reduction algorithms.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_empty_reserve</code> </td> + * <td>OUT: Boolean flag indicating whether an empty reserve should be maintained under either of the + * ageout cache size reduction algorithms.</td> + * </tr> + * <tr> + * <td><em>double</em> <code>empty_reserve</code> </td> + * <td>OUT: Empty reserve for use with the ageout cache size reduction algorithms, if applicable.</td> + * </tr> + * </table> + * + * \par Parallel configuration section + * <table> + * <tr><td><em>int</em> <code>dirty_bytes_threshold</code> </td> + * <td>OUT: Threshold number of bytes of dirty metadata generation for triggering synchronizations of the + * metadata caches serving the target file in the parallel case.<p>Synchronization occurs whenever the + * number of bytes of dirty metadata created since the last synchronization exceeds this limit.</p></td> + * </tr> + * </table> + * + * \since 1.8.0 + * + * \todo Fix the reference! + * */ H5_DLL herr_t H5Fget_mdc_config(hid_t file_id, H5AC_cache_config_t *config_ptr); /** * \ingroup MDC * - * \todo Finish this! + * \brief Attempts to configure metadata cache of target file + * + * \file_id + * \param[in,out] config_ptr Pointer to the H5AC_cache_config_t instance + * containing the desired configuration. + * The fields of this structure are discussed + * \ref H5AC-cache-config-t "here". + * \return \herr_t + * + * \details H5Fset_mdc_config() attempts to configure the file's metadata cache + * according configuration supplied in \p config_ptr. + * + * \par General configuration fields + * <table> + * <tr> + * <td><em>int</em> <code>version</code></td> + * <td>IN: Integer field indicating the the version of the H5AC_cache_config_t in use. This + * field should be set to #H5AC__CURR_CACHE_CONFIG_VERSION (defined + * in H5ACpublic.h).</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>rpt_fcn_enabled</code></td> + * <td>IN: Boolean flag indicating whether the adaptive cache resize report function is enabled. This + * field should almost always be set to disabled (<code>0</code>). Since resize algorithm activity is reported + * via stdout, it MUST be set to disabled (<code>0</code>) on Windows machines.<p>The report function is not + * supported code, and can be expected to change between versions of the library. Use it at your own + * risk.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>open_trace_File</code></td> + * <td>IN: Boolean field indicating whether the <code>trace_file_name</code> field should be used to open + * a trace file for the cache.<p>The trace file is a debuging feature that allows the capture of top level + * metadata cache requests for purposes of debugging and/or optimization. This field should normally be set + * to <code>0</code>, as trace file collection imposes considerable overhead.</p><p>This field should only be + * set to <code>1</code> when the <code>trace_file_name</code> contains the full path of the desired trace + * file, and either there is no open trace file on the cache, or the <code>close_trace_file</code> field is + * also <code>1</code>.</p><p>The trace file feature is unsupported unless used at the direction of The HDF + * Group. It is intended to allow The HDF Group to collect a trace of cache activity in cases of occult + * failures and/or poor performance seen in the field, so as to aid in reproduction in the lab. If you use it + * absent the direction of The HDF Group, you are on your + * own.</p></td> + * </tr> + * <tr><td><em>hbool_t</em> <code>close_trace_file</code></td> + * <td>IN: Boolean field indicating whether the current trace file (if any) should be closed.<p>See the + * above comments on the <code>open_trace_file</code> field. This field should be set to <code>0</code> unless + * there is an open trace file on the cache that you wish to close.</p><p>The trace file feature is + * unsupported unless used at the direction of The HDF Group. It is intended to allow The HDF Group to collect + * a trace of cache activity in cases of occult failures and/or poor performance seen in the field, so as to + * aid in reproduction in the lab. If you use it absent the direction of The HDF Group, you are on your + * own.</p></td> + * </tr> + * <tr> + * <td><em>char</em> <code>trace_file_name[]</code></td> + * <td>IN: Full path of the trace file to be opened if the <code>open_trace_file</code> field is set + * to <code>1</code>.<p>In the parallel case, an ascii representation of the mpi rank of the process will be + * appended to the file name to yield a unique trace file name for each process.</p><p>The length of the path + * must not exceed #H5AC__MAX_TRACE_FILE_NAME_LEN characters.</p><p>The trace file feature is + * unsupported unless used at the direction of The HDF Group. It is intended to allow The HDF Group to collect + * a trace of cache activity in cases of occult failures and/or poor performance seen in the field, so as to + * aid in reproduction in the lab. If you use it absent the direction of The HDF Group, you are on your + * own.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>evictions_enabled</code></td> + * <td>IN: A boolean flag indicating whether evictions from the metadata cache are enabled. This flag is + * initially set to enabled (<code>1</code>).<p>In rare circumstances, the raw data throughput requirements + * may be so high that the user wishes to postpone metadata writes so as to reserve I/O throughput for raw + * data. The <code>evictions_enabled</code> field exists to allow this. However, this is an extreme step, and + * you have no business doing it unless you have read the User Guide section on metadata caching, and have + * considered all other options carefully.</p><p>The <code>evictions_enabled</code> field may not be set to + * disabled (<code>0</code>) unless all adaptive cache resizing code is disabled via + * the <code>incr_mode</code>, <code>flash_incr_mode</code>, and <code>decr_mode</code> fields.</p><p>When + * this flag is set to disabled (<code>0</code>), the metadata cache will not attempt to evict entries to make + * space for new entries, and thus will grow without bound.</p><p>Evictions will be re-enabled when this field + * is set back to <code>1</code>. This should be done as soon as + * possible.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>set_initial_size</code></td> + * <td>IN: Boolean flag indicating whether the cache should be forced to the user specified initial + * size.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>initial_size</code></td> + * <td>IN: If <code>set_initial_size</code> is set to <code>1</code>, then <code>initial_size</code> must + * contain the desired initial size in bytes. This value must lie in the closed interval <code>[min_size, + * max_size]</code>. (see below)</td> + * </tr> + * <tr><td><em>double</em> <code>min_clean_fraction</code></td> + * <td>IN: This field specifies the minimum fraction of the cache that must be kept either clean or + * empty.<p>The value must lie in the interval [0.0, 1.0]. 0.01 is a good place to start in the serial case. + * In the parallel case, a larger value is needed -- + * see <a href="/display/HDF5/Metadata+Caching+in+HDF5">Metadata Caching in HDF5</a> in the collection + * "Advanced Topics in HDF5."</p></td> + * </tr> + * <tr><td><em>size_t</em> <code>max_size</code></td> + * <td>IN: Upper bound (in bytes) on the range of values that the adaptive cache resize code can select as + * the maximum cache size.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>min_size</code></td> + * <td>IN: Lower bound (in bytes) on the range of values that the adaptive cache resize code can select as + * the maximum cache size.</td> + * </tr> + * <tr><td><em>long int</em> <code>epoch_length</code></td> + * <td>IN: Number of cache accesses between runs of the adaptive cache resize code. 50,000 is a good + * starting number.</td> + * </tr> + * </table> + * + * \par Increment configuration fields + * <table> + * <tr> + * <td><em>enum H5C_cache_incr_mode</em> <code>incr_mode</code></td> + * <td>IN: Enumerated value indicating the operational mode of the automatic cache size increase code. At + * present, only two values are legal:<p>\c H5C_incr__off: Automatic cache size increase is disabled, and the + * remaining increment fields are ignored.</p><p>\c H5C_incr__threshold: Automatic cache size increase is enabled + * using the hit rate threshold + * algorithm.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>lower_hr_threshold</code></td> + * <td>IN: Hit rate threshold used by the hit rate threshold cache size increment algorithm.<p>When the + * hit rate over an epoch is below this threshold and the cache is full, the maximum size of the cache is + * multiplied by increment (below), and then clipped as necessary to stay within max_size, and possibly + * max_increment.</p><p>This field must lie in the interval [0.0, 1.0]. 0.8 or 0.9 is a good starting + * point.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>increment</code></td> + * <td>IN: Factor by which the hit rate threshold cache size increment algorithm multiplies the current + * maximum cache size to obtain a tentative new cache size.<p>The actual cache size increase will be clipped + * to satisfy the max_size specified in the general configuration, and possibly max_increment below.</p><p>The + * parameter must be greater than or equal to 1.0 -- 2.0 is a reasonable value.</p><p>If you set it to 1.0, + * you will effectively disable cache size + * increases.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_max_increment</code></td> + * <td>IN: Boolean flag indicating whether an upper limit should be applied to the size of cache size + * increases.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>max_increment</code></td> + * <td>IN: Maximum number of bytes by which cache size can be increased in a single step -- if + * applicable.</td> + * </tr> + * <tr> + * <td><em>enum H5C_cache_flash_incr_mode</em> <code>flash_incr_mode</code></td> + * <td>IN: Enumerated value indicating the operational mode of the flash cache size increase code. At + * present, only the following values are legal:<p>\c H5C_flash_incr__off: Flash cache size increase is + * disabled.</p><p>\c H5C_flash_incr__add_space: Flash cache size increase is enabled using the add space + * algorithm.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>flash_threshold</code></td> + * <td>IN: The factor by which the current maximum cache size is multiplied to obtain the minimum size + * entry / entry size increase which may trigger a flash cache size increase.<p>At present, this value must + * lie in the range [0.1, 1.0].</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>flash_multiple</code></td> + * <td>IN: The factor by which the size of the triggering entry / entry size increase is multiplied to + * obtain the initial cache size increment. This increment may be reduced to reflect existing free space in + * the cache and the <code>max_size</code> field above.<p>At present, this field must lie in the range [0.1, + * 10.0].</p></td> + * </tr> + * </table> + * + * \par Decrement configuration fields + * <table> + * <tr> + * <td><em>enum H5C_cache_decr_mode</em> <code>decr_mode</code></td> + * <td>IN: Enumerated value indicating the operational mode of the automatic cache size decrease code. At + * present, the following values are legal:<p>\c H5C_decr__off: Automatic cache size decrease is + * disabled.</p><p>\c H5C_decr__threshold: Automatic cache size decrease is enabled using the hit rate threshold + * algorithm.</p><p>\c H5C_decr__age_out: Automatic cache size decrease is enabled using the ageout + * algorithm.</p><p>\c H5C_decr__age_out_with_threshold: Automatic cache size decrease is enabled using the + * ageout with hit rate threshold + * algorithm</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>upper_hr_threshold</code></td> + * <td>IN: Hit rate threshold for the hit rate threshold and ageout with hit rate threshold cache size + * decrement algorithms.<p>When \c decr_mode is \c H5C_decr__threshold, and the hit rate over a given epoch exceeds + * the supplied threshold, the current maximum cache size is multiplied by decrement to obtain a tentative new + * (and smaller) maximum cache size.</p><p>When \c decr_mode is \c H5C_decr__age_out_with_threshold, there is no + * attempt to find and evict aged out entries unless the hit rate in the previous epoch exceeded the supplied + * threshold.</p><p>This field must lie in the interval [0.0, 1.0].</p><p>For \c H5C_incr__threshold, .9995 or + * .99995 is a good place to start.</p><p>For \c H5C_decr__age_out_with_threshold, .999 might be more + * useful.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>decrement</code></td> + * <td>IN: In the hit rate threshold cache size decrease algorithm, this parameter contains the factor by + * which the current max cache size is multiplied to produce a tentative new cache size.<p>The actual cache + * size decrease will be clipped to satisfy the min_size specified in the general configuration, and possibly + * max_decrement below.</p><p>The parameter must be be in the interval [0.0, 1.0].</p><p>If you set it to 1.0, + * you will effectively disable cache size decreases. 0.9 is a reasonable starting + * point.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_max_decrement</code></td> + * <td>IN: Boolean flag indicating whether an upper limit should be applied to the size of cache size + * decreases.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>max_decrement</code></td> + * <td>IN: Maximum number of bytes by which the maximum cache size can be decreased in any single step -- + * if applicable.</td> + * </tr> + * <tr> + * <td><em>int</em> <code>epochs_before_eviction</code></td> + * <td>IN: In the ageout based cache size reduction algorithms, this field contains the minimum number of + * epochs an entry must remain unaccessed in cache before the cache size reduction algorithm tries to evict + * it. 3 is a reasonable value.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_empty_reserve</code></td> + * <td>IN: Boolean flag indicating whether the ageout based decrement algorithms will maintain a empty + * reserve when decreasing cache size.</td> + * </tr> + * <tr> + * <td><em>double</em> <code>empty_reserve</code></td> + * <td>IN: Empty reserve as a fraction of maximum cache size if applicable.<p>When so directed, the ageout + * based algorithms will not decrease the maximum cache size unless the empty reserve can be met.</p><p>The + * parameter must lie in the interval [0.0, 1.0]. 0.1 or 0.05 is a good place to + * start.</p></td> + * </tr> + * </table> + * + * \par Parallel configuration fields + * <table> + * <tr> + * <td><em>int</em> <code>dirty_bytes_threshold</code></td> + * <td>IN: Threshold number of bytes of dirty metadata generation for triggering synchronizations of the + * metadata caches serving the target file in the parallel case.<p>Synchronization occurs whenever the number + * of bytes of dirty metadata created since the last synchronization exceeds this limit.</p><p>This field only + * applies to the parallel case. While it is ignored elsewhere, it can still draw a value out of bounds + * error.</p><p>It must be consistant across all caches on any given file.</p><p>By default, this field is set + * to 256 KB. It shouldn't be more than half the current maximum cache size times the minimum clean + * fraction.</p></td> + * </tr> + * </table> + * + * \since 1.8.0 + * + * \todo Fix the MDC document reference! */ H5_DLL herr_t H5Fset_mdc_config(hid_t file_id, H5AC_cache_config_t *config_ptr); /** * \ingroup MDC * - * \todo Finish this! + * \brief Obtains target file's metadata cache hit rate + * + * \file_id + * \param[out] hit_rate_ptr Pointer to the double in which the hit rate is returned. Note that + * \p hit_rate_ptr is undefined if the API call fails + * \return \herr_t + * + * \details H5Fget_mdc_hit_rate() queries the metadata cache of the target file to obtain its hit rate + * \Code{(cache hits / (cache hits + cache misses))} since the last time hit rate statistics + * were reset. If the cache has not been accessed since the last time the hit rate stats were + * reset, the hit rate is defined to be 0.0. + * + * The hit rate stats can be reset either manually (via H5Freset_mdc_hit_rate_stats()), or + * automatically. If the cache's adaptive resize code is enabled, the hit rate stats will be + * reset once per epoch. If they are reset manually as well, the cache may behave oddly. + * + * See the overview of the metadata cache in the special topics section of the user manual for + * details on the metadata cache and its adaptive resize algorithms. + * */ H5_DLL herr_t H5Fget_mdc_hit_rate(hid_t file_id, double *hit_rate_ptr); /** * \ingroup MDC * - * \todo Finish this! + * \brief Obtains current metadata cache size data for specified file + * + * \file_id + * \param[out] max_size_ptr Pointer to the location in which the current cache maximum size is to be + * returned, or NULL if this datum is not desired + * \param[out] min_clean_size_ptr Pointer to the location in which the current cache minimum clean + * size is to be returned, or NULL if that datum is not desired + * \param[out] cur_size_ptr Pointer to the location in which the current cache size is to be returned, + * or NULL if that datum is not desired + * \param[out] cur_num_entries_ptr Pointer to the location in which the current number of entries in + * the cache is to be returned, or NULL if that datum is not desired + * \returns \herr_t + * + * \details H5Fget_mdc_size() queries the metadata cache of the target file for the desired size + * information, and returns this information in the locations indicated by the pointer + * parameters. If any pointer parameter is NULL, the associated data is not returned. + * + * If the API call fails, the values returned via the pointer parameters are undefined. + * + * If adaptive cache resizing is enabled, the cache maximum size and minimum clean size + * may change at the end of each epoch. Current size and current number of entries can + * change on each cache access. + * + * Current size can exceed maximum size under certain conditions. See the overview of the + * metadata cache in the special topics section of the user manual for a discussion of this. + * */ H5_DLL herr_t H5Fget_mdc_size(hid_t file_id, size_t *max_size_ptr, size_t *min_clean_size_ptr, size_t *cur_size_ptr, int *cur_num_entries_ptr); /** * \ingroup MDC * - * \todo Finish this! + * \brief Resets hit rate statistics counters for the target file + * + * \file_id + * \returns \herr_t + * + * \details + * \parblock + * H5Freset_mdc_hit_rate_stats() resets the hit rate statistics counters in the metadata cache + * associated with the specified file. + * + * If the adaptive cache resizing code is enabled, the hit rate statistics are reset at the beginning + * of each epoch. This API call allows you to do the same thing from your program. + * + * The adaptive cache resizing code may behave oddly if you use this call when adaptive cache resizing + * is enabled. However, the call should be useful if you choose to control metadata cache size from your + * program. + * + * See "Metadata Caching in HDF5" for details about the metadata cache and the adaptive cache resizing + * algorithms. If you have not read, understood, and thought about the material covered in that + * documentation, + * you should not be using this API call. + * \endparblock + * + * \todo Fix the MDC document reference! */ H5_DLL herr_t H5Freset_mdc_hit_rate_stats(hid_t file_id); /** @@ -1067,13 +1579,118 @@ H5_DLL herr_t H5Fget_info2(hid_t obj_id, H5F_info2_t *file_info); /** * \ingroup SWMR * - * \todo Finish this! + * \brief Retrieves the collection of read retries for metadata entries with checksum + * + * \file_id + * \param[out] info Struct containing the collection of read retries for metadata + * entries with checksum + * \return \herr_t\n + * + * \details \Bold{Failure Modes:} + * \li When the input identifier is not a file identifier. + * \li When the pointer to the output structure is NULL. + * \li When the memory allocation for \p retries failed. + * + * \details H5Fget_metadata_read_retry_info() retrieves information regarding the number + * of read retries for metadata entries with checksum for the file \p file_id. + * This information is reported in the H5F_retry_info_t struct defined in + * H5Fpublic.h as follows: + * \snippet this H5F_retry_info_t_snip + * \c nbins is the number of bins for each \c retries[i] of metadata entry \c i. + * It is calculated based on the current number of read attempts used in the + * library and logarithmic base 10. + * + * If read retries are incurred for a metadata entry \c i, the library will + * allocate memory for \Code{retries[i] (nbins * sizeof(uint32_t)} and store + * the collection of retries there. If there are no retries for a metadata entry + * \c i, \Code{retries[i]} will be NULL. After a call to this routine, users should + * free each \Code{retries[i]} that is non-NULL, otherwise resource leak will occur. + * + * For the library default read attempts of 100 for SWMR access, nbins will be 2 + * as depicted below: + * \li \Code{retries[i][0]} is the number of 1 to 9 read retries. + * \li \Code{retries[i][1]} is the number of 10 to 99 read retries. + * For the library default read attempts of 1 for non-SWMR access, \c nbins will + * be 0 and each \Code{retries[i]} will be NULL. + * + * The following table lists the 21 metadata entries of \Code{retries[]}: + * <table> + * <tr> + * <th>Index for \Code{retries[]}</th> + * <th>Metadata entries<sup>*</sup></th> + * </tr> + * <tr><td>0</td><td>Object header (version 2)</td></tr> + * <tr><td>1</td><td>Object header chunk (version 2)</td></tr> + * <tr><td>2</td><td>B-tree header (version 2)</td></tr> + * <tr><td>3</td><td>B-tree internal node (version 2)</td></tr> + * <tr><td>4</td><td>B-tree leaf node (version 2)</td></tr> + * <tr><td>5</td><td>Fractal heap header</td></tr> + * <tr><td>6</td><td>Fractal heap direct block (optional checksum)</td></tr> + * <tr><td>7</td><td>Fractal heap indirect block</td></tr> + * <tr><td>8</td><td>Free-space header</td></tr> + * <tr><td>9</td><td>Free-space sections</td></tr> + * <tr><td>10</td><td>Shared object header message table</td></tr> + * <tr><td>11</td><td>Shared message record list</td></tr> + * <tr><td>12</td><td>Extensive array header</td></tr> + * <tr><td>13</td><td>Extensive array index block</td></tr> + * <tr><td>14</td><td>Extensive array super block</td></tr> + * <tr><td>15</td><td>Extensive array data block</td></tr> + * <tr><td>16</td><td>Extensive array data block page</td></tr> + * <tr><td>17</td><td>Fixed array super block</td></tr> + * <tr><td>18</td><td>Fixed array data block</td></tr> + * <tr><td>19</td><td>Fixed array data block page</td></tr> + * <tr><td>20</td><td>File's superblock (version 2)</td></tr> + * <tr><td colspan=2><sup>*</sup> All entries are of version 0 (zero) unless indicated otherwise.</td></tr> + * </table> + * + * \note On a system that is not atomic, the library might possibly read inconsistent + * metadata with checksum when performing single-writer/multiple-reader (SWMR) + * operations for an HDF5 file. Upon encountering such situations, the library + * will try reading the metadata again for a set number of times to attempt to + * obtain consistent data. The maximum number of read attempts used by the library + * will be either the value set via H5Pset_metadata_read_attempts() or the library + * default value when a value is not set.\n + * When the current number of metadata read attempts used in the library is unable + * to remedy the reading of inconsistent metadata on a system, the user can assess + * the information obtained via this routine to derive a different maximum value. + * The information can also be helpful for debugging purposes to identify potential + * issues with metadata flush dependencies and SWMR implementation in general. + * + * \since 1.10.0 + * */ H5_DLL herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info); /** * \ingroup SWMR * - * \todo Finish this! + * \brief Retrieves free-space section information for a file + * + * \file_id + * + * \return \herr_t + * + * \details H5Fstart_swmr_write() will activate SWMR writing mode for a file + * associated with \p file_id. This routine will prepare and ensure + * the file is safe for SWMR writing as follows: + * \li Check that the file is opened with write access (#H5F_ACC_RDWR). + * \li Check that the file is opened with the latest library format to + * ensure data structures with check-summed metadata are used. + * \li Check that the file is not already marked in SWMR writing mode. + * \li Enable reading retries for check-summed metadata to remedy + * possible checksum failures from reading inconsistent metadata + * on a system that is not atomic. + * \li Turn off usage of the library's accumulator to avoid possible + * ordering problem on a system that is not atomic. + * \li Perform a flush of the file’s data buffers and metadata to set + * a consistent state for starting SWMR write operations. + * + * Library objects are groups, datasets, and committed datatypes. For + * the current implementation, groups and datasets can remain open when + * activating SWMR writing mode, but not committed datatypes. Attributes + * attached to objects cannot remain open either. + * + * \since 1.10.0 + * */ H5_DLL herr_t H5Fstart_swmr_write(hid_t file_id); /** @@ -1174,19 +1791,141 @@ H5_DLL herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver /** * \ingroup MDC * - * \todo Finish this! + * \brief Starts logging metadata cache events if logging was previously enabled + * + * \file_id + * + * \return \herr_t + * + * \details The metadata cache is a central part of the HDF5 library through + * which all \Emph{file metadata} reads and writes take place. File + * metadata is normally invisible to the user and is used by the + * library for purposes such as locating and indexing data. File + * metadata should not be confused with user metadata, which consists + * of attributes created by users and attached to HDF5 objects such + * as datasets via H5A API calls. + * + * Due to the complexity of the cache, a trace/logging feature has been + * created that can be used by HDF5 developers for debugging and performance + * analysis. The functions that control this functionality will normally be + * of use to a very limited number of developers outside of The HDF Group. + * The functions have been documented to help users create logs that can + * be sent with bug reports. + * + * Control of the log functionality is straightforward. Logging is enabled + * via the H5Pset_mdc_log_options() function, which will modify the file + * access property list used to open or create a file. This function has + * a flag that determines whether logging begins at file open or starts + * in a paused state. Log messages can then be controlled via the + * H5Fstart_mdc_logging() and H5Fstop_mdc_logging() functions. + * H5Pget_mdc_log_options() can be used to examine a file access property + * list, and H5Fget_mdc_logging_status() will return the current state of + * the logging flags. + * + * The log format is described in the \Emph{Metadata Cache Logging} document. + * + * \note Logging can only be started or stopped if metadata cache logging was enabled + * via H5Pset_mdc_log_options().\n + * When enabled and currently logging, the overhead of the logging feature will + * almost certainly be significant.\n + * The log file is opened when the HDF5 file is opened or created and not when + * this function is called for the first time.\n + * This function opens the log file and starts logging metadata cache operations + * for a particular file. Calling this function when logging has already been + * enabled will be considered an error. + * + * \since 1.10.0 + * + * \todo Fix the document reference! + * */ H5_DLL herr_t H5Fstart_mdc_logging(hid_t file_id); /** * \ingroup MDC * - * \todo Finish this! + * \brief Stops logging metadata cache events if logging was previously enabled and is currently ongoing + * + * \file_id + * + * \return \herr_t + * + * \details The metadata cache is a central part of the HDF5 library through + * which all \Emph{file metadata} reads and writes take place. File + * metadata is normally invisible to the user and is used by the + * library for purposes such as locating and indexing data. File + * metadata should not be confused with user metadata, which consists + * of attributes created by users and attached to HDF5 objects such + * as datasets via H5A API calls. + * + * Due to the complexity of the cache, a trace/logging feature has been + * created that can be used by HDF5 developers for debugging and performance + * analysis. The functions that control this functionality will normally be + * of use to a very limited number of developers outside of The HDF Group. + * The functions have been documented to help users create logs that can + * be sent with bug reports. + * + * Control of the log functionality is straightforward. Logging is enabled + * via the H5Pset_mdc_log_options() function, which will modify the file + * access property list used to open or create a file. This function has + * a flag that determines whether logging begins at file open or starts + * in a paused state. Log messages can then be controlled via the + * H5Fstart_mdc_logging() and H5Fstop_mdc_logging() functions. + * H5Pget_mdc_log_options() can be used to examine a file access property + * list, and H5Fget_mdc_logging_status() will return the current state of + * the logging flags. + * + * The log format is described in the \Emph{Metadata Cache Logging} document. + * + * \note Logging can only be started or stopped if metadata cache logging was enabled + * via H5Pset_mdc_log_options().\n + * This function only suspends the logging operations. The log file will remain + * open and will not be closed until the HDF5 file is closed. + * + * \since 1.10.0 + * */ H5_DLL herr_t H5Fstop_mdc_logging(hid_t file_id); /** * \ingroup MDC * - * \todo Finish this! + * \brief Gets the current metadata cache logging status + * + * \file_id + * \param[out] is_enabled Whether logging is enabled + * \param[out] is_currently_logging Whether events are currently being logged + * \return \herr_t + * + * \details The metadata cache is a central part of the HDF5 library through + * which all \Emph{file metadata} reads and writes take place. File + * metadata is normally invisible to the user and is used by the + * library for purposes such as locating and indexing data. File + * metadata should not be confused with user metadata, which consists + * of attributes created by users and attached to HDF5 objects such + * as datasets via H5A API calls. + * + * Due to the complexity of the cache, a trace/logging feature has been + * created that can be used by HDF5 developers for debugging and performance + * analysis. The functions that control this functionality will normally be + * of use to a very limited number of developers outside of The HDF Group. + * The functions have been documented to help users create logs that can + * be sent with bug reports. + * + * Control of the log functionality is straightforward. Logging is enabled + * via the H5Pset_mdc_log_options() function, which will modify the file + * access property list used to open or create a file. This function has + * a flag that determines whether logging begins at file open or starts + * in a paused state. Log messages can then be controlled via the + * H5Fstart_mdc_logging() and H5Fstop_mdc_logging() functions. + * H5Pget_mdc_log_options() can be used to examine a file access property + * list, and H5Fget_mdc_logging_status() will return the current state of + * the logging flags. + * + * The log format is described in the \Emph{Metadata Cache Logging} document. + * + * \note Unlike H5Fstart_mdc_logging() and H5Fstop_mdc_logging(), this function can + * be called on any open file identifier. + * + * \since 1.10.0 */ H5_DLL herr_t H5Fget_mdc_logging_status(hid_t file_id, /*OUT*/ hbool_t *is_enabled, @@ -1245,7 +1984,32 @@ H5_DLL herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2], /** * \ingroup MDC * - * \todo Finish this! + * \brief Obtains information about a cache image if it exists + * + * \file_id + * \param[out] image_addr Offset of the cache image if it exists, or #HADDR_UNDEF if it does not + * \param[out] image_size Length of the cache image if it exists, or 0 if it does not + * \returns \herr_t + * + * \details + * \parblock + * H5Fget_mdc_image_info() returns information about a cache image if it exists. + * + * When an HDF5 file is opened in Read/Write mode, any metadata cache image will + * be read and deleted from the file on the first metadata cache access (or, if + * persistent free space managers are enabled, on the first file space + * allocation / deallocation, or read of free space manager status, whichever + * comes first). + * + * Thus, if the file is opened Read/Write, H5Fget_mdc_image_info() should be called + * immediately after file open and before any other operation. If H5Fget_mdc_image_info() + * is called after the cache image is loaded, it will correctly report that no cache image + * exists, as the image will have already been read and deleted from the file. In the Read Only + * case, the function may be called at any time, as any cache image will not be deleted + * from the file. + * \endparblock + * + * \since 1.10.1 */ H5_DLL herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t *image_size); /** @@ -1307,13 +2071,91 @@ H5_DLL herr_t H5Fset_dset_no_attrs_hint(hid_t file_id, hbool_t minimize); /** * \ingroup PH5F * - * \todo Finish this! + * \brief Sets the MPI atomicity mode + * + * \file_id + * \param[in] flag Logical flag for atomicity setting. Valid values are: + * \li \c 1 -- Sets MPI file access to atomic mode. + * \li \c 0 -- Sets MPI file access to nonatomic mode. + * \returns \herr_t + * + * \par Motivation + * H5Fset_mpi_atomicity() is applicable only in parallel environments using MPI I/O. + * The function is one of the tools used to ensure sequential consistency. This means + * that a set of operations will behave as though they were performed in a serial + * order consistent with the program order. + * + * \details + * \parblock + * H5Fset_mpi_atomicity() sets MPI consistency semantics for data access to the file, + * \p file_id. + * + * If \p flag is set to \c 1, all file access operations will appear atomic, guaranteeing + * sequential consistency. If \p flag is set to \c 0, enforcement of atomic file access + * will be turned off. + * + * H5Fset_mpi_atomicity() is a collective function and all participating processes must + * pass the same values for \p file_id and \p flag. + * + * This function is available only when the HDF5 library is configured with parallel support + * (\Code{--enable-parallel}). It is useful only when used with the #H5FD_MPIO driver + * (see H5Pset_fapl_mpio()). + * \endparblock + * + * \attention + * \parblock + * H5Fset_mpi_atomicity() calls \Code{MPI_File_set_atomicity} underneath and is not supported + * if the execution platform does not support \Code{MPI_File_set_atomicity}. When it is + * supported and used, the performance of data access operations may drop significantly. + * + * In certain scenarios, even when \Code{MPI_File_set_atomicity} is supported, setting + * atomicity with H5Fset_mpi_atomicity() and \p flag set to 1 does not always yield + * strictly atomic updates. For example, some H5Dwrite() calls translate to multiple + * \Code{MPI_File_write_at} calls. This happens in all cases where the high-level file + * access routine translates to multiple lower level file access routines. + * The following scenarios will raise this issue: + * \li Non-contiguous file access using independent I/O + * \li Partial collective I/O using chunked access + * \li Collective I/O using filters or when data conversion is required + * + * This issue arises because MPI atomicity is a matter of MPI file access operations rather + * than HDF5 access operations. But the user is normally seeking atomicity at the HDF5 level. + * To accomplish this, the application must set a barrier after a write, H5Dwrite(), but before + * the next read, H5Dread(), in addition to calling H5Fset_mpi_atomicity().The barrier will + * guarantee that all underlying write operations execute atomically before the read + * operations starts. This ensures additional ordering semantics and will normally produce + * the desired behavior. + * \endparblock + * + * \see Enabling a Strict Consistency Semantics Model in Parallel HDF5 + * + * \since 1.8.9 + * + * \todo Fix the reference! */ H5_DLL herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag); /** * \ingroup PH5F * - * \todo Finish this! + * \brief Retrieves the atomicity mode in use + * + * \file_id + * \param[out] flag Logical flag for atomicity setting. Valid values are: + * \li 1 -- MPI file access is set to atomic mode. + * \li 0 -- MPI file access is set to nonatomic mode. + * \returns \herr_t + * + * \details H5Fget_mpi_atomicity() retrieves the current consistency semantics mode for + * data access for the file \p file_id. + * + * Upon successful return, \p flag will be set to \c 1 if file access is set + * to atomic mode and \c 0 if file access is set to nonatomic mode. + * + * \see Enabling a Strict Consistency Semantics Model in Parallel HDF5 + * + * \since 1.8.9 + * + * \todo Fix the reference! */ H5_DLL herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag); #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Imodule.h b/src/H5Imodule.h index 768fa81..7fc6af0 100644 --- a/src/H5Imodule.h +++ b/src/H5Imodule.h @@ -29,4 +29,9 @@ #define H5_MY_PKG_ERR H5E_ATOM #define H5_MY_PKG_INIT NO +/**\defgroup H5I H5I + * \brief Identifier Interface + * \todo Describe concisely what the functions in this module are about. + */ + #endif /* _H5Imodule_H */ diff --git a/src/H5Ipublic.h b/src/H5Ipublic.h index 2b8a978..f981d2e2 100644 --- a/src/H5Ipublic.h +++ b/src/H5Ipublic.h @@ -21,34 +21,36 @@ /* Public headers needed by this file */ #include "H5public.h" -/* - * Library type values. Start with `1' instead of `0' because it makes the - * tracing output look better when hid_t values are large numbers. Change the - * TYPE_BITS in H5I.c if the MAXID gets larger than 32 (an assertion will - * fail otherwise). +/** + * Library type values. + * \internal Library type values. Start with `1' instead of `0' because it + * makes the tracing output look better when hid_t values are large + * numbers. Change the TYPE_BITS in H5I.c if the MAXID gets larger + * than 32 (an assertion will fail otherwise). * - * When adding types here, add a section to the 'misc19' test in test/tmisc.c - * to verify that the H5I{inc|dec|get}_ref() routines work correctly with it. + * When adding types here, add a section to the 'misc19' test in + * test/tmisc.c to verify that the H5I{inc|dec|get}_ref() routines + * work correctly with it. \endinternal */ typedef enum H5I_type_t { - H5I_UNINIT = (-2), /* uninitialized type */ - H5I_BADID = (-1), /* invalid Type */ - H5I_FILE = 1, /* type ID for File objects */ - H5I_GROUP, /* type ID for Group objects */ - H5I_DATATYPE, /* type ID for Datatype objects */ - H5I_DATASPACE, /* type ID for Dataspace objects */ - H5I_DATASET, /* type ID for Dataset objects */ - H5I_MAP, /* type ID for Map objects */ - H5I_ATTR, /* type ID for Attribute objects */ - H5I_VFL, /* type ID for virtual file layer */ - H5I_VOL, /* type ID for virtual object layer */ - H5I_GENPROP_CLS, /* type ID for generic property list classes */ - H5I_GENPROP_LST, /* type ID for generic property lists */ - H5I_ERROR_CLASS, /* type ID for error classes */ - H5I_ERROR_MSG, /* type ID for error messages */ - H5I_ERROR_STACK, /* type ID for error stacks */ - H5I_SPACE_SEL_ITER, /* type ID for dataspace selection iterator */ - H5I_NTYPES /* number of library types, MUST BE LAST! */ + H5I_UNINIT = (-2), /**< uninitialized type */ + H5I_BADID = (-1), /**< invalid Type */ + H5I_FILE = 1, /**< type ID for File objects */ + H5I_GROUP, /**< type ID for Group objects */ + H5I_DATATYPE, /**< type ID for Datatype objects */ + H5I_DATASPACE, /**< type ID for Dataspace objects */ + H5I_DATASET, /**< type ID for Dataset objects */ + H5I_MAP, /**< type ID for Map objects */ + H5I_ATTR, /**< type ID for Attribute objects */ + H5I_VFL, /**< type ID for virtual file layer */ + H5I_VOL, /**< type ID for virtual object layer */ + H5I_GENPROP_CLS, /**< type ID for generic property list classes */ + H5I_GENPROP_LST, /**< type ID for generic property lists */ + H5I_ERROR_CLASS, /**< type ID for error classes */ + H5I_ERROR_MSG, /**< type ID for error messages */ + H5I_ERROR_STACK, /**< type ID for error stacks */ + H5I_SPACE_SEL_ITER, /**< type ID for dataspace selection iterator */ + H5I_NTYPES /**< number of library types, MUST BE LAST! */ } H5I_type_t; /* Type of IDs to return to users */ @@ -59,13 +61,18 @@ typedef int64_t hid_t; #define PRIXHID PRIX64 #define PRIoHID PRIo64 -#define H5_SIZEOF_HID_T H5_SIZEOF_INT64_T +/** + * The size of identifiers + */ +#define H5_SIZEOF_HID_T H5_SIZEOF_INT64_T -/* An invalid object ID. This is also negative for error return. */ -#define H5I_INVALID_HID (-1) +/** + * An invalid object ID. This is also negative for error return. + */ +#define H5I_INVALID_HID (-1) -/* - * Function for freeing objects. This function will be called with an object +/** + * A function for freeing objects. This function will be called with an object * ID type number and a pointer to the object. The function should free the * object and return non-negative to indicate that the object * can be removed from the ID type. If the function returns negative @@ -73,11 +80,19 @@ typedef int64_t hid_t; */ typedef herr_t (*H5I_free_t)(void *); -/* Type of the function to compare objects & keys */ +/** + * The type of a function to compare objects & keys + */ +//! [H5I_search_func_t_snip] typedef int (*H5I_search_func_t)(void *obj, hid_t id, void *key); +//! [H5I_search_func_t_snip] -/* Type of the H5Iiterate callback function */ +/** + * The type of H5Iiterate() callback functions + */ +//! [H5I_iterate_func_t_snip] typedef herr_t (*H5I_iterate_func_t)(hid_t id, void *udata); +//! [H5I_iterate_func_t_snip] #ifdef __cplusplus extern "C" { @@ -85,25 +100,561 @@ extern "C" { /* Public API functions */ +/** + * \ingroup H5I + * + * \brief Registers an object under a type and returns an ID for it + * + * \param[in] type The identifier of the type of the new ID + * \param[in] object Pointer to object for which a new ID is created + * + * \return \hid_t{object} + * + * \details H5Iregister() allocates and returns a new ID for an object. + * + * \details The \p type parameter is the identifier for the ID type to which + * this new ID will belong. This identifier must have been created by + * a call to H5Iregister_type(). + * + * \details The \p object parameter is a pointer to the memory which the new ID + * will be a reference to. This pointer will be stored by the library + * and returned via a call to H5Iobject_verify(). + * + */ H5_DLL hid_t H5Iregister(H5I_type_t type, const void *object); +/** + * \ingroup H5I + * + * \brief Returns the object referenced by an ID + * + * \param[in] id ID to be dereferenced + * \param[in] id_type The identifier type + + * + * \return Pointer to the object referenced by \p id on success, NULL on failure. + * + * \details H5Iobject_verify() returns a pointer to the memory referenced by id + * after verifying that \p id is of type \p id_type. This function is + * analogous to dereferencing a pointer in C with type checking. + * + * \note H5Iobject_verify() does not change the ID it is called on in any way + * (as opposed to H5Iremove_verify(), which removes the ID from its + * type’s hash table). + * + * \see H5Iregister() + * + */ H5_DLL void * H5Iobject_verify(hid_t id, H5I_type_t id_type); +/** + * \ingroup H5I + * + * \brief Removes an ID from its type + * + * \param[in] id The ID to be removed from its type + * \param[in] id_type The identifier type + + * + * \return Returns a pointer to the memory referred to by \p id on success, + * NULL on failure. + * + * \details H5Iremove_verify() first ensures that \p id belongs to \p id_type. + * If so, it removes \p id from its type and returns the pointer + * to the memory it referred to. This pointer is the same pointer that + * was placed in storage by H5Iregister(). If id does not belong to + * \p id_type, then NULL is returned. + * + * The \p id parameter is the ID which is to be removed from its type. + * + * The \p type parameter is the identifier for the ID type which \p id + * is supposed to belong to. This identifier must have been created by + * a call to H5Iregister_type(). + * + * \note This function does NOT deallocate the memory that \p id refers to. + * The pointer returned by H5Iregister() must be deallocated by the user + * to avoid memory leaks. + * + */ H5_DLL void * H5Iremove_verify(hid_t id, H5I_type_t id_type); +/** + * \ingroup H5I + * + * \brief Retrieves the type of an object + * + * \obj_id{id} + * + * \return Returns the object type if successful; otherwise #H5I_BADID. + * + * \details H5Iget_type() retrieves the type of the object identified by + * \p id. + * + * Valid types returned by the function are: + * \id_types + * + * If no valid type can be determined or the identifier submitted is + * invalid, the function returns #H5I_BADID. + * + * This function is of particular use in determining the type of + * object closing function (H5Dclose(), H5Gclose(), etc.) to call + * after a call to H5Rdereference(). + * + * \note Note that this function returns only the type of object that \p id + * would identify if it were valid; it does not determine whether \p id + * is valid identifier. Validity can be determined with a call to + * H5Iis_valid(). + * + */ H5_DLL H5I_type_t H5Iget_type(hid_t id); +/** + * \ingroup H5I + * + * \brief Retrieves an identifier for the file containing the specified object + * + * \obj_id{id} + * + * \return \hid_t{file} + * + * \details H5Iget_file_id() returns the identifier of the file associated with + * the object referenced by \p id. + * + * \note Note that the HDF5 library permits an application to close a file + * while objects within the file remain open. If the file containing the + * object \p id is still open, H5Iget_file_id() will retrieve the + * existing file identifier. If there is no existing file identifier for + * the file, i.e., the file has been closed, H5Iget_file_id() will reopen + * the file and return a new file identifier. In either case, the file + * identifier must eventually be released using H5Fclose(). + * + * \since 1.6.3 + * + */ H5_DLL hid_t H5Iget_file_id(hid_t id); +/** + * \ingroup H5I + * + * \brief Retrieves a name of an object based on the object identifier + * + * \obj_id{id} + * \param[out] name A buffer for thename associated with the identifier + * \param[in] size The size of the \p name buffer; usually the size of + * the name in bytes plus 1 for a NULL terminator + * + * \return ssize_t + * + * \details H5Iget_name() retrieves a name for the object identified by \p id. + * + * \details Up to size characters of the name are returned in \p name; + * additional characters, if any, are not returned to the user + * application. + * + * If the length of the name, which determines the required value of + * \p size, is unknown, a preliminary H5Iget_name() call can be made. + * The return value of this call will be the size in bytes of the + * object name. That value, plus 1 for a NULL terminator, is then + * assigned to size for a second H5Iget_name() call, which will + * retrieve the actual name. + * + * If the object identified by \p id is an attribute, as determined + * via H5Iget_type(), H5Iget_name() retrieves the name of the object + * to which that attribute is attached. To retrieve the name of the + * attribute itself, use H5Aget_name(). + * + * If there is no name associated with the object identifier or if the + * name is NULL, H5Iget_name() returns 0 (zero). + * + * \note Note that an object in an HDF5 file may have multiple paths if there + * are multiple links pointing to it. This function may return any one of + * these paths. When possible, H5Iget_name() returns the path with which + * the object was opened. + * + * \since 1.6.0 + * + */ H5_DLL ssize_t H5Iget_name(hid_t id, char *name /*out*/, size_t size); +/** + * \ingroup H5I + * + * \brief Increments the reference count for an object + * + * \obj_id{id} + * + * \return Returns a non-negative reference count of the object ID after + * incrementing it if successful; otherwise a negative value is + * returned. + * + * \details H5Iinc_ref() increments the reference count of the object + * identified by \p id. + * + * The reference count for an object ID is attached to the information + * about an object in memory and has no relation to the number of + * links to an object on disk. + * + * The reference count for a newly created object will be 1. Reference + * counts for objects may be explicitly modified with this function or + * with H5Idec_ref(). When an object ID's reference count reaches + * zero, the object will be closed. Calling an object ID's \c close + * function decrements the reference count for the ID which normally + * closes the object, but if the reference count for the ID has been + * incremented with this function, the object will only be closed when + * the reference count reaches zero with further calls to H5Idec_ref() + * or the object ID's \c close function. + * + * If the object ID was created by a collective parallel call (such as + * H5Dcreate(), H5Gopen(), etc.), the reference count should be + * modified by all the processes which have copies of the ID. + * Generally this means that group, dataset, attribute, file and named + * datatype IDs should be modified by all the processes and that all + * other types of IDs are safe to modify by individual processes. + * + * This function is of particular value when an application is + * maintaining multiple copies of an object ID. The object ID can be + * incremented when a copy is made. Each copy of the ID can then be + * safely closed or decremented and the HDF5 object will be closed + * when the reference count for that that object drops to zero. + * + * \since 1.6.2 + * + */ H5_DLL int H5Iinc_ref(hid_t id); +/** + * \ingroup H5I + * + * \brief Decrements the reference count for an object + * + * \obj_id{id} + * + * \return Returns a non-negative reference count of the object ID after + * decrementing it, if successful; otherwise a negative value is + * returned. + * + * \details H5Idec_ref() decrements the reference count of the object + * identified by \p id. + * + * The reference count for an object ID is attached to the information + * about an object in memory and has no relation to the number of + * links to an object on disk. + * + * The reference count for a newly created object will be 1. Reference + * counts for objects may be explicitly modified with this function or + * with H5Iinc_ref(). When an object identifier’s reference count + * reaches zero, the object will be closed. Calling an object + * identifier’s \c close function decrements the reference count for + * the identifier which normally closes the object, but if the + * reference count for the identifier has been incremented with + * H5Iinc_ref(), the object will only be closed when the reference + * count reaches zero with further calls to this function or the + * object identifier’s \c close function. + * + * If the object ID was created by a collective parallel call (such as + * H5Dcreate(), H5Gopen(), etc.), the reference count should be + * modified by all the processes which have copies of the ID. + * Generally this means that group, dataset, attribute, file and named + * datatype IDs should be modified by all the processes and that all + * other types of IDs are safe to modify by individual processes. + * + * This function is of particular value when an application is + * maintaining multiple copies of an object ID. The object ID can be + * incremented when a copy is made. Each copy of the ID can then be + * safely closed or decremented and the HDF5 object will be closed + * when the reference count for that that object drops to zero. + * + * \since 1.6.2 + * + */ H5_DLL int H5Idec_ref(hid_t id); +/** + * \ingroup H5I + * + * \brief Retrieves the reference count for an object + * + * \obj_id{id} + * + * \return Returns a non-negative current reference count of the object + * identifier if successful; otherwise a negative value is returned. + * + * \details H5Iget_ref() retrieves the reference count of the object identified + * by \p id. + * + * The reference count for an object identifier is attached to the + * information about an object in memory and has no relation to the + * number of links to an object on disk. + * + * The function H5Iis_valid() is used to determine whether a specific + * object identifier is valid. + * + * \since 1.6.2 + * + */ H5_DLL int H5Iget_ref(hid_t id); +/** + * \ingroup H5I + * + * \brief Creates and returns a new ID type + * + * \param[in] hash_size Minimum hash table size (in entries) used to store IDs + * for the new type + * \param[in] reserved Number of reserved IDs for the new type + * \param[in] free_func Function used to deallocate space for a single ID + * + * \return Returns the type identifier on success, negative on failure. + * + * \details H5Iregister_type() allocates space for a new ID type and returns an + * identifier for it. + * + * The \p hash_size parameter indicates the minimum size of the hash + * table used to store IDs in the new type. + * + * The \p reserved parameter indicates the number of IDs in this new + * type to be reserved. Reserved IDs are valid IDs which are not + * associated with any storage within the library. + * + * The \p free_func parameter is a function pointer to a function + * which returns an herr_t and accepts a \c void*. The purpose of this + * function is to deallocate memory for a single ID. It will be called + * by H5Iclear_type() and H5Idestroy_type() on each ID. This function + * is NOT called by H5Iremove_verify(). The \c void* will be the same + * pointer which was passed in to the H5Iregister() function. The \p + * free_func function should return 0 on success and -1 on failure. + * + */ H5_DLL H5I_type_t H5Iregister_type(size_t hash_size, unsigned reserved, H5I_free_t free_func); +/** + * \ingroup H5I + * + * \brief Deletes all identifiers of the given type + * + * \param[in] type Identifier of identifier type which is to be cleared of identifiers + * \param[in] force Whether or not to force deletion of all identifiers + * + * \return \herr_t + * + * \details H5Iclear_type() deletes all identifiers of the type identified by + * the argument \p type. + * + * The identifier type's free function is first called on all of these + * identifiers to free their memory, then they are removed from the + * type. + * + * If the \p force flag is set to false, only those identifiers whose + * reference counts are equal to 1 will be deleted, and all other + * identifiers will be entirely unchanged. If the force flag is true, + * all identifiers of this type will be deleted. + * + */ H5_DLL herr_t H5Iclear_type(H5I_type_t type, hbool_t force); +/** + * \ingroup H5I + * + * \brief Removes an identifier type and all identifiers within that type + * + * \param[in] type Identifier of identifier type which is to be destroyed + * + * \return \herr_t + * + * \details H5Idestroy_type deletes an entire identifier type \p type. All + * identifiers of this type are destroyed and no new identifiers of + * this type can be registered. + * + * The type’s free function is called on all of the identifiers which + * are deleted by this function, freeing their memory. In addition, + * all memory used by this type’s hash table is freed. + * + * Since the H5I_type_t values of destroyed identifier types are + * reused when new types are registered, it is a good idea to set the + * variable holding the value of the destroyed type to #H5I_UNINIT. + * + */ H5_DLL herr_t H5Idestroy_type(H5I_type_t type); +/** + * \ingroup H5I + * + * \brief Increments the reference count on an ID type + * + * \param[in] type The identifier of the type whose reference count is to be incremented + * + * \return Returns the current reference count on success, negative on failure. + * + * \details 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. + * + * The type parameter is the identifier for the ID type whose + * reference count is to be incremented. This identifier must have + * been created by a call to H5Iregister_type(). + * + */ H5_DLL int H5Iinc_type_ref(H5I_type_t type); +/** + * \ingroup H5I + * + * \brief Decrements the reference count on an identifier type + * + * \param[in] type The identifier of the type whose reference count is to be decremented + * + * \return Returns the current reference count on success, negative on failure. + * + * \details 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. + * + * The type parameter is the identifier for the identifier type whose + * reference count is to be decremented. This identifier must have + * been created by a call to H5Iregister_type(). + * + */ H5_DLL int H5Idec_type_ref(H5I_type_t type); +/** + * \ingroup H5I + * + * \brief Retrieves the reference count on an ID type + * + * \param[in] type The identifier of the type whose reference count is to be retieved + * + * \return Returns the current reference count on success, negative on failure. + * + * \details 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. + * + * The type parameter is the identifier for the ID type whose + * reference count is to be retrieved. This identifier must have been + * created by a call to H5Iregister_type(). + * + */ H5_DLL int H5Iget_type_ref(H5I_type_t type); +/** + * \ingroup H5I + * + * \brief Finds the memory referred to by an ID within the given ID type such + * that some criterion is satisfied + * + * \param[in] type The identifier of the type to be searched + * \param[in] func The function defining the search criteria + * \param[in] key A key for the search function + * + * \return Returns a pointer to the object which satisfies the search function + * on success, NULL on failure. + * + * \details H5Isearch() searches through a given ID type to find an object that + * satisfies the criteria defined by \p func. If such an object is + * found, the pointer to the memory containing this object is + * returned. Otherwise, NULL is returned. To do this, \p func is + * called on every member of type \p type. The first member to satisfy + * \p func is returned. + * + * The \p type parameter is the identifier for the ID type which is to + * be searched. This identifier must have been created by a call to + * H5Iregister_type(). + * + * The parameter \p func is a function pointer to a function which + * takes three parameters. The first parameter is a \c void* and will + * be a pointer to the object to be tested. This is the same object + * that was placed in storage using H5Iregister(). The second + * parameter is a hid_t and is the ID of the object to be tested. The + * last parameter is a \c void*. This is the \p key parameter and can + * be used however the user finds helpful, or it can be ignored if it + * is not needed. \p func returns 0 if the object it is testing does + * not pass its criteria. A non-zero value should be returned if the + * object does pass its criteria. H5I_search_func_t is defined in + * H5Ipublic.h and is shown below. + * \snippet this H5I_search_func_t_snip + * The \p key parameter will be passed to the search function as a + * parameter. It can be used to further define the search at run-time. + * + */ H5_DLL void * H5Isearch(H5I_type_t type, H5I_search_func_t func, void *key); +/** + * \ingroup H5I + * + * \brief Calls a callback for each member of the identifier type specified + * + * \param[in] type The identifier type + * \param[in] op The callback function + * \param[in,out] op_data The data for the callback function + * + * \return The last value returned by \p op + * + * \details H5Iiterate() calls the callback function \p op for each member of + * the identifier type \p type. The callback function type for \p op, + * H5I_iterate_func_t, is defined in H5Ipublic.h as: + * \snippet this H5I_iterate_func_t_snip + * \p op takes as parameters the identifier and a pass through of + * \p op_data, and returns an herr_t. + * + * A positive return from op will cause the iteration to stop and + * H5Iiterate() will return the value returned by \p op. A negative + * return from \p op will cause the iteration to stop and H5Iiterate() + * will return failure. A zero return from \p op will allow iteration + * to continue, as long as there are other identifiers remaining in + * type. + * + * \since 1.12.0 + * + */ H5_DLL herr_t H5Iiterate(H5I_type_t type, H5I_iterate_func_t op, void *op_data); +/** + * \ingroup H5I + * + * \brief Returns the number of identifiers in a given identifier type + * + * \param[in] type The identifier type + * \param[out] num_members Number of identifiers of the specified identifier type + * + * \return \herr_t + * + * \details H5Inmembers() returns the number of identifiers of the identifier + * type specified in \p type. + * + * The number of identifiers is returned in \p num_members. If no + * identifiers of this type have been registered, the type does not + * exist, or it has been destroyed, \p num_members is returned with + * the value 0. + * + */ H5_DLL herr_t H5Inmembers(H5I_type_t type, hsize_t *num_members); +/** + * \ingroup H5I + * + * \brief Determines whether an identifier type is registered + * + * \param[in] type Identifier type + * + * \return \htri_t + * + * \details H5Itype_exists() determines whether the given identifier type, + * \p type, is registered with the library. + * + * \since 1.8.0 + * + */ H5_DLL htri_t H5Itype_exists(H5I_type_t type); +/** + * \ingroup H5I + * + * \brief Determines whether an identifier is valid + * + * \obj_id{id} + * + * \return \htri_t + * + * \details H5Iis_valid() determines whether the identifier \p id is valid. + * + * \details Valid identifiers are those that have been obtained by an + * application and can still be used to access the original target. + * Examples of invalid identifiers include: + * \li Out of range values: negative, for example + * \li Previously-valid identifiers that have been released: + * for example, a dataset identifier for which the dataset has + * been closed + * + * H5Iis_valid() can be used with any type of identifier: object + * identifier, property list identifier, attribute identifier, error + * message identifier, etc. When necessary, a call to H5Iget_type() + * can determine the type of the object that \p id identifies. + * + * \since 1.8.3 + * + */ H5_DLL htri_t H5Iis_valid(hid_t id); #ifdef __cplusplus diff --git a/src/H5Lmodule.h b/src/H5Lmodule.h index 043a865..ad737d6 100644 --- a/src/H5Lmodule.h +++ b/src/H5Lmodule.h @@ -29,4 +29,12 @@ #define H5_MY_PKG_ERR H5E_LINK #define H5_MY_PKG_INIT YES +/**\defgroup H5L H5L + * \brief Link Interface + * \todo Describe concisely what the functions in this module are about. + * + * \defgroup TRAV Link Traversal + * \ingroup H5L + */ + #endif /* _H5Lmodule_H */ diff --git a/src/H5Lpublic.h b/src/H5Lpublic.h index be920c2..14975bc 100644 --- a/src/H5Lpublic.h +++ b/src/H5Lpublic.h @@ -34,14 +34,21 @@ /* Public Macros */ /*****************/ -/* Maximum length of a link's name */ -/* (encoded in a 32-bit unsigned integer) */ +/** + * \brief Maximum length of a link's name + * + * The maximum length of a link's name is encoded in a 32-bit unsigned integer. + */ #define H5L_MAX_LINK_NAME_LEN ((uint32_t)(-1)) /* (4GB - 1) */ -/* Macro to indicate operation occurs on same location */ +/** + * \brief Macro to indicate operation occurs on same location + */ #define H5L_SAME_LOC (hid_t)0 -/* Current version of the H5L_class_t struct */ +/** + * \brief Current version of the H5L_class_t struct + */ #define H5L_LINK_CLASS_T_VERS 1 #ifdef __cplusplus @@ -52,91 +59,128 @@ extern "C" { /* Public Typedefs */ /*******************/ -/* Link class types. - * Values less than 64 are reserved for the HDF5 library's internal use. - * Values 64 to 255 are for "user-defined" link class types; these types are - * defined by HDF5 but their behavior can be overridden by users. - * Users who want to create new classes of links should contact the HDF5 - * development team at help@hdfgroup.org. - * These values can never change because they appear in HDF5 files. +/** + * \brief Link class types. + * + * Values less than 64 are reserved for the HDF5 library's internal use. Values + * 64 to 255 are for "user-defined" link class types; these types are defined + * by HDF5 but their behavior can be overridden by users. Users who want to + * create new classes of links should contact the HDF5 development team at + * mailto:help@hdfgroup.org. These values can never change because they appear + * in HDF5 files. */ typedef enum { - H5L_TYPE_ERROR = (-1), /* Invalid link type id */ - H5L_TYPE_HARD = 0, /* Hard link id */ - H5L_TYPE_SOFT = 1, /* Soft link id */ - H5L_TYPE_EXTERNAL = 64, /* External link id */ - H5L_TYPE_MAX = 255 /* Maximum link type id */ + H5L_TYPE_ERROR = (-1), /**< Invalid link type id */ + H5L_TYPE_HARD = 0, /**< Hard link id */ + H5L_TYPE_SOFT = 1, /**< Soft link id */ + H5L_TYPE_EXTERNAL = 64, /**< External link id */ + H5L_TYPE_MAX = 255 /**< Maximum link type id */ } H5L_type_t; -/* Maximum value link value for "built-in" link types */ +/** + * \brief Maximum value link value for "built-in" link types + */ #define H5L_TYPE_BUILTIN_MAX H5L_TYPE_SOFT -/* Link ids at or above this value are "user-defined" link types. */ -#define H5L_TYPE_UD_MIN H5L_TYPE_EXTERNAL +/** + * \brief Link ids at or above this value are "user-defined" link types. + */ +#define H5L_TYPE_UD_MIN H5L_TYPE_EXTERNAL +/** + * \brief Maximum link id value for "user-defined" link types. + */ +#define H5L_TYPE_UD_MAX H5L_TYPE_MAX -/* Information struct for link (for H5Lget_info2/H5Lget_info_by_idx2) - * H5O_token_t version used in VOL layer and future public API calls +/** + * \brief Information struct for links */ +//! [H5L_info2_t_snip] typedef struct { - H5L_type_t type; /* Type of link */ - hbool_t corder_valid; /* Indicate if creation order is valid */ - int64_t corder; /* Creation order */ - H5T_cset_t cset; /* Character set of link name */ + H5L_type_t type; /**< Type of link */ + hbool_t corder_valid; /**< Indicate if creation order is valid */ + int64_t corder; /**< Creation order */ + H5T_cset_t cset; /**< Character set of link name */ union { - H5O_token_t token; /* Token of location that hard link points to */ - size_t val_size; /* Size of a soft link or UD link value */ + H5O_token_t token; /**< Token of location that hard link points to */ + size_t val_size; /**< Size of a soft link or user-defined link value */ } u; } H5L_info2_t; +//! [H5L_info2_t_snip] /* The H5L_class_t struct can be used to override the behavior of a * "user-defined" link class. Users should populate the struct with callback * functions defined below. */ /* Callback prototypes for user-defined links */ -/* Link creation callback */ -typedef herr_t (*H5L_create_func_t)(const char *link_name, hid_t loc_group, const void *lnkdata, - size_t lnkdata_size, hid_t lcpl_id); - -/* Callback for when the link is moved */ -typedef herr_t (*H5L_move_func_t)(const char *new_name, hid_t new_loc, const void *lnkdata, - size_t lnkdata_size); - -/* Callback for when the link is copied */ -typedef herr_t (*H5L_copy_func_t)(const char *new_name, hid_t new_loc, const void *lnkdata, - size_t lnkdata_size); - -/* Callback during link traversal */ -typedef hid_t (*H5L_traverse_func_t)(const char *link_name, hid_t cur_group, const void *lnkdata, - size_t lnkdata_size, hid_t lapl_id, hid_t dxpl_id); - -/* Callback for when the link is deleted */ -typedef herr_t (*H5L_delete_func_t)(const char *link_name, hid_t file, const void *lnkdata, - size_t lnkdata_size); - -/* Callback for querying the link */ -/* Returns the size of the buffer needed */ -typedef ssize_t (*H5L_query_func_t)(const char *link_name, const void *lnkdata, size_t lnkdata_size, - void *buf /*out*/, size_t buf_size); +/** + * \brief Link creation callback + */ +typedef herr_t (*H5L_create_func_t)(const char *link_name, hid_t loc_group, + const void *lnkdata, size_t lnkdata_size, hid_t lcpl_id); +/** + * \brief Callback for link move + */ +typedef herr_t (*H5L_move_func_t)(const char *new_name, hid_t new_loc, + const void *lnkdata, size_t lnkdata_size); +/** + * \brief Callback for link copy + */ +typedef herr_t (*H5L_copy_func_t)(const char *new_name, hid_t new_loc, + const void *lnkdata, size_t lnkdata_size); +/** + * \brief Callback during link traversal + */ +typedef hid_t (*H5L_traverse_func_t)(const char *link_name, hid_t cur_group, + const void *lnkdata, size_t lnkdata_size, hid_t lapl_id, hid_t dxpl_id); +/** + * \brief Callback for link deletion + */ +typedef herr_t (*H5L_delete_func_t)(const char *link_name, hid_t file, + const void *lnkdata, size_t lnkdata_size); +/** + * \brief Callback for querying the link. + * + * Returns the size of the buffer needed. + */ +typedef ssize_t (*H5L_query_func_t)(const char *link_name, const void *lnkdata, + size_t lnkdata_size, void *buf /*out*/, size_t buf_size); +/** + * \brief Link prototype + * + * The H5L_class_t struct can be used to override the behavior of a + * "user-defined" link class. Users should populate the struct with callback + * functions defined elsewhere. + */ +//! [H5L_class_t_snip] typedef struct { - int version; /* Version number of this struct */ - H5L_type_t id; /* Link type ID */ - const char * comment; /* Comment for debugging */ - H5L_create_func_t create_func; /* Callback during link creation */ - H5L_move_func_t move_func; /* Callback after moving link */ - H5L_copy_func_t copy_func; /* Callback after copying link */ - H5L_traverse_func_t trav_func; /* Callback during link traversal */ - H5L_delete_func_t del_func; /* Callback for link deletion */ - H5L_query_func_t query_func; /* Callback for queries */ + int version; /**< Version number of this struct */ + H5L_type_t id; /**< Link type ID */ + const char *comment; /**< Comment for debugging */ + H5L_create_func_t create_func; /**< Callback during link creation */ + H5L_move_func_t move_func; /**< Callback after moving link */ + H5L_copy_func_t copy_func; /**< Callback after copying link */ + H5L_traverse_func_t trav_func; /**< Callback during link traversal */ + H5L_delete_func_t del_func; /**< Callback for link deletion */ + H5L_query_func_t query_func; /**< Callback for queries */ } H5L_class_t; +//! [H5L_class_t_snip] -/* Prototype for H5Literate2/H5Literate_by_name2() operator - * H5O_token_t version used in VOL layer and future public API calls +/** + * \brief Prototype for H5Literate2(), H5Literate_by_name2() operator + * + * The H5O_token_t version is used in the VOL layer and future public API calls. */ -typedef herr_t (*H5L_iterate2_t)(hid_t group, const char *name, const H5L_info2_t *info, void *op_data); +//! [H5L_iterate2_t_snip] +typedef herr_t (*H5L_iterate2_t)(hid_t group, const char *name, const H5L_info2_t *info, + void *op_data); +//! [H5L_iterate2_t_snip] -/* Callback for external link traversal */ -typedef herr_t (*H5L_elink_traverse_t)(const char *parent_file_name, const char *parent_group_name, - const char *child_file_name, const char *child_object_name, - unsigned *acc_flags, hid_t fapl_id, void *op_data); +/** + * \brief Callback for external link traversal + */ +typedef herr_t (*H5L_elink_traverse_t)(const char *parent_file_name, + const char *parent_group_name, const char *child_file_name, + const char *child_object_name, unsigned *acc_flags, hid_t fapl_id, + void *op_data); /********************/ /* Public Variables */ @@ -145,49 +189,1409 @@ typedef herr_t (*H5L_elink_traverse_t)(const char *parent_file_name, const char /*********************/ /* Public Prototypes */ /*********************/ +/** + * \ingroup H5L + * + * \brief Moves a link within an HDF5 file + * + * \fgdta_loc_id{src_loc} + * \param[in] src_name Original link name + * \fgdta_loc_id{dst_loc} + * \param[in] dst_name New link name + * \lcpl_id + * \lapl_id + * + * \return \herr_t + * + * \todo We need to get the location ID story straight! + * + * \details H5Lmove() moves a link within an HDF5 file. The original link, + * \p src_name, is removed from \p src_loc and the new link, + * \p dst_name, is inserted at dst_loc. This change is + * accomplished as an atomic operation. + * + * \p src_loc and \p src_name identify the original link. + * \p src_loc is the original location identifier; \p src_name is + * the path to the link and is interpreted relative to \p src_loc. + * + * \p dst_loc and \p dst_name identify the new link. \p dst_loc is + * either a file or group identifier; \p dst_name is the path to + * the link and is interpreted relative to \p dst_loc. + * + * \p lcpl_id and \p lapl_id are the link creation and link access + * property lists, respectively, associated with the new link, + * \p dst_name. + * + * Through these property lists, several properties are available to + * govern the behavior of H5Lmove(). The property controlling creation + * of missing intermediate groups is set in the link creation property + * list with H5Pset_create_intermediate_group(); H5Lmove() ignores any + * other properties in the link creation property list. Properties + * controlling character encoding, link traversals, and external link + * prefixes are set in the link access property list with + * H5Pset_char_encoding(), H5Pset_nlinks(), and H5Pset_elink_prefix(), + * respectively. + * + * \note Note that H5Lmove() does not modify the value of the link; the new + * link points to the same object as the original link pointed to. + * Furthermore, if the object pointed to by the original link was already + * open with a valid object identifier, that identifier will remain valid + * after the call to H5Lmove(). + * + * \attention Exercise care in moving links as it is possible to render data in + * a file inaccessible with H5Lmove(). If the link being moved is on + * the only path leading to an HDF5 object, that object may become + * permanently inaccessible in the file. + * + * \since 1.8.0 + * + *------------------------------------------------------------------------- + */ H5_DLL herr_t H5Lmove(hid_t src_loc, const char *src_name, hid_t dst_loc, const char *dst_name, hid_t lcpl_id, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Creates an identical copy of a link with the same creation time and + * target. The new link can have a different name and be in a different + * location than the original. + * + * \fgdt_loc_id{src_loc} + * \param[in] src_name Name of the link to be copied + * \fgdt_loc_id{dst_loc} + * \param[in] dst_name Name to be assigned to the new copy + * \lcpl_id + * \lapl_id + * \return \herr_t + * + * \details H5Lcopy() copies the link specified by \p src_name from the location + * specified by \p src_loc_id to the location specified by + * \p dst_loc_id. The new copy of the link is created with the name + * \p dst_name. + * + * If \p dst_loc_id is a file identifier, \p dst_name will be + * interpreted relative to that file’s root group. + * + * The new link is created with the creation and access property lists + * specified by \p lcpl_id and \p lapl_id. The interpretation of + * \p lcpl_id is limited in the manner described in the next paragraph. + * + * H5Lcopy() retains the creation time and the target of the original + * link. However, since the link may be renamed, the character + * encoding is that specified in \p lcpl_id rather than that of the + * original link. Other link creation properties are ignored. + * + * If the link is a soft link, also known as a symbolic link, its + * target is interpreted relative to the location of the copy. + * + * Several properties are available to govern the behavior of + * H5Lcopy(). These properties are set in the link creation and access + * property lists, \p lcpl_id and \p lapl_id, respectively. The + * property controlling creation of missing intermediate groups is set + * in the link creation property list with + * H5Pset_create_intermediate_group(); this function ignores any + * other properties in the link creation property list. Properties + * controlling character encoding, link traversals, and external link + * prefixes are set in the link access property list with + * H5Pset_char_encoding(), H5Pset_nlinks(), and + * H5Pset_elink_prefix(). + * + * \note H5Lcopy() does not affect the object that the link points to. + * + * \attention H5Lcopy() cannot copy hard links across files as a hard link is + * not valid without a target object; to copy objects from one file + * to another, see H5Ocopy(). + * + * \see H5Ocopy() + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Lcopy(hid_t src_loc, const char *src_name, hid_t dst_loc, const char *dst_name, hid_t lcpl_id, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Creates a hard link to an object + * + * \fgdta_loc_id{cur_loc} + * \param[in] cur_name Name of the target object, which must already exist + * \fgdta_loc_id{dst_loc} + * \param[in] dst_name The name of the new link + * \lcpl_id + * \lapl_id + * + * \return \herr_t + * + * \todo We need to get the location ID story straight! + * + * \details H5Lcreate_hard() creates a new hard link to a pre-existing object + * in an HDF5 file. + * + * \p cur_loc and \p cur_name specify the location + * and name, respectively, of the target object, i.e., the object that + * the new hard link points to. \p dst_loc and \p dst_name specify the + * location and name, respectively, of the new hard link. + * + * \p cur_name and \p dst_name are interpreted relative to \p cur_loc + * and \p dst_loc, respectively. If \p cur_loc and \p dst_loc are the + * same location, the HDF5 macro #H5L_SAME_LOC can be used for either + * parameter (but not both). + * + * \p lcpl_id and \p lapl_id are the link creation and access property + * lists associated with the new link. + * + * \note Hard and soft links are for use only if the target object is in the + * current file. If the desired target object is in a different file from + * the new link, an external link may be created with + * H5Lcreate_external(). + * + * \note The HDF5 library keeps a count of all hard links pointing to an + * object; if the hard link count reaches zero (0), the object will be + * deleted from the file. Creating new hard links to an object will + * prevent it from being deleted if other links are removed. The + * library maintains no similar count for soft links and they can dangle. + * + * \note The new link may be one of many that point to that object. + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Lcreate_hard(hid_t cur_loc, const char *cur_name, hid_t dst_loc, const char *dst_name, hid_t lcpl_id, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Creates a soft link + * + * \param[in] link_target An HDF5 path name + * \fgdta_loc_id{link_loc_id} + * \param[in] link_name The name of the new link + * \lcpl_id + * \lapl_id + * + * \return \herr_t + * + * \todo We need to get the location ID story straight! + * + * \details H5Lcreate_soft() creates a new soft link to an object in an HDF5 + * file. + * + * \p link_target specifies the HDF5 path name the soft link contains. + * \p link_target can be an arbitrary HDF5 path name and is + * interpreted only at lookup time. This path may be absolute in the + * file or relative to \p link_loc_id. + * + * \p link_loc_id and \p link_name specify the location and name, + * respectively, of the new soft link. \p link_name is interpreted + * relative to \p link_loc_id and must contain only the name of the soft + * link; \p link_name may not contain any additional path elements. + * + * If \p link_loc_id is a group identifier, the object pointed to by + * \p link_name will be accessed as a member of that group. If + * \p link_loc_id is a file identifier, the object will be accessed as a + * member of the file's root group. + * + * \p lcpl_id and \p lapl_id are the link creation and access property + * lists associated with the new link. + * + * For instance, if target_path is \c ./foo, \p link_loc_id specifies + * \c ./x/y/bar, and the name of the new link is \c new_link, then a + * subsequent request for \c ./x/y/bar/new_link will return same the + * object as would be found at \c ./foo. + * + * \note H5Lcreate_soft() is for use only if the target object is in the + * current file. If the desired target object is in a different file from + * the new link, use H5Lcreate_external() to create an external link. + * + * \note Soft links and external links are also known as symbolic links as they + * use a name to point to an object; hard links employ an object’s + * address in the file. + * + * \note Unlike hard links, a soft link in an HDF5 file is allowed to dangle, + * meaning that the target object need not exist at the time that the + * link is created. + * + * \note The HDF5 library does not keep a count of soft links as it does of + * hard links. + * + * \note The new link may be one of many that point to that object. + * + * \see H5Lcreate_hard(), H5Lcreate_external() + * + * \since 1.8.0 + * + + */ H5_DLL herr_t H5Lcreate_soft(const char *link_target, hid_t link_loc_id, const char *link_name, hid_t lcpl_id, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Removes a link from a group + * + * \fgdta_loc_id + * \param[in] name Name of the link to delete + * \lapl_id + * + * \return \herr_t + * + * \todo We need to get the location ID story straight! + * + * \details H5Ldelete() removes the link specified by \p name from the location + * \p loc_id. + * + * If the link being removed is a hard link, H5Ldelete() also + * decrements the link count for the object to which name points. + * Unless there is a duplicate hard link in that group, this action + * removes the object to which name points from the group that + * previously contained it. + * + * Object headers keep track of how many hard links refer to an + * object; when the hard link count, also referred to as the reference + * count, reaches zero, the object can be removed from the file. The + * file space associated will then be released, i.e., identified in + * memory as freespace. Objects which are open are not removed until + * all identifiers to the object are closed. + * + * \attention Exercise caution in the use of H5Ldelete(); if the link being + * removed is on the only path leading to an HDF5 object, that + * object may become permanently inaccessible in the file. + * + * \see H5Lcreate_hard(), H5Lcreate_soft(), H5Lcreate_external() + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Ldelete(hid_t loc_id, const char *name, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Removes the \Emph{n}-th link in a group + * + * \fgdta_loc_id + * \param[in] group_name Name of subject group + * \param[in] idx_type Index or field which determines the order + * \param[in] order Order within field or index + * \param[in] n Link for which to retrieve information + * \lapl_id + * + * \return \herr_t + * + * \todo We need to get the location ID story straight! + * + * \details H5Ldelete_by_idx() removes the \Emph{n}-th link in a group + * according to the specified order, \p order, in the specified index, + * \p index. + * + * If \p loc_id specifies the group in which the link resides, + * \p group_name can be a dot (\c .). + * + * \see H5Ldelete() + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Ldelete_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Returns the value of a link + * + * \fgdta_loc_id + * \param[in] name Link name + * \param[out] buf The buffer to hold the link value + * \param[in] size Maximum number of bytes of link value to be returned + * \lapl_id + * + * \return \herr_t + * + * \todo We need to get the location ID story straight! + * + * \details H5Lget_val() returns tha value of link \p name. For smbolic links, + * this is the path to which the link points, including the null + * terminator. For external and user-defined links, it is the link + * buffer. + * + * \p size is the size of \p buf and should be the size of the link + * value being returned. This size value can be determined through a + * call to H5Lget_info(); it is returned in the \c val_size field of + * the \ref H5L_info_t \c struct. + * + * If \p size is smaller than the size of the returned value, then the + * string stored in \p buf will be truncated to \p size bytes. For + * soft links, this means that the value will not be null terminated. + * + * In the case of external links, the target file and object names are + * extracted from \p buf by calling H5Lunpack_elink_val(). + * + * The link class of link \p name can be determined with a call to + * H5Lget_info(). + * + * \p lapl_id specifies the link access property list associated with + * the link \p name. In the general case, when default link access + * properties are acceptable, this can be passed in as #H5P_DEFAULT. An + * example of a situation that requires a non-default link access + * property list is when the link is an external link; an external + * link may require that a link prefix be set in a link access + * property list (see H5Pset_elink_prefix()). + * + * This function should be used only after H5Lget_info() has been + * called to verify that \p name is a symbolic link. This can be + * deteremined from the \c link_type field of the \ref H5L_info_t + * \c struct. + * + * \note This function will fail if called on a hard link. + * + * \see H5Lget_val_by_idx() + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Lget_val(hid_t loc_id, const char *name, void *buf /*out*/, size_t size, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Retrieves value of the \Emph{n}-th link in a group, according to the order within an index + * + * \fgdta_loc_id + * \param[in] group_name Group name + * \param[in] idx_type Type of index + * \param[in] order Order within field or index + * \param[in] n Link position for which to retrieve information + * \param[out] buf The buffer to hold the link value + * \param[in] size Maximum number of bytes of link value to be returned + * \lapl_id + * + * \return \herr_t + * + * \todo We need to get the location ID story straight! + * + * \details H5Lget_val_by_idx() retrieves the value of the \Emph{n}-th link in + * a group, according to the specified order, \p order, within an + * index, \p index. + * + * For soft links, the value is an HDF5 path name. + * + * For external links, this is a compound value containing file and + * path name information; to use this external link information, it + * must first be decoded with H5Lunpack_elink_val() + * + * For user-defined links, this value will be described in the + * definition of the user-defined link type. + * + * \p loc_id specifies the location identifier of the group specified + * by \p group_name. + * + * \p group_name specifies the group in which the link exists. If + * \p loc_id already specifies the group in which the link exists, + * \p group_name must be a dot (\c .). + * + * The size in bytes of link_val is specified in \p size. The size + * value can be determined through a call to H5Lget_info_by_idx(); it + * is returned in the \c val_size field of the \ref H5L_info_t + * \c struct. If + * size is smaller than the size of the returned value, then the + * string stored in link_val will be truncated to size bytes. For soft + * links, this means that the value will not be null terminated. + * + * If the type of the link is unknown or uncertain, H5Lget_val_by_idx() + * should be called only after the type has been determined via a call + * to H5Lget_info_by_idx(). + * + * \note This function will fail if called on a hard link. + * + * \see H5Lget_val() + * + * \since 1.8.0 + * + */ H5_DLL 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); +/** + * \ingroup H5L + * + * \brief Determines whether a link with the specified name exists in a group + * + * \fgdta_loc_id + * \param[in] name Link name + * \lapl_id + * + * \return \herr_t + * + * \todo We need to get the location ID story straight! + * + * \details H5Lexists() allows an application to determine whether the link \p + * name exists in the location specified by \p loc_id. The link may be + * of any type; only the presence of a link with that name is checked. + * + * Note that H5Lexists() verifies only that the target link exists. If + * name includes either a relative path or an absolute path to the + * target link, intermediate steps along the path must be verified + * before the existence of the target link can be safely checked. If + * the path is not verified and an intermediate element of the path + * does not exist, H5Lexists() will fail. The example in the next + * paragraph illustrates one step-by-step method for verifying the + * existence of a link with a relative or absolute path. + * + * \Bold{Example:} Use the following steps to verify the existence of + * the link \c datasetD in the \c group group1/group2/softlink_to_group3/, + * where \c group1 is a member of the group specified by \c loc_id: + * + * 1. First use H5Lexists() to verify that \c group1 exists. + * 2. If \c group1 exists, use H5Lexists() again, this time with name + * set to \c group1/group2, to verify that \c group2 exists. + * 3. If \c group2 exists, use H5Lexists() with name set to + * \c group1/group2/softlink_to_group3 to verify that + * \c softlink_to_group3 exists. + * 4. If \c softlink_to_group3 exists, you can now safely use + * H5Lexists() with \c name set to + * \c group1/group2/softlink_to_group3/datasetD to verify that the + * target link, \c datasetD, exists. + * + * If the link to be verified is specified with an absolute path, the + * same approach should be used, but starting with the first link in + * the file’s root group. For instance, if \c datasetD were in + * \c /group1/group2/softlink_to_group3, the first call to H5Lexists() + * would have name set to \c /group1. + * + * Note that this is an outline and does not include all necessary + * details. Depending on circumstances, for example, you may need to + * verify that an intermediate link points to a group and that a soft + * link points to an existing target. + * + * \note The behavior of H5Lexists() was changed in the 1.10 release in the + * case where the root group, \c "/", is the name of the link. This + * change is described below: + * <ol> + * <li>Let \c file denote a valid HDF5 file identifier, and let \c lapl + * denote a valid link access property list identifier. A call to + * H5Lexists() with arguments \c file, \c "/", and \c lapl + * returns a positive value; in other words, + * \Code{H5Lexists(file, "/", lapl)} returns a positive value. + * In HDF5 version 1.8.16, this function returns 0.</li> + * <li>Let \c root denote a valid HDF5 group identifier that refers to the + * root group of an HDF5 file, and let \c lapl denote a valid link + * access property list identifier. A call to H5Lexists() with + * arguments c root, \c "/", and \c lapl returns a positive value; + * in other words, \Code{H5Lexists(root, "/", lapl)} returns a postive + * value. In HDF5 version 1.8.16, this function returns 0.</li> + * </ol> + * Note that the function accepts link names and path names. This is + * potentially misleading to callers, and we plan to separate the + * functionality for link names and path names in a future release. + * + * \attention H5Lexists() checks the existence of only the final element in a + * relative or absolute path; it does not check any other path + * elements. The function will therefore fail when both of the + * following conditions exist: + * - \c name is not local to the group specified by \c loc_id or, + * if \c loc_id is something other than a group identifier, \c name + * is not local to the root group. + * - Any element of the relative path or absolute path in name, + * except the target link, does not exist. + * + * \version 1.10.0 Function behavior changed in this release. (See the note.) + * \since 1.8.0 + * + */ H5_DLL htri_t H5Lexists(hid_t loc_id, const char *name, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Returns information about a link + * + * \fgdta_loc_id + * \param[in] name Link name + * \param[out] linfo Buffer in which link information is returned + * \lapl_id + * + * \return \herr_t + * + * \todo We need to get the location ID story straight! + * + * \details H5Lget_info2() returns information about the specified link through + * the \p linfo argument. + * + * The location identifier, \p loc_id, specifies the location of the + * link. A link name, \p name, interpreted relative to \p loc_id, + * specifies the link being queried. + * + * \p lapl_id is the link access property list associated with the + * link name. In the general case, when default link access properties + * are acceptable, this can be passed in as #H5P_DEFAULT. An example + * of a situation that requires a non-default link access property + * list is when the link is an external link; an external link may + * require that a link prefix be set in a link access property list + * (see H5Pset_elink_prefix()). + * + * H5Lget_info2() returns information about name in the data structure + * H5L_info2_t, which is described below and defined in H5Lpublic.h. + * This structure is returned in the buffer \p linfo. + * \snippet this H5L_info2_t_snip + * In the above struct, \c type specifies the link class. Valid values + * include the following: + * \link_types + * There will be additional valid values if user-defined links have + * been registered. + * + * \p corder specifies the link’s creation order position while + * \p corder_valid indicates whether the value in corder is valid. + * + * If \p corder_valid is \c TRUE, the value in \p corder is known to + * be valid; if \p corder_valid is \c FALSE, the value in \p corder is + * presumed to be invalid; \p corder starts at zero (0) and is + * incremented by one (1) as new links are created. But + * higher-numbered entries are not adjusted when a lower-numbered link + * is deleted; the deleted link's creation order position is simply + * left vacant. In such situations, the value of \p corder for the + * last link created will be larger than the number of links remaining + * in the group. + * + * \p cset specifies the character set in which the link name is + * encoded. Valid values include the following: + * \csets + * This value is set with H5Pset_char_encoding(). + * + * \c token is the location that a hard link points to, and + * \c val_size is the size of a soft link or user defined link value. + * H5O_token_t is used in the VOL layer. It is defined in H5public.h + * as: + * \snippet H5public.h H5O_token_t_snip + * + * If the link is a symbolic link, \c val_size will be the length of + * the link value, e.g., the length of the HDF5 path name with a null + * terminator. + * + * \since 1.12.0 + * + */ H5_DLL herr_t H5Lget_info2(hid_t loc_id, const char *name, H5L_info2_t *linfo /*out*/, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Retrieves metadata for a link in a group, according to the order + * within a field or index + * + * \loc_id + * \param[in] group_name Group name + * \idx_type + * \order + * \param[in] n Link position for which to retrieve information + * \param[out] linfo Buffer in which link information is returned + * \lapl_id + * + * \return \herr_t + * + * \details H5get_info_by_idx2() returns the metadata for a link in a group + * according to a specified field or index and a specified order. The + * link for which information is to be returned is specified by \p + * idx_type, \p order, and \p n as follows: + * + * - \p idx_type specifies the field by which the links in \p + * group_name are ordered. The links may be indexed on this field, + * in which case operations seeking specific links are likely to + * complete more quickly. + * - \p order specifies the order in which + * the links are to be referenced for the purposes of this function. + * - \p n specifies the position of the subject link. Note that this + * count is zero-based; 0 (zero) indicates that the function will + * return the value of the first link; if \p n is 5, the function + * will return the value of the sixth link; etc. + * + * For example, assume that \p idx_type, \p order, and \p n are + * #H5_INDEX_NAME, #H5_ITER_DEC, and 5, respectively. #H5_INDEX_NAME + * indicates that the links are accessed in lexicographic order by + * their names. #H5_ITER_DEC specifies that the list be traversed in + * reverse order, or in decremented order. And 5 specifies that this + * call to the function will return the metadata for the 6th link + * (\c n + 1) from the end. + * + * See H5Literate2() for a list of valid values and further discussion + * regarding \p idx_type and \p order. + * + * If \p loc_id specifies the group in which the link resides, + * \p group_name can be a dot (\c .). + * + * \since 1.12.0 + * + * \see H5Lget_info2() + * + * \todo Document H5Lget_info_by_idx() + * + */ H5_DLL herr_t H5Lget_info_by_idx2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, H5L_info2_t *linfo /*out*/, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Retrieves name of the \Emph{n}-th link in a group, according to the + * order within a specified field or index + * + * \loc_id + * \param[in] group_name Group name + * \idx_type + * \order + * \param[in] n Link position for which to retrieve information + * \param[out] name Buffer in which link name is returned + * \param[in] size Size in bytes of \p name + * \lapl_id + * + * \return Returns the size of the link name if successful; otherwise returns a + * negative value. + * + * \details H5get_name_by_idx() retrieves the name of the \Emph{n}-th link in a + * group, according to the specified order, \p order, within a specified + * field or index, \p idx_type. + * + * \p idx_type specifies the index that is used. Valid values include + * the following: + * \indexes + * + * \p order specifies the order in which objects are inspected along + * the index specified in \p idx_type. Valid values include the + * following: + * \orders + * + * If \p loc_id specifies the group in which the link resides, + * \p group_name can be a dot (\c .). + * + * The size in bytes of name is specified in \p size. If \p size is + * unknown, it can be determined via an initial H5Lget_name_by_idx() + * call with name set to NULL; the function's return value will be the + * size of the name. + * + * \note Please note that in order for the specified index to correspond to the + * creation order index, \p order must be set to #H5_ITER_INC or + * #H5_ITER_DEC when calling H5Lget_name_by_idx(). \note The index \p n + * passed to H5Lget_name_by_idx() is the index of the link within the + * link table, sorted according to \p order and \p idx_type. If order is + * #H5_ITER_NATIVE, then the link table is not sorted, and it does not + * matter what \p idx_type is. Specifying #H5_ITER_NATIVE does not + * guarantee any particular order, only that it remains consistent. + * + * \since 1.8.0 + * + */ H5_DLL ssize_t H5Lget_name_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, char *name /*out*/, size_t size, hid_t lapl_id); +/** + * \ingroup TRAV + * + * \brief Iterates over links in a group, with user callback routine, + * according to the order within an index. + * + * \group_id{grp_id} + * \idx_type + * \order + * \param[in,out] idx Pointer to an iteration index to allow + * continuing a previous iteration + * \op + * \op_data + * \return \success{The return value of the first operator that returns + * non-zero, or zero if all members were processed with no + * operator returning non-zero.} + * \return \failure{Negative if an error occurs in the library, or the negative + * value returned by one of the operators.} + * + * \details H5Literate2() iterates through the links in a file or + * group, \p group_id, in the order of the specified + * index, \p idx_type, using a user-defined callback routine + * \p op. H5Literate2() does not recursively follow links into + * subgroups of the specified group. + * + * Three parameters are used to manage progress of the iteration: + * \p idx_type, \p order, and \p idx_p. + * + * \p idx_type specifies the index to be used. If the links have + * not been indexed by the index type, they will first be sorted by + * that index then the iteration will begin; if the links have been + * so indexed, the sorting step will be unnecessary, so the iteration + * may begin more quickly. + * + * \p order specifies the order in which objects are to be inspected + * along the index \p idx_type. + * + * \p idx_p tracks the iteration and allows an iteration to be + * resumed if it was stopped before all members were processed. It is + * passed in by the application with a starting point and returned by + * the library with the point at which the iteration stopped. + * + * \p op_data is a user-defined pointer to the data required to + * process links in the course of the iteration. This pointer is + * passed back to each step of the iteration in the \p op callback + * function's \p op_data parameter. \p op is invoked for each link + * encounter. + * + * \p op_data is passed to and from each iteration and can be used to + * supply or aggregate information across iterations. + * + * \remark Same pattern of behavior as H5Giterate(). + * + * \note This function is also available through the H5Literate() macro. + * + * \warning The behavior of H5Literate2() is undefined if the link + * membership of \p group_id changes during the iteration. + * This does not limit the ability to change link destinations + * while iterating, but caution is advised. + * + * + * \since 1.12.0 + * + * \see H5Literate_by_name2(), H5Lvisit2(), H5Lvisit_by_name2() + * + */ H5_DLL herr_t H5Literate2(hid_t grp_id, H5_index_t idx_type, H5_iter_order_t order, hsize_t *idx, H5L_iterate2_t op, void *op_data); +/** + * \ingroup TRAV + * + * \brief Iterates through links in a group + * + * \loc_id + * \param[in] group_name Group name + * \idx_type + * \order + * \param[in,out] idx iteration position at which to start (\Emph{IN}) or + * position at which an interrupted iteration may be restarted + * (\Emph{OUT}) + * \op + * \op_data + * \lapl_id + * \return \success{The return value of the first operator that returns + * non-zero, or zero if all members were processed with no + * operator returning non-zero.} + * \return \failure{Negative if an error occurs in the library, or the negative + * value returned by one of the operators.} + * + * \details H5Literate_by_name2() iterates through the links in a group + * specified by \p loc_id and \p group_name, in the order of the + * specified index, \p idx_type, using a user-defined callback routine + * \p op. H5Literate_by_name2() does not recursively follow links into + * subgroups of the specified group. + * + * \p idx_type specifies the index to be used. If the links have not + * been indexed by the index type, they will first be sorted by that + * index then the iteration will begin; if the links have been so + * indexed, the sorting step will be unnecessary, so the iteration may + * begin more quickly. Valid values include the following: + * \indexes + * + * \p order specifies the order in which objects are to be inspected + * along the index specified in \p idx_type. Valid values include the + * following: + * \orders + * + * \p idx_p allows an interrupted iteration to be resumed; it is + * passed in by the application with a starting point and returned by + * the library with the point at which the iteration stopped. + * + * \note H5Literate_by_name2() is not recursive. In particular, if a member of + * \p group_name is found to be a group, call it \c subgroup_a, + * H5Literate_by_name2() does not examine the members of \c subgroup_a. + * When recursive iteration is required, the application must handle the + * recursion, explicitly calling H5Literate_by_name2() on discovered + * subgroups. + * + * \note H5Literate_by_name2() assumes that the membership of the group being + * iterated over remains unchanged through the iteration; if any of the + * links in the group change during the iteration, the function’s + * behavior is undefined. Note, however, that objects pointed to by the + * links can be modified. + * + * \note H5Literate_by_name2() is the same as H5Literate2(), except that + * H5Literate2() always proceeds in alphanumeric order. + * + * \since 1.12.0 + * + * \see H5Literate(), H5Lvisit() + * + */ H5_DLL herr_t H5Literate_by_name2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t *idx, H5L_iterate2_t op, void *op_data, hid_t lapl_id); +/** + * \ingroup TRAV + * + * \brief Recursively visits all links starting from a specified group + * + * \group_id{grp_id} + * \idx_type + * \order + * \op + * \op_data + * \return \success{The return value of the first operator that returns + * non-zero, or zero if all members were processed with no + * operator returning non-zero.} + * \return \failure{Negative if an error occurs in the library, or the negative + * value returned by one of the operators.} + * + * \details H5Lvisit2() is a recursive iteration function to visit all links in + * and below a group in an HDF5 file, thus providing a mechanism for + * an application to perform a common set of operations across all of + * those links or a dynamically selected subset. For non-recursive + * iteration across the members of a group, see H5Literate2(). + * + * The group serving as the root of the iteration is specified by its + * group or file identifier, \p group_id. + * + * Two parameters are used to establish the iteration: \p idx_type and + * \p order. + * + * \p idx_type specifies the index to be used. If the links have not + * been indexed by the index type, they will first be sorted by that + * index then the iteration will begin; if the links have been so + * indexed, the sorting step will be unnecessary, so the iteration may + * begin more quickly. Valid values include the following: + * \indexes + * + * Note that the index type passed in \p idx_type is a best effort + * setting. If the application passes in a value indicating iteration + * in creation order and a group is encountered that was not tracked + * in creation order, that group will be iterated over in + * lexicographic order by name, or name order. (Name order is the + * native order used by the HDF5 library and is always available.) + * + * \p order specifies the order in which objects are to be inspected + * along the index specified in \p idx_type. Valid values include the + * following: + * \orders + * + * \p op is a callback function of type \ref H5L_iterate2_t that is invoked + * for each link encountered. + * \snippet this H5L_iterate2_t_snip + * + * The \ref H5L_info2_t struct is defined (in H5Lpublic.h) as follows: + * \snippet this H5L_info2_t_snip + * + * The possible return values from the callback function, and the + * effect of each, are as follows: + * \li Zero causes the visit iterator to continue, returning zero when + * all group members have been processed. + * \li A positive value causes the visit iterator to immediately + * return that positive value, indicating short-circuit success. + * \li A negative value causes the visit iterator to immediately + * return that value, indicating failure. + * + * The H5Lvisit2() \p op_data parameter is a user-defined pointer to + * the data required to process links in the course of the iteration. + * This pointer is passed back to each step of the iteration in the + * \p op callback function's \p op_data parameter. + * + * H5Lvisit2() and H5Ovisit2() are companion functions: one for + * examining and operating on links; the other for examining and + * operating on the objects that those links point to. Both functions + * ensure that by the time the function completes successfully, every + * link or object below the specified point in the file has been + * presented to the application for whatever processing the + * application requires. + * + * \since 1.12.0 + * + * \see H5Literate() + * + */ H5_DLL herr_t H5Lvisit2(hid_t grp_id, H5_index_t idx_type, H5_iter_order_t order, H5L_iterate2_t op, void *op_data); +/** + * \ingroup TRAV + * + * \brief Recursively visits all links starting from a specified group + * + * \loc_id + * \param[in] group_name Group name + * \idx_type + * \order + * \op + * \op_data + * \lapl_id + * + * \return \herr_t + * + * \details H5Lvisit_by_name2() is a recursive iteration function to visit all + * links in and below a group in an HDF5 file, thus providing a + * mechanism for an application to perform a common set of operations + * across all of those links or a dynamically selected subset. For + * non-recursive iteration across the members of a group, see + * H5Literate2(). + * + * The group serving as the root of the iteration is specified by the + * \p loc_id / \p group_name parameter pair. \p loc_id specifies a + * file or group; group_name specifies either a group in the file + * (with an absolute name based in the file’s root group) or a group + * relative to \p loc_id. If \p loc_id fully specifies the group that + * is to serve as the root of the iteration, group_name should be '.' + * (a dot). (Note that when \p loc_id fully specifies the the group + * that is to serve as the root of the iteration, the user may wish to + * consider using H5Lvisit2() instead of H5Lvisit_by_name2().) + * + * Two parameters are used to establish the iteration: \p idx_type and + * \p order. + * + * \p idx_type specifies the index to be used. If the links have not + * been indexed by the index type, they will first be sorted by that + * index then the iteration will begin; if the links have been so + * indexed, the sorting step will be unnecesary, so the iteration may + * begin more quickly. Valid values include the following: + * \indexes + * + * Note that the index type passed in \p idx_type is a best effort + * setting. If the application passes in a value indicating iteration + * in creation order and a group is encountered that was not tracked + * in creation order, that group will be iterated over in + * lexicographic order by name, or name order. (Name order is the + * native order used by the HDF5 library and is always available.) + * + * \p order specifies the order in which objects are to be inspected + * along the index specified in \p idx_type. Valid values include the + * following: + * \orders + * + * The \p op callback function, the related \ref H5L_info2_t + * \c struct, and the effect that the callback function's return value + * has on the application are described in H5Lvisit2(). + * + * The H5Lvisit_by_name2() \p op_data parameter is a user-defined + * pointer to the data required to process links in the course of the + * iteration. This pointer is passed back to each step of the + * iteration in the callback function's \p op_data parameter. + * + * \p lapl_id is a link access property list. In the general case, + * when default link access properties are acceptable, this can be + * passed in as #H5P_DEFAULT. An example of a situation that requires + * a non-default link access property list is when the link is an + * external link; an external link may require that a link prefix be + * set in a link access property list (see H5Pset_elink_prefix()). + * + * H5Lvisit_by_name2() and H5Ovisit_by_name2() are companion + * functions: one for examining and operating on links; the other for + * examining and operating on the objects that those links point to. + * Both functions ensure that by the time the function completes + * successfully, every link or object below the specified point in the + * file has been presented to the application for whatever processing + * the application requires. + * + * \since 1.12.0 + * + */ H5_DLL herr_t H5Lvisit_by_name2(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_iter_order_t order, H5L_iterate2_t op, void *op_data, hid_t lapl_id); /* UD link functions */ +/** + * \ingroup H5L + * + * \brief Creates a link of a user-defined type + * + * \loc_id{link_loc_id} + * \param[in] link_name Link name + * \param[in] link_type User-defined link class + * \param[in] udata User-supplied link information + * \param[in] udata_size Size of udata buffer + * \lcpl_id + * \lapl_id + * + * \return \herr_t + * + * \details H5Lcreate_ud() creates a link of user-defined type \p link_type + * named \p link_name at the location specified in \p link_loc_id with + * user-specified data \p udata. + * + * \p link_name is interpreted relative to \p link_loc_id. + * + * Valid values for the link class of the new link, \p link_type, + * include #H5L_TYPE_EXTERNAL and any user-defined link classes that + * have been registered with the library. See H5Lregister() for + * further information. + * + * The format of the information pointed to by \p udata is defined by + * the user. \p udata_size specifies the size of the \p udata buffer. + * \p udata may be NULL if \p udata_size is zero (0). + * + * The property lists specified by \p lcpl_id and \p lapl_id specify + * properties used to create and access the link. + * + * \note The external link type, #H5L_TYPE_EXTERNAL, included in the HDF5 + * library distribution, is implemented as a user-defined link type. This + * was done, in part, to provide a model for the implementation of other + * user-defined links. + * + * \since 1.8.0 + * + */ H5_DLL 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); +/** + * \ingroup H5LA + * + * \brief Registers a user-defined link class or changes behavior of an + * existing class + * + * \param[in] cls Pointer to a buffer containing the struct describing the + * user-defined link class + * + * \return \herr_t + * + * \details H5Lregister() registers a class of user-defined links, or changes + * the behavior of an existing class. + * + * \p cls is a pointer to a buffer containing a copy of the + * H5L_class_t struct. This struct is defined in H5Lpublic.h as + * follows: + * \snippet this H5L_class_t_snip + * + * The class definition passed with \p cls must include at least the + * following: + * \li An H5L_class_t version (which should be #H5L_LINK_CLASS_T_VERS) + * \li A link class identifier, \c class_id + * \li A traversal function, \c trav_func + * + * Remaining \c struct members are optional and may be passed as NULL. + * + * The link class passed in \c class_id must be in the user-definable + * range between #H5L_TYPE_UD_MIN and #H5L_TYPE_UD_MAX + * (see the table below) and will override + * any existing link class with that identifier. + * + * As distributed, valid values of \c class_id used in HDF5 include + * the following (defined in H5Lpublic.h): + * \link_types + * + * The hard and soft link class identifiers cannot be modified or + * reassigned, but the external link class is implemented as an + * example in the user-definable link class identifier range. + * H5Lregister() is used to register additional link classes. It could + * also be used to modify the behavior of the external link class, + * though that is not recommended. + * + * The following table summarizes existing link types and values and + * the reserved and user-definable link class identifier value ranges. + * <table> + * <tr> + * <th>Link class identifier or Value range</th> + * <th>Description</th> + * <th>Link class or label</th> + * </tr> + * <tr> + * <td>0 to 63</td> + * <td>Reserved range</td> + * <td></td> + * </tr> + * <tr> + * <td>64 to 255</td> + * <td>User-definable range</td> + * <td></td> + * </tr> + * <tr> + * <td>64</td> + * <td>Minimum user-defined value</td> + * <td>#H5L_TYPE_UD_MIN</td> + * </tr> + * <tr> + * <td>64</td> + * <td>External link</td> + * <td>#H5L_TYPE_EXTERNAL</td> + * </tr> + * <tr> + * <td>255</td> + * <td>Maximum user-defined value</td> + * <td>#H5L_TYPE_UD_MAX</td> + * </tr> + * <tr> + * <td>255</td> + * <td>Maximum value</td> + * <td>#H5L_TYPE_MAX</td> + * </tr> + * <tr> + * <td>-1</td> + * <td>Error</td> + * <td>#H5L_TYPE_ERROR</td> + * </tr> + * </table> + * + * Note that HDF5 internally registers user-defined link classes only + * by the numeric value of the link class identifier. An application, + * on the other hand, will generally use a name for a user-defined + * class, if for no other purpose than as a variable name. Assume, + * for example, that a complex link type is registered with the link + * class identifier 73 and that the code includes the following + * assignment: + * \code + * H5L_TYPE_COMPLEX_A = 73 + * \endcode + * The application can refer to the link class with a term, + * \c H5L_TYPE_COMPLEX_A, that conveys meaning to a human reviewing + * the code, while HDF5 recognizes it by the more cryptic numeric + * identifier, 73. + * + * \attention Important details and considerations include the following: + * \li If you plan to distribute files or software with a + * user-defined link class, please contact the Help Desk at + * The HDF Group to help prevent collisions between \c class_id + * values. See below. + * \li As distributed with HDF5, the external link class is + * implemented as an example of a user-defined link class with + * #H5L_TYPE_EXTERNAL equal to #H5L_TYPE_UD_MIN. \c class_id in + * the H5L_class_t \c struct must not equal #H5L_TYPE_UD_MIN + * unless you intend to overwrite or modify the behavior of + * external links. + * \li H5Lregister() can be used only with link class identifiers + * in the user-definable range (see table above). + * \li The hard and soft links defined by the HDF5 library, + * #H5L_TYPE_HARD and #H5L_TYPE_SOFT, reside in the reserved + * range below #H5L_TYPE_UD_MIN and cannot be redefined or + * modified. + * \li H5Lis_registered() can be used to determine whether a desired + * link class identifier is available. \Emph{Note that this + * function will tell you only whether the link class identifier + * has been registered with the installed copy of HDF5; it + * cannot tell you whether the link class has been registered + * with The HDF Group.} + * \li #H5L_TYPE_MAX is the maximum allowed value for a link type + * identifier. + * \li #H5L_TYPE_UD_MIN equals #H5L_TYPE_EXTERNAL. + * \li #H5L_TYPE_UD_MAX equals #H5L_TYPE_MAX. + * \li #H5L_TYPE_ERROR indicates that an error has occurred. + * + * \note \Bold{Registration with The HDF Group:}\n + * There are sometimes reasons to take a broader approach to registering + * a user-defined link class than just invoking H5Lregister(). For + * example: + * \li A user-defined link class is intended for use across an + * organization, among collaborators, or across a community of users. + * \li An application or library overlying HDF5 invokes a user-defined + * link class that must be shipped with the software. + * \li Files are distributed that make use of a user-defined link class. + * \li Or simply, a specific user-defined link class is thought to be + * widely useful. + * + * In such cases, you are encouraged to register that link class with + * The HDF Group's Helpdesk. The HDF Group maintains a registry of known + * user-defined link classes and tracks the selected link class + * identifiers. This registry is intended to reduce the risk of + * collisions between \c class_id values and to help coordinate the use + * of specialized link classes. + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Lregister(const H5L_class_t *cls); +/** + * \ingroup H5LA + * + * \brief Unregisters a class of user-defined links + * + * \param[in] id User-defined link class identifier + * + * \return \herr_t + * + * \details H5Lunregister() unregisters a class of user-defined links, + * preventing them from being traversed, queried, moved, etc. + * + * \note A link class can be re-registered using H5Lregister(). + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Lunregister(H5L_type_t id); +/** + * \ingroup H5LA + * + * \brief Determines whether a class of user-defined links is registered + * + * \param[in] id User-defined link class identifier + * + * \return \htri_t + * + * \details 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(). + * + * \note A link class must be registered to create new links of that type or to + * traverse existing links of that type. + * + * \since 1.8.0 + * + */ H5_DLL htri_t H5Lis_registered(H5L_type_t id); /* External link functions */ +/** + * \ingroup H5L + * + * \brief Decodes external link information + * + * \param[in] ext_linkval Buffer containing external link information + * \param[in] link_size Size, in bytes, of the \p ext_linkval buffer + * \param[out] flags External link flags, packed as a bitmap (\Emph{Reserved as + * a bitmap for flags; no flags are currently defined, so the + * only valid value * is 0.}) + * \param[out] filename Returned filename \param[out] obj_path Returned + * object path, relative to \p filename + * + * \return \herr_t + * + * \details H5Lunpack_elink_val() decodes the external link information + * returned by H5Lget_val() in the \p ext_linkval buffer. + * + * \p ext_linkval should be the buffer set by H5Lget_val() and will + * consist of two NULL-terminated strings, the filename and object + * path, one after the other. + * + * Given this buffer, H5Lunpack_elink_val() creates pointers to the + * filename and object path within the buffer and returns them in + * \p filename and \p obj_path, unless they are passed in as NULL. + * + * H5Lunpack_elink_val() requires that \p ext_linkval contain a + * concatenated pair of null-terminated strings, so use of this + * function on a string that is not an external link \p udata buffer + * may result in a segmentation fault. This failure can be avoided by + * adhering to the following procedure: + * <ol> + * <li>Call H5Lget_info() to get the link type and the size of the + * link value.<li> + * <li>Verify that the link is an external link, i.e., that its link + * type is #H5L_TYPE_EXTERNAL.</li> + * <li>Call H5Lget_val() to get the link value.</li> + * <li>Call H5Lunpack_elink_val() to unpack that value.</li> + * </ol> + * + * \since 1.8.0 + * + */ H5_DLL 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*/); +/** + * \ingroup H5L + * + * \brief Creates an external link, a soft link to an object in a different file. + * + * \param[in] file_name Name of the target file containing the target object. + * \param[in] obj_name Path within the target file to the target object + * \fgdt_loc_id{link_loc_id} + * \param[in] link_name Name of the new link, relative to \p link_loc_id + * \lcpl_id + * \lapl_id + * \return \herr_t + * + * \details H5Lcreate_external() creates a new external link. An external link + * is a soft link to an object in a different HDF5 file from the + * location of the link, i.e., to an external object. + * + * \p file_name identifies the target file containing the target + * object; \p obj_name specifies the path of the target object within + * that file. \p obj_name must be an absolute pathname in + * \p file_name, i.e., it must start at the target file’s root group, + * but it is not interpreted until an application attempts to traverse + * it. + * + * \p link_loc_id and \p link_name specify the location and name, + * respectively, of the new link. \p link_name is interpreted relative + * to \p link_loc_id. + * + * \p lcpl_id is the link creation property list used in creating the + * new link. + * + * \p lapl_id is the link access property list used in traversing the + * new link. Note that an external file opened by the traversal of an + * external link is always opened with the weak file close degree + * property setting, #H5F_CLOSE_WEAK (see H5Pset_fclose_degree()); + * any file close degree property setting in \p lapl_id is ignored. + * + * An external link behaves similarly to a soft link, and like a soft + * link in an HDF5 file, it may dangle: the target file and object + * need not exist at the time that the external link is created. + * + * When the external link \p link_name is accessed, the library will + * search for the target file \p file_name as described below: + * + * - If \p file_name is a relative pathname, the following steps are + * performed: + * - The library will get the prefix(es) set in the environment + * variable \c HDF5_EXT_PREFIX and will try to prepend each prefix + * to \p file_name to form a new \p file_name. + * - If the new \p file_name does not exist or if \c HDF5_EXT_PREFIX + * is not set, the library will get the prefix set via + * H5Pset_elink_prefix() and prepend it to \p file_name to form a + * new \p file_name. + * - If the new \p file_name does not exist or no prefix is being + * set by H5Pset_elink_prefix(), then the path of the file + * associated with \p link_loc_id is obtained. This path can be + * the absolute path or the current working directory plus the + * relative path of that file when it is created/opened. The + * library will prepend this path to \p file_name to form a new + * \p file_name. + * - If the new \p file_name does not exist, then the library will + * look for \p file_name and will return failure/success + * accordingly. + * - If \p file_name is an absolute pathname, the library will first + * try to find \p file_name. If \p file_name does not exist, + * \p file_name is stripped of directory paths to form a new + * \p file_name. The search for the new \p file_name then follows + * the same steps as described above for a relative pathname. See + * examples below illustrating how target_file_name is stripped to + * form a new \p file_name. + * + * Note that \p file_name is considered to be an absolute pathname + * when the following condition is true: + * + * - For Unix, the first character of \p file_name is a slash (\c /). + * For example, consider a \p file_name of \c /tmp/A.h5. + * If that target file does not exist, the new \p file_name after + * stripping will be \c A.h5. + * - For Windows, there are 6 cases: + * -# \p file_name is an absolute drive with absolute pathname. + * For example, consider a \p file_name of \c /tmp/A.h5. If that + * target file does not exist, the new \p file_name after + * stripping will be \c A.h5. + * -# \p file_name is an absolute pathname without specifying drive + * name. For example, consider a \p file_name of \c /tmp/A.h5. + * If that target file does not exist, the new \p file_name after + * stripping will be \c A.h5. + * -# \p file_name is an absolute drive with relative pathname. + * For example, consider a \p file_name of \c /tmp/A.h5. If that + * target file does not exist, the new \p file_name after + * stripping will be \c tmp\A.h5. + * -# \p file_name is in UNC (Uniform Naming Convention) format with + * server name, share name, and pathname. For example, consider + * a \p file_name of \c /tmp/A.h5. If that target file does not + * exist, the new \p file_name after stripping will be \c A.h5. + * -# \p file_name is in Long UNC (Uniform Naming Convention) format + * with server name, share name, and pathname. For example, + * consider a \p file_name of \c /tmp/A.h5. If that target file + * does not exist, the new \p file_name after stripping will be + * \c A.h5. + * -# \p file_name is in Long UNC (Uniform Naming Convention) format + * with an absolute drive and an absolute pathname. For example, + * consider a \p file_name of \c /tmp/A.h5. If that target file + * does not exist, the new \p file_name after stripping will be + * \c A.h5. + * + * The library opens target file \p file_name with the file access + * property list that is set via H5Pset_elink_fapl() when the external + * link link_name is accessed. If no such property list is set, the + * library uses the file access property list associated with the file + * of \p link_loc_id to open the target file. + * + * If an application requires additional control over file access + * flags or the file access property list, see H5Pset_elink_cb(); this + * function enables the use of an external link callback function as + * described in H5L_elink_traverse_t(). + * + * \attention A file close degree property setting (H5Pset_fclose_degree()) in + * the external link file access property list or in the external + * link callback function will be ignored. A file opened by means of + * traversing an external link is always opened with the weak file + * close degree property setting, #H5F_CLOSE_WEAK . + * + * \see H5Lcreate_hard(), H5Lcreate_soft(), H5Lcreate_ud() + * + * \since 1.8.0 + */ H5_DLL herr_t H5Lcreate_external(const char *file_name, const char *obj_name, hid_t link_loc_id, const char *link_name, hid_t lcpl_id, hid_t lapl_id); @@ -205,49 +1609,508 @@ H5_DLL herr_t H5Lcreate_external(const char *file_name, const char *obj_name, hi /* Typedefs */ /* Information struct for link (for H5Lget_info1/H5Lget_info_by_idx1) */ +//! [H5L_info1_t_snip] typedef struct { - H5L_type_t type; /* Type of link */ - hbool_t corder_valid; /* Indicate if creation order is valid */ - int64_t corder; /* Creation order */ - H5T_cset_t cset; /* Character set of link name */ + H5L_type_t type; /**< Type of link */ + hbool_t corder_valid; /**< Indicate if creation order is valid */ + int64_t corder; /**< Creation order */ + H5T_cset_t cset; /**< Character set of link name */ union { - haddr_t address; /* Address hard link points to */ - size_t val_size; /* Size of a soft link or UD link value */ + haddr_t address; /**< Address hard link points to */ + size_t val_size; /**< Size of a soft link or UD link value */ } u; } H5L_info1_t; +//! [H5L_info1_t_snip] -/* Callback during link traversal */ +/** Callback during link traversal */ typedef hid_t (*H5L_traverse_0_func_t)(const char *link_name, hid_t cur_group, const void *lnkdata, size_t lnkdata_size, hid_t lapl_id); -/* User-defined link types */ +/** User-defined link types */ typedef struct { - int version; /* Version number of this struct */ - H5L_type_t id; /* Link type ID */ - const char * comment; /* Comment for debugging */ - H5L_create_func_t create_func; /* Callback during link creation */ - H5L_move_func_t move_func; /* Callback after moving link */ - H5L_copy_func_t copy_func; /* Callback after copying link */ - H5L_traverse_0_func_t trav_func; /* Callback during link traversal */ - H5L_delete_func_t del_func; /* Callback for link deletion */ - H5L_query_func_t query_func; /* Callback for queries */ + int version; /**< Version number of this struct */ + H5L_type_t id; /**< Link type ID */ + const char *comment; /**< Comment for debugging */ + H5L_create_func_t create_func; /**< Callback during link creation */ + H5L_move_func_t move_func; /**< Callback after moving link */ + H5L_copy_func_t copy_func; /**< Callback after copying link */ + H5L_traverse_0_func_t trav_func; /**< Callback during link traversal */ + H5L_delete_func_t del_func; /**< Callback for link deletion */ + H5L_query_func_t query_func; /**< Callback for queries */ } H5L_class_0_t; -/* Prototype for H5Literate1/H5Literate_by_name1() operator */ -typedef herr_t (*H5L_iterate1_t)(hid_t group, const char *name, const H5L_info1_t *info, void *op_data); +/** Prototype for H5Literate1() / H5Literate_by_name1() operator */ +//! [H5L_iterate1_t_snip] +typedef herr_t (*H5L_iterate1_t)(hid_t group, const char *name, const H5L_info1_t *info, + void *op_data); +//! [H5L_iterate1_t_snip] /* Function prototypes */ +/** + * \ingroup H5L + * + * \brief Returns information about a link + * + * \fgdta_loc_id + * \param[in] name Link name + * \param[out] linfo Buffer in which link information is returned + * \lapl_id + * + * \return \herr_t + * + * \deprecated As of HDF5-1.12 this function has been deprecated in favor of + * the function H5Lget_info2() or the macro H5Lget_info(). + * + * \todo We need to get the location ID story straight! + * + * \details H5Lget_info1() returns information about the specified link through + * the \p linfo argument. + * + * The location identifier, \p loc_id, specifies the location of the + * link. A link name, \p name, interpreted relative to \p loc_id, + * specifies the link being queried. + * + * \p lapl_id is the link access property list associated with the + * link \p name. In the general case, when default link access + * properties are acceptable, this can be passed in as #H5P_DEFAULT. + * An example of a situation that requires a non-default link access + * property list is when the link is an external link; an external + * link may require that a link prefix be set in a link access + * property list (see H5Pset_elink_prefix()). + * + * H5Lget_info1() returns information about name in the data structure + * \ref H5L_info1_t, which is described below and defined in + * H5Lpublic.h. This structure is returned in the buffer \p linfo. + * \snippet this H5L_info1_t_snip + * In the above struct, type specifies the link class. Valid values + * include the following: + * \link_types + * There will be additional valid values if user-defined links have + * been registered. + * + * \c corder specifies the link’s creation order position while + * \c corder_valid indicates whether the value in \c corder is valid. + * + * If \c corder_valid is \c TRUE, the value in \c corder is known to + * be valid; if \c corder_valid is \c FALSE, the value in \c corder is + * presumed to be invalid; + * + * \c corder starts at zero (0) and is incremented by one (1) as new + * links are created. But higher-numbered entries are not adjusted + * when a lower-numbered link is deleted; the deleted link’s creation + * order position is simply left vacant. In such situations, the value + * of \c corder for the last link created will be larger than the + * number of links remaining in the group. + * + * \c cset specifies the character set in which the link name is + * encoded. Valid values include the following: + * \csets + * This value is set with H5Pset_char_encoding(). + * + * \c address and \c val_size are returned for hard and symbolic + * links, respectively. Symbolic links include soft and external links + * and some user-defined links. + * + * If the link is a hard link, \c address specifies the file address + * that the link points to. + * + * If the link is a symbolic link, \c val_size will be the length of + * the link value, e.g., the length of the HDF5 path name with a null + * terminator. + * + * \version 1.12.0 Function was deprecated. + * \version 1.8.2 Fortran subroutine added in this release. + * \version 1.8.4 Fortran subroutine syntax changed in this release. + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Lget_info1(hid_t loc_id, const char *name, H5L_info1_t *linfo /*out*/, hid_t lapl_id); +/** + * \ingroup H5L + * + * \brief Retrieves metadata for a link in a group, according to the order + * within a field or index + * + * \loc_id + * \param[in] group_name Group name + * \idx_type + * \order + * \param[in] n Link position for which to retrieve information + * \param[out] linfo Buffer in which link information is returned + * \lapl_id + * + * \return \herr_t + * + * \deprecated As of HDF5-1.12 this function has been deprecated in favor of + * the function H5Lget_info_by_idx2() and the macro + * H5Lget_info_by_idx(). + * + * \details H5get_info_by_idx1() returns the metadata for a link in a group + * according to a specified field or index and a specified order. + * + * The link for which information is to be returned is specified by \p + * idx_type, \p order, and \p n as follows: + * + * - \p idx_type specifies the field by which the links in \p + * group_name are ordered. The links may be indexed on this field, + * in which case operations seeking specific links are likely to + * complete more quickly. + * - \p order specifies the order in which + * the links are to be referenced for the purposes of this function. + * - \p n specifies the position of the subject link. Note that this + * count is zero-based; 0 (zero) indicates that the function will + * return the value of the first link; if \p n is 5, the function + * will return the value of the sixth link; etc. + * + * For example, assume that \p idx_type, \p order, and \p n are + * #H5_INDEX_NAME, #H5_ITER_DEC, and 5, respectively. #H5_INDEX_NAME + * indicates that the links are accessed in lexicographic order by + * their names. #H5_ITER_DEC specifies that the list be traversed in + * reverse order, or in decremented order. And 5 specifies that this + * call to the function will return the metadata for the 6th link + * (\c n + 1) from the end. + * + * See H5Literate1() for a list of valid values and further discussion + * regarding \p idx_type and \p order. + * + * If \p loc_id specifies the group in which the link resides, + * \p group_name can be a dot (\c .). + * + * \version 1.12.0 Function was renamed to H5Lget_index_by_idx1() and deprecated. + * \version 1.8.4 Fortran subroutine syntax changed in this release. + * \version 1.8.2 Fortran subroutine added in this release. + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Lget_info_by_idx1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, H5L_info1_t *linfo /*out*/, hid_t lapl_id); +/** + * \ingroup TRAV + * + * \brief Iterates over links in a group, with user callback routine, + * according to the order within an index. + * + * \group_id{grp_id} + * \idx_type + * \order + * \param[in,out] idx Pointer to an iteration index to allow + * continuing a previous iteration + * \op + * \op_data + * \return \success{The return value of the first operator that returns + * non-zero, or zero if all members were processed with no + * operator returning non-zero.} + * \return \failure{Negative if an error occurs in the library, or the negative + * value returned by one of the operators.} + * + * \deprecated Deprecated in favor of H5Literate2(). + * + * \details H5Literate1() iterates through the links in a file or + * group, \p group_id, in the order of the specified + * index, \p idx_type, using a user-defined callback routine + * \p op. H5Literate1() does not recursively follow links into + * subgroups of the specified group. + * + * Three parameters are used to manage progress of the iteration: + * \p idx_type, \p order, and \p idx_p. + * + * \p idx_type specifies the index to be used. If the links have + * not been indexed by the index type, they will first be sorted by + * that index then the iteration will begin; if the links have been + * so indexed, the sorting step will be unnecessary, so the iteration + * may begin more quickly. + * + * \p order specifies the order in which objects are to be inspected + * along the index \p idx_type. + * + * \p idx_p tracks the iteration and allows an iteration to be + * resumed if it was stopped before all members were processed. It is + * passed in by the application with a starting point and returned by + * the library with the point at which the iteration stopped. + * + * \p op_data is a user-defined pointer to the data required to + * process links in the course of the iteration. This pointer is + * passed back to each step of the iteration in the \p op callback + * function's \p op_data parameter. \p op is invoked for each link + * encounter. + * + * \p op_data is passed to and from each iteration and can be used to + * supply or aggregate information across iterations. + * + * \remark Same pattern of behavior as H5Giterate(). + * + * \note This function is also available through the H5Literate() macro. + * + * \warning The behavior of H5Literate1() is undefined if the link + * membership of \p group_id changes during the iteration. + * This does not limit the ability to change link destinations + * while iterating, but caution is advised. + * + * + * \version 1.12.0 Function was deprecated in this release. + * \since 1.8.0 + * + * \see H5Literate_by_name2(), H5Lvisit2(), H5Lvisit_by_name2() + * + */ H5_DLL herr_t H5Literate1(hid_t grp_id, H5_index_t idx_type, H5_iter_order_t order, hsize_t *idx, H5L_iterate1_t op, void *op_data); +/** + * \ingroup TRAV + * + * \brief Iterates through links in a group by its name + * + * \loc_id + * \param[in] group_name Group name + * \idx_type + * \order + * \param[in,out] idx iteration position at which to start (\Emph{IN}) or + * position at which an interrupted iteration may be restarted + * (\Emph{OUT}) + * \op + * \op_data + * \lapl_id + * + * \return \success{The return value of the first operator that returns + * non-zero, or zero if all members were processed with no + * operator returning non-zero.} + * \return \failure{Negative if an error occurs in the library, or the negative + * value returned by one of the operators.} + * + * \deprecated As of HDF5-1.12 this function has been deprecated in favor of + * the function H5Literate_by_name2() or the macro + * H5Literate_by_name(). + * + * \details H5Literate_by_name1() iterates through the links in a group + * specified by \p loc_id and \p group_name, in the order of the + * specified index, \p idx_type, using a user-defined callback routine + * \p op. H5Literate_by_name1() does not recursively follow links into + * subgroups of the specified group. + * + * \p idx_type specifies the index to be used. If the links have not + * been indexed by the index type, they will first be sorted by that + * index then the iteration will begin; if the links have been so + * indexed, the sorting step will be unnecessary, so the iteration may + * begin more quickly. Valid values include the following: + * \indexes + * + * \p order specifies the order in which objects are to be inspected + * along the index specified in \p idx_type. Valid values include the + * following: + * \orders + * + * \p idx allows an interrupted iteration to be resumed; it is + * passed in by the application with a starting point and returned by + * the library with the point at which the iteration stopped. + * + * \note H5Literate_by_name1() is not recursive. In particular, if a member of + * \p group_name is found to be a group, call it \c subgroup_a, + * H5Literate_by_name1() does not examine the members of \c subgroup_a. + * When recursive iteration is required, the application must handle the + * recursion, explicitly calling H5Literate_by_name1() on discovered + * subgroups. + * + * \note H5Literate_by_name1() assumes that the membership of the group being + * iterated over remains unchanged through the iteration; if any of the + * links in the group change during the iteration, the function’s + * behavior is undefined. Note, however, that objects pointed to by the + * links can be modified. + * + * \note H5Literate_by_name1() is the same as H5Giterate(), except that + * H5Giterate() always proceeds in lexicographic order. + * + * \version 1.12.0 Function H5Literate_by_name() was renamed to + * H5Literate_by_name1() and deprecated. + * \version 1.8.8 Fortran subroutine added. + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Literate_by_name1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t *idx, H5L_iterate1_t op, void *op_data, hid_t lapl_id); +/** + * \ingroup TRAV + * + * \brief Recursively visits all links starting from a specified group + * + * \group_id{grp_id} + * \idx_type + * \order + * \op + * \op_data + * + * \return \success{The return value of the first operator that returns + * non-zero, or zero if all members were processed with no + * operator returning non-zero.} + * \return \failure{Negative if an error occurs in the library, or the negative + * value returned by one of the operators.} + * + * \deprecated As of HDF5-1.12 this function has been deprecated in favor of + * the function H5Lvisit2() or the macro H5Lvisit(). + * + * \details H5Lvisit1() is a recursive iteration function to visit all links in + * and below a group in an HDF5 file, thus providing a mechanism for + * an application to perform a common set of operations across all of + * those links or a dynamically selected subset. For non-recursive + * iteration across the members of a group, see H5Literate1(). + * + * The group serving as the root of the iteration is specified by its + * group or file identifier, \p group_id. + * + * Two parameters are used to establish the iteration: \p idx_type and + * \p order. + * + * \p idx_type specifies the index to be used. If the links have not + * been indexed by the index type, they will first be sorted by that + * index then the iteration will begin; if the links have been so + * indexed, the sorting step will be unnecessary, so the iteration may + * begin more quickly. Valid values include the following: + * \indexes + * + * Note that the index type passed in \p idx_type is a best effort + * setting. If the application passes in a value indicating iteration + * in creation order and a group is encountered that was not tracked + * in creation order, that group will be iterated over in + * lexicographic order by name, or name order. (Name order is the + * native order used by the HDF5 library and is always available.) + * + * \p order specifies the order in which objects are to be inspected + * along the index specified in \p idx_type. Valid values include the + * following: + * \orders + * + * \p op is a callback function of type \ref H5L_iterate1_t that is invoked + * for each link encountered. + * \snippet this H5L_iterate1_t_snip + * + * The \ref H5L_info1_t struct is defined (in H5Lpublic.h) as follows: + * \snippet this H5L_info1_t_snip + * + * The possible return values from the callback function, and the + * effect of each, are as follows: + * \li Zero causes the visit iterator to continue, returning zero when + * all group members have been processed. + * \li A positive value causes the visit iterator to immediately + * return that positive value, indicating short-circuit success. + * \li A negative value causes the visit iterator to immediately + * return that value, indicating failure. + * + * The H5Lvisit1() \p op_data parameter is a user-defined pointer to + * the data required to process links in the course of the iteration. + * This pointer is passed back to each step of the iteration in the + * \p op callback function's \p op_data parameter. + * + * H5Lvisit1() and H5Ovisit1() are companion functions: one for + * examining and operating on links; the other for examining and + * operating on the objects that those links point to. Both functions + * ensure that by the time the function completes successfully, every + * link or object below the specified point in the file has been + * presented to the application for whatever processing the + * application requires. + * + * \version 1.12.0 Function was renamed from H5Lvisit() to H5Lvisit1() and + * deprecated. + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Lvisit1(hid_t grp_id, H5_index_t idx_type, H5_iter_order_t order, H5L_iterate1_t op, void *op_data); +/** + * \ingroup TRAV + * + * \brief Recursively visits all links starting from a specified group + * + * \loc_id + * \param[in] group_name Group name + * \idx_type + * \order + * \op + * \op_data + * \lapl_id + * + * \return \success{The return value of the first operator that returns + * non-zero, or zero if all members were processed with no + * operator returning non-zero.} + * \return \failure{Negative if an error occurs in the library, or the negative + * value returned by one of the operators.} + * + * \deprecated As of HDF5-1.12 this function has been deprecated in favor of + * the function H5Lvisit_by_name2() or the macro H5Lvisit_by_name(). + * + * \details H5Lvisit_by_name1() is a recursive iteration function to visit all + * links in and below a group in an HDF5 file, thus providing a + * mechanism for an application to perform a common set of operations + * across all of those links or a dynamically selected subset. For + * non-recursive iteration across the members of a group, see + * H5Literate1(). + * + * The group serving as the root of the iteration is specified by the + * \p loc_id / \p group_name parameter pair. \p loc_id specifies a + * file or group; group_name specifies either a group in the file + * (with an absolute name based in the file’s root group) or a group + * relative to \p loc_id. If \p loc_id fully specifies the group that + * is to serve as the root of the iteration, group_name should be '.' + * (a dot). (Note that when \p loc_id fully specifies the the group + * that is to serve as the root of the iteration, the user may wish to + * consider using H5Lvisit1() instead of H5Lvisit_by_name1().) + * + * Two parameters are used to establish the iteration: \p idx_type and + * \p order. + * + * \p idx_type specifies the index to be used. If the links have not + * been indexed by the index type, they will first be sorted by that + * index then the iteration will begin; if the links have been so + * indexed, the sorting step will be unnecesary, so the iteration may + * begin more quickly. Valid values include the following: + * \indexes + * + * Note that the index type passed in \p idx_type is a best effort + * setting. If the application passes in a value indicating iteration + * in creation order and a group is encountered that was not tracked + * in creation order, that group will be iterated over in + * lexicographic order by name, or name order. (Name order is the + * native order used by the HDF5 library and is always available.) + * + * \p order specifies the order in which objects are to be inspected + * along the index specified in \p idx_type. Valid values include the + * following: + * \orders + * + * The \p op callback function, the related \ref H5L_info1_t + * \c struct, and the effect that the callback function's return value + * has on the application are described in H5Lvisit1(). + * + * The H5Lvisit_by_name1() \p op_data parameter is a user-defined + * pointer to the data required to process links in the course of the + * iteration. This pointer is passed back to each step of the + * iteration in the callback function's \p op_data parameter. + * + * \p lapl_id is a link access property list. In the general case, + * when default link access properties are acceptable, this can be + * passed in as #H5P_DEFAULT. An example of a situation that requires + * a non-default link access property list is when the link is an + * external link; an external link may require that a link prefix be + * set in a link access property list (see H5Pset_elink_prefix()). + * + * H5Lvisit_by_name1() and H5Ovisit_by_name1() are companion + * functions: one for examining and operating on links; the other for + * examining and operating on the objects that those links point to. + * Both functions ensure that by the time the function completes + * successfully, every link or object below the specified point in the + * file has been presented to the application for whatever processing + * the application requires. + * + * \version 1.12.0 Function renamed from H5Lvisit_by_name() to + * H5Lvisit_by_name1() and deprecated. + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Lvisit_by_name1(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_iter_order_t order, H5L_iterate1_t op, void *op_data, hid_t lapl_id); diff --git a/src/H5PLmodule.h b/src/H5PLmodule.h index 8bf11ce..6e6a088 100644 --- a/src/H5PLmodule.h +++ b/src/H5PLmodule.h @@ -27,4 +27,9 @@ #define H5_MY_PKG_ERR H5E_PLUGIN #define H5_MY_PKG_INIT YES +/**\defgroup H5PL H5PL + * \brief Plugins + * \todo Describe what programmatically controlling dynamically loaded plugins (H5PL) is all about + */ + #endif /* _H5PLmodule_H */ diff --git a/src/H5PLpublic.h b/src/H5PLpublic.h index a54cce0..b345188 100644 --- a/src/H5PLpublic.h +++ b/src/H5PLpublic.h @@ -28,14 +28,20 @@ */ #define H5PL_NO_PLUGIN "::" -/* Plugin type used by the plugin library */ +//! [H5PL_type_t_snip] + +/** + * Plugin type (bit-position) used by the plugin library + */ typedef enum H5PL_type_t { - H5PL_TYPE_ERROR = -1, /* Error */ - H5PL_TYPE_FILTER = 0, /* Filter */ - H5PL_TYPE_VOL = 1, /* VOL driver */ - H5PL_TYPE_NONE = 2 /* This must be last! */ + H5PL_TYPE_ERROR = -1, /**< Error */ + H5PL_TYPE_FILTER = 0, /**< Filter */ + H5PL_TYPE_VOL = 1, /**< VOL driver */ + H5PL_TYPE_NONE = 2 /**< Sentinel: This must be last! */ } H5PL_type_t; +//! [H5PL_type_t_snip] + /* Common dynamic plugin type flags used by the set/get_loading_state functions */ #define H5PL_FILTER_PLUGIN 0x0001 #define H5PL_VOL_PLUGIN 0x0002 @@ -46,14 +52,174 @@ extern "C" { #endif /* plugin state */ +/** + * \ingroup H5PL + * \brief Controls the loadability of dynamic plugin types + * + * \param[in] plugin_control_mask The list of dynamic plugin types to enable or disable.\n + * A plugin bit set to 0 (zero) prevents use of that dynamic plugin.\n + * A plugin bit set to 1 (one) enables use of that dynamic plugin.\n + * Setting \p plugin_control_mask to a negative value enables all dynamic + * plugin types.\n + * Setting \p plugin_control_mask to 0 (zero) disables all dynamic plugin\n + * types. + * \return \herr_t + * + * \details H5PLset_loading_state() uses one argument to enable or disable individual plugin types. + * + * \details The \p plugin_control_mask parameter is an encoded integer in which each bit controls a specific + * plugin type. Bit positions allocated to date are specified in \ref H5PL_type_t as follows: + * \snippet this H5PL_type_t_snip + * + * A plugin bit set to 0 (zero) prevents the use of the dynamic plugin type corresponding to that bit + * position. A plugin bit set to 1 (one) allows the use of that dynamic plugin type. + * + * All dynamic plugin types can be enabled by setting \p plugin_control_mask to a negative value. A + * value of 0 (zero) will disable all dynamic plugin types. + * + * The loading of external dynamic plugins can be controlled during runtime with an environment + * variable, \c HDF5_PLUGIN_PRELOAD. H5PLset_loading_state() inspects the \c HDF5_PLUGIN_PRELOAD + * environment variable every time it is called. If the environment variable is set to the special + * \c :: string, all dynamic plugins are disabled. + * + * \warning The environment variable \c HDF5_PLUGIN_PRELOAD controls the loading of dynamic plugin types at + * runtime. If it is set to disable all plugin types, then it will disable them for \Emph{all} + * running programs that access the same variable instance. + * + * \since 1.8.15 + * + */ H5_DLL herr_t H5PLset_loading_state(unsigned int plugin_control_mask); +/** + * \ingroup H5PL + * \brief Queries the loadability of dynamic plugin types + * + * \param[out] plugin_control_mask List of dynamic plugin types that are enabled or disabled.\n + * A plugin bit set to 0 (zero) indicates that that the dynamic plugin type is + * disabled.\n + * A plugin bit set to 1 (one) indicates that that the dynamic plugin type is + * enabled.\n + * If the value of \p plugin_control_mask is negative, all dynamic plugin types + * are enabled.\n + * If the value of \p plugin_control_mask is 0 (zero), all dynamic plugins + * are disabled. + * \return \herr_t + * + * \details H5PLget_loading_state() retrieves the bitmask that controls whether a certain type of plugins + * (e.g.: filters, VOL drivers) will be loaded by the HDF5 library. + * + * Bit positions allocated to date are specified in \ref H5PL_type_t as follows: + * \snippet this H5PL_type_t_snip + * + * \since 1.8.15 + * + */ H5_DLL herr_t H5PLget_loading_state(unsigned int *plugin_control_mask /*out*/); +/** + * \ingroup H5PL + * \brief Inserts a plugin path at the end of the plugin search path list + * + * \param[in] search_path A plugin path + * \return \herr_t + * + * \details H5PLappend() inserts a plugin path at the end of the plugin search path list. + * + * \since 1.10.1 + * + */ H5_DLL herr_t H5PLappend(const char *search_path); +/** + * \ingroup H5PL + * \brief Inserts a plugin path at the beginning of the plugin search path list + * + * \param[in] search_path A plugin path + * \return \herr_t + * + * \details H5PLprepend() inserts a plugin path at the end of the plugin search path list. + * + * \since 1.10.1 + * + */ H5_DLL herr_t H5PLprepend(const char *search_path); +/** + * \ingroup H5PL + * \brief Replaces the path at the specified index in the plugin search path list + * + * \param[in] search_path A plugin path + * \param[in] index Index + * \return \herr_t + * + * \details H5PLreplace() replaces a plugin path at the specified index in the plugin search path list. + * + * \since 1.10.1 + * + */ H5_DLL herr_t H5PLreplace(const char *search_path, unsigned int index); +/** + * \ingroup H5PL + * \brief Inserts a path at the specified index in the plugin search path list + * + * \param[in] search_path A plugin path + * \param[in] index Index + * \return \herr_t + * + * \details H5PLinsert() inserts a plugin path at the specified index in the plugin search path list, + * moving other paths after \p index. + * + * \since 1.10.1 + * + */ H5_DLL herr_t H5PLinsert(const char *search_path, unsigned int index); +/** + * \ingroup H5PL + * \brief Removes a plugin path at a specified index from the plugin search path list + * + * \param[in] index Index + * \return \herr_t + * + * \details H5PLremove() removes a plugin path at the specified \p index and compacts the plugin search path + * list. + * + * \since 1.10.1 + * + */ H5_DLL herr_t H5PLremove(unsigned int index); +/** + * \ingroup H5PL + * \brief Queries the plugin search path list at the specified index + * + * \param[in] index Index + * \param[out] path_buf Pathname + * \param[in] buf_size Size of \p path_buf + * \return Returns the length of the path, a non-negative value, if successful; otherwise returns a negative + * value. + * + * \details H5PLget() queries the plugin path at a specified index. If \p path_buf is non-NULL then it writes + * up to \p buf_size bytes into that buffer and always returns the length of the path name. + * + * If \p path_buf is NULL, this function will simply return the number of characters required to + * store the path name, ignoring \p path_buf and \p buf_size. + * + * If an error occurs then the buffer pointed to by \p path_buf (NULL or non-NULL) is unchanged and + * the function returns a negative value. If a zero is returned for the name's length, then there is + * no path name associated with the index. and the \p path_buf buffer will be unchanged. + * + * \since 1.10.1 + * + */ H5_DLL ssize_t H5PLget(unsigned int index, char *path_buf /*out*/, size_t buf_size); +/** + * \ingroup H5PL + * \brief Retrieves the number of stored plugin paths + * + * \param[out] num_paths Current length of the plugin search path list + * \return \herr_t + * + * \details H5PLsize() retrieves the number of paths stored in the plugin search path list. + * + * \since 1.10.1 + * + */ H5_DLL herr_t H5PLsize(unsigned int *num_paths /*out*/); #ifdef __cplusplus diff --git a/src/H5Pmodule.h b/src/H5Pmodule.h index d8cc430..b9e1180 100644 --- a/src/H5Pmodule.h +++ b/src/H5Pmodule.h @@ -29,4 +29,47 @@ #define H5_MY_PKG_ERR H5E_PLIST #define H5_MY_PKG_INIT YES +/**\defgroup H5P H5P + * \brief Property List Interface + * + * \details The HDF5 Property List Interface provides a mechanism to take + * advantage of more powerful or unusual features in HDF5. + * + * HDF5 objects have properties or characteristics associated with + * them, and there are default properties that handle the most + * common needs. These default properties can be modified using the + * HDF5 Property List Interface. For example, the data storage + * layout property of a dataset is contiguous by default. For better + * performance, the layout can be modified to be chunked or chunked + * and compressed. + * + * \todo Describe concisely what the functions in this module are about. + * \todo Clicking on "more" after "Property List Interface" at the top does not work + * + * \defgroup GPLO General Property List Operations + * \ingroup H5P + * \defgroup GPLOA General Property List Operations (Advanced) + * \ingroup H5P + * \defgroup FCPL File Creation Properties + * \ingroup H5P + * \defgroup FAPL File Access Properties + * \ingroup H5P + * \defgroup GCPL Group Creation Properties + * \ingroup H5P + * \defgroup ALCAPL Attribute and Link Creation Properties + * \ingroup H5P + * \defgroup LAPL Link Access Properties + * \ingroup H5P + * \defgroup DCPL Dataset Creation Properties + * \ingroup H5P + * \defgroup DAPL Dataset Access Properties + * \ingroup H5P + * \defgroup DXPL Dataset Transfer Properties + * \ingroup H5P + * \defgroup OCPL Object Creation Properties + * \ingroup H5P + * \defgroup OCPPL Object Copy Properties + * \ingroup H5P + */ + #endif /* _H5Pmodule_H */ diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h index ffcdd99..a978895 100644 --- a/src/H5Ppublic.h +++ b/src/H5Ppublic.h @@ -232,11 +232,153 @@ H5_DLLVAR hid_t H5P_LST_REFERENCE_ACCESS_ID_g; /*********************/ /* Generic property list routines */ + +/** + * \ingroup GPLO + * + * \brief Terminates access to a property list + * + * \plist_id + * + * \return \herr_t + * + * \details H5Pclose() terminates access to a property list. All property + * lists should be closed when the application is finished + * accessing them. This frees resources used by the property + * list. + * + * \since 1.0.0 + * + */ +H5_DLL herr_t H5Pclose(hid_t plist_id); +/** + * \ingroup GPLO + * + * \brief Creates a new property list as an instance of a property list class + * + * \plistcls_id{cls_id} + * + * \return \hid_t{property list} + * + * \details H5Pcreate() creates a new property list as an instance of + * some property list class. The new property list is initialized + * with default values for the specified class. The classes are as + * follows: + * + * <table> + * <tr> + * <th>Class Identifier</th> + * <th>Class Name</th> + * <th>Comments</th> + * </tr> + * <tr> + * <td>#H5P_ATTRIBUTE_CREATE</td> + * <td>attribute create</td> + * <td>Properties for attribute creation</td> + * </tr> + * <tr> + * <td>#H5P_DATASET_ACCESS</td> + * <td>dataset access</td> + * <td>Properties for dataset access</td> + * </tr> + * <tr> + * <td>#H5P_DATASET_CREATE</td> + * <td>dataset create</td> + * <td>Properties for dataset creation</td> + * </tr> + * <tr> + * <td>#H5P_DATASET_XFER</td> + * <td>data transfer</td> + * <td>Properties for raw data transfer</td> + * </tr> + * <tr> + * <td>#H5P_DATATYPE_ACCESS</td> + * <td>datatype access</td> + * <td>Properties for datatype access</td> + * </tr> + * <tr> + * <td>#H5P_DATATYPE_CREATE</td> + * <td>datatype create</td> + * <td>Properties for datatype creation</td> + * </tr> + * <tr> + * <td>#H5P_FILE_ACCESS</td> + * <td>file access</td> + * <td>Properties for file access</td> + * </tr> + * <tr> + * <td>#H5P_FILE_CREATE</td> + * <td>file create</td> + * <td>Properties for file creation</td> + * </tr> + * <tr> + * <td>#H5P_FILE_MOUNT</td> + * <td>file mount</td> + * <td>Properties for file mounting</td> + * </tr> + * <tr valign="top"> + * <td>#H5P_GROUP_ACCESS</td> + * <td>group access</td> + * <td>Properties for group access</td> + * </tr> + * <tr> + * <td>#H5P_GROUP_CREATE</td> + * <td>group create</td> + * <td>Properties for group creation</td> + * </tr> + * <tr> + * <td>#H5P_LINK_ACCESS</td> + * <td>link access</td> + * <td>Properties governing link traversal when accessing objects</td> + * </tr> + * <tr> + * <td>#H5P_LINK_CREATE</td> + * <td>link create</td> + * <td>Properties governing link creation</td> + * </tr> + * <tr> + * <td>#H5P_OBJECT_COPY</td> + * <td>object copy</td> + * <td>Properties governing the object copying process</td> + * </tr> + * <tr> + * <td>#H5P_OBJECT_CREATE</td> + * <td>object create</td> + * <td>Properties for object creation</td> + * </tr> + * <tr> + * <td>#H5P_STRING_CREATE</td> + * <td>string create</td> + * <td>Properties for character encoding when encoding strings or + * object names</td> + * </tr> + * <tr> + * <td>#H5P_VOL_INITIALIZE</td> + * <td>vol initialize</td> + * <td>Properties for VOL initialization</td> + * </tr> + * </table> + * + * This property list must eventually be closed with H5Pclose(); + * otherwise, errors are likely to occur. + * + * \version 1.12.0 The #H5P_VOL_INITIALIZE property list class was added + * \version 1.8.15 For each class, the class name returned by + * H5Pget_class_name() was added. + * The list of possible Fortran values was updated. + * \version 1.8.0 The following property list classes were added at this + * release: #H5P_DATASET_ACCESS, #H5P_GROUP_CREATE, + * #H5P_GROUP_ACCESS, #H5P_DATATYPE_CREATE, + * #H5P_DATATYPE_ACCESS, #H5P_ATTRIBUTE_CREATE + * + * \since 1.0.0 + * + */ +H5_DLL hid_t H5Pcreate(hid_t cls_id); H5_DLL hid_t H5Pcreate_class(hid_t parent, const char *name, H5P_cls_create_func_t cls_create, void *create_data, H5P_cls_copy_func_t cls_copy, void *copy_data, H5P_cls_close_func_t cls_close, void *close_data); H5_DLL char * H5Pget_class_name(hid_t pclass_id); -H5_DLL hid_t H5Pcreate(hid_t cls_id); H5_DLL herr_t H5Pregister2(hid_t cls_id, const char *name, size_t size, void *def_value, H5P_prp_create_func_t prp_create, H5P_prp_set_func_t prp_set, H5P_prp_get_func_t prp_get, H5P_prp_delete_func_t prp_del, @@ -262,10 +404,80 @@ H5_DLL herr_t H5Pcopy_prop(hid_t dst_id, hid_t src_id, const char *name); H5_DLL herr_t H5Premove(hid_t plist_id, const char *name); H5_DLL herr_t H5Punregister(hid_t pclass_id, const char *name); H5_DLL herr_t H5Pclose_class(hid_t plist_id); -H5_DLL herr_t H5Pclose(hid_t plist_id); H5_DLL hid_t H5Pcopy(hid_t plist_id); /* Object creation property list (OCPL) routines */ + +/** + * \ingroup OCPL + * + * \brief Returns information about a filter in a pipeline + * + * \todo Signature for H5Pget_filter2 is different in H5Pocpl.c than in + * H5Ppublic.h + * + * \plist_id{plist_id} + * \param[in] idx Sequence number within the filter pipeline of the filter + * for which information is sought + * \param[out] flags Bit vector specifying certain general properties of the + * filter + * \param[in,out] cd_nelmts Number of elements in \p cd_values + * \param[out] cd_values Auxiliary data for the filter + * \param[in] namelen Anticipated number of characters in \p name + * \param[out] name Name of the filter + * \param[out] filter_config Bit field, as described in H5Zget_filter_info() + * + * \return Returns a negative value on failure, and the filter identifier + * if successful (see #H5Z_filter_t): + * - #H5Z_FILTER_DEFLATE Data compression filter, + * employing the gzip algorithm + * - #H5Z_FILTER_SHUFFLE Data shuffling filter + * - #H5Z_FILTER_FLETCHER32 Error detection filter, employing the + * Fletcher32 checksum algorithm + * - #H5Z_FILTER_SZIP Data compression filter, employing the + * SZIP algorithm + * - #H5Z_FILTER_NBIT Data compression filter, employing the + * N-bit algorithm + * - #H5Z_FILTER_SCALEOFFSET Data compression filter, employing the + * scale-offset algorithm + * + * \details 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. + * + * \p plist_id must be a dataset or group creation property list. + * + * \p idx is a value between zero and N-1, as described in + * H5Pget_nfilters(). The function will return a negative value if + * the filter number is out of range. + * + * The structure of the \p flags argument is discussed in + * H5Pset_filter(). + * + * On input, \p cd_nelmts indicates the number of entries in the + * \p cd_values array, as allocated by the caller; on return, + * \p cd_nelmts contains the number of values defined by the filter. + * + * If \p name is a pointer to an array of at least \p namelen bytes, + * the filter name will be copied into that array. The name will be + * null terminated if \p namelen is large enough. The filter name + * returned will be the name appearing in the file, the name + * registered for the filter, or an empty string. + * + * \p filter_config is the bit field described in + * H5Zget_filter_info(). + * + * \version 1.8.5 Function extended to work with group creation property + * lists. + * \since 1.8.0 + * + */ +H5_DLL H5Z_filter_t H5Pget_filter2(hid_t plist_id, unsigned idx, + unsigned int *flags/*out*/, + size_t *cd_nelmts/*out*/, + unsigned cd_values[]/*out*/, + size_t namelen, char name[], + unsigned *filter_config /*out*/); H5_DLL herr_t H5Pset_attr_phase_change(hid_t plist_id, unsigned max_compact, unsigned min_dense); H5_DLL herr_t H5Pget_attr_phase_change(hid_t plist_id, unsigned *max_compact, unsigned *min_dense); H5_DLL herr_t H5Pset_attr_creation_order(hid_t plist_id, unsigned crt_order_flags); @@ -277,9 +489,6 @@ H5_DLL herr_t H5Pmodify_filter(hid_t plist_id, H5Z_filter_t filter, unsigned int H5_DLL herr_t H5Pset_filter(hid_t plist_id, H5Z_filter_t filter, unsigned int flags, size_t cd_nelmts, const unsigned int c_values[]); H5_DLL int H5Pget_nfilters(hid_t plist_id); -H5_DLL H5Z_filter_t H5Pget_filter2(hid_t plist_id, unsigned filter, unsigned int *flags /*out*/, - size_t *cd_nelmts /*out*/, unsigned cd_values[] /*out*/, size_t namelen, - char name[], unsigned *filter_config /*out*/); H5_DLL herr_t H5Pget_filter_by_id2(hid_t plist_id, H5Z_filter_t id, unsigned int *flags /*out*/, size_t *cd_nelmts /*out*/, unsigned cd_values[] /*out*/, size_t namelen, char name[] /*out*/, unsigned *filter_config /*out*/); @@ -379,10 +588,592 @@ H5_DLL herr_t H5Pget_page_buffer_size(hid_t plist_id, size_t *buf_size, unsigned unsigned *min_raw_per); /* Dataset creation property list (DCPL) routines */ -H5_DLL herr_t H5Pset_layout(hid_t plist_id, H5D_layout_t layout); + +/** + * \ingroup DCPL + * + * \brief Retrieves the size of chunks for the raw data of a chunked + * layout dataset + * + * \dcpl_id{plist_id} + * \param[in] max_ndims Size of the \p dims array + * \param[out] dim Array to store the chunk dimensions + * + * \return Returns chunk dimensionality if successful; + * otherwise returns a negative value. + * + * \details H5Pget_chunk() retrieves the size of chunks for the raw data + * of a chunked layout dataset. This function is only valid for + * dataset creation property lists. At most, \p max_ndims elements + * of \p dim will be initialized. + * + * \since 1.0.0 + * + */ +H5_DLL int H5Pget_chunk(hid_t plist_id, int max_ndims, hsize_t dim[]/*out*/); +/** + *------------------------------------------------------------------------- + * + * \ingroup DCPL + * + * \brief Retrieves the edge chunk option setting from a dataset creation + * property list + * + * \dcpl_id{plist_id} + * \param[out] opts Edge chunk option flag. Valid values are described in + * H5Pset_chunk_opts(). The option status can be + * retrieved using the bitwise AND operator ( & ). For + * example, the expression + * (opts&#H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS) will + * evaluate to #H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS if + * that option has been enabled. Otherwise, it will + * evaluate to 0 (zero). + * + * \return \herr_t + * + * \details H5Pget_chunk_opts() retrieves the edge chunk option setting + * stored in the dataset creation property list \p plist_id. + * + * \since 1.10.0 + * + */ +H5_DLL herr_t H5Pget_chunk_opts(hid_t plist_id, unsigned *opts); +/** + *------------------------------------------------------------------------- + * + * \ingroup DCPL + * + * \brief Retrieves the time when fill values are written to a dataset + * + * \dcpl_id{plist_id} + * \param[out] fill_time Setting for the timing of writing fill values to + * the dataset + * + * \return \herr_t + * + * \details H5Pget_fill_time() examines the dataset creation property list + * \p plist_id to determine when fill values are to be written to + * a dataset. Valid values returned in \p fill_time are as + * follows: + * + * <table> + * <tr> + * <td>#H5D_FILL_TIME_IFSET</td> + * <td>Fill values are written to the dataset when storage + * space is allocated only if there is a user-defined fill + * value, i.e., one set with H5Pset_fill_value(). (Default) + * </td> + * </tr> + * <tr> + * <td>#H5D_FILL_TIME_ALLOC</td> + * <td>Fill values are written to the dataset when storage + * space is allocated.</td> + * </tr> + * <tr> + * <td>#H5D_FILL_TIME_NEVER</td> + * <td>Fill values are never written to the dataset.</td> + * </tr> + * </table> + * + * \note H5Pget_fill_time() is designed to work in coordination with the + * dataset fill value and dataset storage allocation time properties, + * retrieved with the functions H5Pget_fill_value() and + * H5Pget_alloc_time(). + * + * \since 1.6.0 + * + */ +H5_DLL herr_t H5Pget_fill_time(hid_t plist_id, H5D_fill_time_t + *fill_time/*out*/); +/** + *------------------------------------------------------------------------- + * + * \ingroup DCPL + * + * \brief Retrieves a dataset fill value + * + * \dcpl_id{plist_id} + * \param[in] type_id Datatype identifier for the value passed via + * \p value + * \param[out] value Pointer to buffer to contain the returned + * fill value + * + * \return \herr_t + * + * \details H5Pget_fill_value() returns the dataset fill value defined in + * the dataset creation property list \p plist_id. The fill value + * is returned through the \p value pointer and will be converted + * to the datatype specified by \p type_id. This datatype may + * differ from the fill value datatype in the property list, but + * the HDF5 library must be able to convert between the two + * datatypes. + * + * If the fill value is undefined, i.e., set to NULL in the + * property list, H5Pget_fill_value() will return an error. + * H5Pfill_value_defined() should be used to check for this + * condition before H5Pget_fill_value() is called. + * + * Memory must be allocated by the calling application. + * + * \note H5Pget_fill_value() is designed to coordinate with the dataset + * storage allocation time and fill value write time properties, + * which can be retrieved with the functions H5Pget_alloc_time() + * and H5Pget_fill_time(), respectively. + * + * \since 1.0.0 + * + */ +H5_DLL herr_t H5Pget_fill_value(hid_t plist_id, hid_t type_id, + void *value/*out*/); +/** + *------------------------------------------------------------------------- + * \ingroup DCPL + * + * \brief Returns the layout of the raw data for a dataset + * + * \dcpl_id{plist_id} + * + * \return Returns the layout type (a non-negative value) of a dataset + * creation property list if successful. Valid return values are: + * - #H5D_COMPACT: Raw data is stored in the object header in the + * file. + * - #H5D_CONTIGUOUS: Raw data is stored separately from the object + * header in one contiguous chunk in the file. + * - #H5D_CHUNKED: Raw data is stored separately from the object + * header in chunks in separate locations in the + * file. + * - #H5D_VIRTUAL: Raw data is drawn from multiple datasets in + * different files. + * \return + * Otherwise, returns a negative value indicating failure. + * + * \details H5Pget_layout() returns the layout of the raw data for a + * dataset. This function is only valid for dataset creation + * property lists. + * + * Note that a compact storage layout may affect writing data to + * the dataset with parallel applications. See the H5Dwrite() + * documentation for details. + * + * \version 1.10.0 #H5D_VIRTUAL added in this release. + * + * \since 1.0.0 + * + */ H5_DLL H5D_layout_t H5Pget_layout(hid_t plist_id); -H5_DLL herr_t H5Pset_chunk(hid_t plist_id, int ndims, const hsize_t dim[/*ndims*/]); -H5_DLL int H5Pget_chunk(hid_t plist_id, int max_ndims, hsize_t dim[] /*out*/); +/** + *------------------------------------------------------------------------- + * \ingroup DCPL + * + * \brief Sets the size of the chunks used to store a chunked layout + * dataset + * + * \dcpl_id{plist_id} + * \param[in] ndims The number of dimensions of each chunk + * \param[in] dim An array defining the size, in dataset elements, of + * each chunk + * + * \return \herr_t + * \details H5Pset_chunk() sets the size of the chunks used to store a + * chunked layout dataset. This function is only valid for dataset + * creation property lists. + * + * The \p ndims parameter currently must be the same size as the + * rank of the dataset. + * + * The values of the \p dim array define the size of the chunks + * to store the dataset's raw data. The unit of measure for \p dim + * values is dataset elements. + * + * As a side-effect of this function, the layout of the dataset is + * changed to #H5D_CHUNKED, if it is not already so set. + * + * \note Chunk size cannot exceed the size of a fixed-size dataset. For + * example, a dataset consisting of a 5x4 fixed-size array cannot be + * defined with 10x10 chunks. Chunk maximums: + * - The maximum number of elements in a chunk is 2<sup>32</sup>-1 which + * is equal to 4,294,967,295. If the number of elements in a chunk is + * set via H5Pset_chunk() to a value greater than 2<sup>32</sup>-1, + * then H5Pset_chunk() will fail. + * - The maximum size for any chunk is 4GB. If a chunk that is larger + * than 4GB attempts to be written with H5Dwrite(), then H5Dwrite() + * will fail. + * + * \see H5Pset_layout(), H5Dwrite() + * + * \since 1.0.0 + * + */ +H5_DLL herr_t H5Pset_chunk(hid_t plist_id, int ndims, const hsize_t dim[/*ndims*/]); +/** + *------------------------------------------------------------------------- + * + * \ingroup DCPL + * + * \brief Sets the edge chunk option in a dataset creation property list + * + * \dcpl_id{plist_id} + * \param[in] opts Edge chunk option flag. Valid values are: + * \li #H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS + * When enabled, filters are not applied to partial + * edge chunks. When disabled, partial edge chunks are + * filtered. Enabling this option will improve + * performance when appending to the dataset and, when + * compression filters are used, prevent reallocation + * of these chunks. Datasets created with this option + * enabled will be inaccessible with HDF5 library + * versions before Release 1.10. Default: \e Disabled + * \li 0 (zero) Disables option; partial edge chunks + * will be compressed. + * + * \return \herr_t + * + * \details H5Pset_chunk_opts() sets the edge chunk option in the + * dataset creation property list \p dcpl_id. + * + * The available option is detailed in the parameters section. + * Only chunks that are not completely filled by the dataset’s + * dataspace are affected by this option. Such chunks are + * referred to as partial edge chunks. + * + * \note \b Motivation: H5Pset_chunk_opts() is used to specify storage + * options for chunks on the edge of a dataset’s dataspace. This + * capability allows the user to tune performance in cases where + * the dataset size may not be a multiple of the chunk size and + * the handling of partial edge chunks can impact performance. + * + * \since 1.10.0 + * + */ +H5_DLL herr_t H5Pset_chunk_opts(hid_t plist_id, unsigned opts); +/** + *------------------------------------------------------------------------- + * + * \ingroup DCPL + * + * \brief Sets the time when fill values are written to a dataset + * + * \dcpl_id{plist_id} + * \param[in] fill_time When to write fill values to a dataset + * + * \return \herr_t + * + * \details H5Pset_fill_time() sets up the timing for writing fill values + * to a dataset. This property is set in the dataset creation + * property list \p plist_id. Timing is specified in \p fill_time + * with one of the following values: + * + * <table> + * <tr> + * <td>#H5D_FILL_TIME_IFSET</td> + * <td>Write fill values to the dataset when storage space is + * allocated only if there is a user-defined fill value, + * i.e.,one set with H5Pset_fill_value(). (Default)</td> + * </tr> + * <tr> + * <td>#H5D_FILL_TIME_ALLOC</td> + * <td>Write fill values to the dataset when storage space is + * allocated.</td> + * </tr> + * <tr> + * <td>#H5D_FILL_TIME_NEVER</td> + * <td>Never write fill values to the dataset.</td> + * </tr> + * </table> + * + * \note H5Pset_fill_time() is designed for coordination with the dataset + * fill value and dataset storage allocation time properties, set + * with the functions H5Pset_fill_value() and H5Pset_alloc_time(). + * See H5Dcreate() for further cross-references. + * + * \since 1.6.0 + * + */ +H5_DLL herr_t H5Pset_fill_time(hid_t plist_id, H5D_fill_time_t fill_time); +/** + *------------------------------------------------------------------------- + * + * \ingroup DCPL + * + * \brief Sets the fill value for a dataset + * + * \dcpl_id{plist_id} + * \param[in] type_id Datatype of \p value + * \param[in] value Pointer to buffer containing value to use as + * fill value + * + * \return \herr_t + * + * \details H5Pset_fill_value() sets the fill value for a dataset in the + * dataset creation property list. \p value is interpreted as + * being of datatype \p type_id. This datatype may differ from + * that of the dataset, but the HDF5 library must be able to + * convert \p value to the dataset datatype when the dataset is + * created. + * + * The default fill value is 0 (zero), which is interpreted + * according to the actual dataset datatype. + * + * Setting \p value to NULL indicates that the fill value is to + * be undefined. + * + * \note Applications sometimes write data only to portions of an allocated + * dataset. It is often useful in such cases to fill the unused space + * with a known fill value. This function allows the user application + * to set that fill value; the functions H5Dfill() and + * H5Pset_fill_time(), respectively, provide the ability to apply the + * fill value on demand or to set up its automatic application. + * + * \note A fill value should be defined so that it is appropriate for the + * application. While the HDF5 default fill value is 0 (zero), it is + * often appropriate to use another value. It might be useful, for + * example, to use a value that is known to be impossible for the + * application to legitimately generate. + * + * \note H5Pset_fill_value() is designed to work in concert with + * H5Pset_alloc_time() and H5Pset_fill_time(). H5Pset_alloc_time() + * and H5Pset_fill_time() govern the timing of dataset storage + * allocation and fill value write operations and can be important in + * tuning application performance. + * + * \note See H5Dcreate() for further cross-references. + * + * \since 1.0.0 + * + */ +H5_DLL herr_t H5Pset_fill_value(hid_t plist_id, hid_t type_id, + const void *value); +/** + *------------------------------------------------------------------------- + * + * \ingroup DCPL + * + * \brief Sets up use of the shuffle filter + * + * \dcpl_id{plist_id} + * + * \return \herr_t + * + * \details H5Pset_shuffle() sets the shuffle filter, #H5Z_FILTER_SHUFFLE, + * in the dataset creation property list \p plist_id. The shuffle + * filter de-interlaces a block of data by reordering the bytes. + * All the bytes from one consistent byte position of each data + * element are placed together in one block; all bytes from a + * second consistent byte position of each data element are placed + * together a second block; etc. For example, given three data + * elements of a 4-byte datatype stored as 012301230123, shuffling + * will re-order data as 000111222333. This can be a valuable step + * in an effective compression algorithm because the bytes in each + * byte position are often closely related to each other and + * putting them together can increase the compression ratio. + * + * As implied above, the primary value of the shuffle filter lies + * in its coordinated use with a compression filter; it does not + * provide data compression when used alone. When the shuffle + * filter is applied to a dataset immediately prior to the use of + * a compression filter, the compression ratio achieved is often + * superior to that achieved by the use of a compression filter + * without the shuffle filter. + * + * \since 1.6.0 + * + */ +H5_DLL herr_t H5Pset_shuffle(hid_t plist_id); +/** + *------------------------------------------------------------------------- + * \ingroup DCPL + * + * \brief Sets the type of storage used to store the raw data for a dataset + * + * \dcpl_id{plist_id} + * \param[in] layout Type of storage layout for raw data + * + * \return \herr_t + * \details H5Pset_layout() sets the type of storage used to store the raw + * data for a dataset. This function is only valid for dataset + * creation property lists. + * + * Valid values for \p layout are: + * - #H5D_COMPACT: Store raw data in the dataset object header + * in file. This should only be used for datasets + * with small amounts of raw data. The raw data + * size limit is 64K (65520 bytes). Attempting + * to create a dataset with raw data larger than + * this limit will cause the H5Dcreate() call to + * fail. + * - #H5D_CONTIGUOUS: Store raw data separately from the object + * header in one large chunk in the file. + * - #H5D_CHUNKED: Store raw data separately from the object header + * as chunks of data in separate locations in + * the file. + * - #H5D_VIRTUAL: Draw raw data from multiple datasets in + * different files. + * + * Note that a compact storage layout may affect writing data to + * the dataset with parallel applications. See the note in + * H5Dwrite() documentation for details. + * \version 1.10.0 #H5D_VIRTUAL added in this release. + * \since 1.0.0 + * + */ +H5_DLL herr_t H5Pset_layout(hid_t plist_id, H5D_layout_t layout); +/** + *------------------------------------------------------------------------- + * \ingroup DCPL + * + * \brief Sets up use of the SZIP compression filter + * + * \dcpl_id{plist_id} + * \param[in] options_mask A bit-mask conveying the desired SZIP options; + * Valid values are #H5_SZIP_EC_OPTION_MASK and + * #H5_SZIP_NN_OPTION_MASK. + * \param[in] pixels_per_block The number of pixels or data elements in each + * data block + * + * \return \herr_t + * + * \details H5Pset_szip() sets an SZIP compression filter, #H5Z_FILTER_SZIP, + * for a dataset. SZIP is a compression method designed for use with + * scientific data. + * + * Before proceeding, all users should review the “Limitations” + * section below. + * + * Users familiar with SZIP outside the HDF5 context may benefit + * from reviewing the Note “For Users Familiar with SZIP in Other + * Contexts” below. + * + * In the text below, the term pixel refers to an HDF5 data element. + * This terminology derives from SZIP compression's use with image + * data, where pixel referred to an image pixel. + * + * The SZIP \p bits_per_pixel value (see Note, below) is automatically + * set, based on the HDF5 datatype. SZIP can be used with atomic + * datatypes that may have size of 8, 16, 32, or 64 bits. + * Specifically, a dataset with a datatype that is 8-, 16-, 32-, or + * 64-bit signed or unsigned integer; char; or 32- or 64-bit float + * can be compressed with SZIP. See Note, below, for further + * discussion of the the SZIP \p bits_per_pixel setting. + * + * SZIP options are passed in an options mask, \p options_mask, + * as follows. + * + * <table> + * <tr> + * <th>Option</th> + * <th>Description (Mutually exclusive; select one.)</th> + * </tr> + * <tr> + * <td>#H5_SZIP_EC_OPTION_MASK</td> + * <td>Selects entropy coding method</td> + * </tr> + * <tr> + * <td>#H5_SZIP_NN_OPTION_MASK</td> + * <td>Selects nearest neighbor coding method</td> + * </tr> + * </table> + * + * The following guidelines can be used in determining which + * option to select: + * + * - The entropy coding method, the EC option specified by + * #H5_SZIP_EC_OPTION_MASK, is best suited for data that has been + * processed. The EC method works best for small numbers. + * - The nearest neighbor coding method, the NN option specified + * by #H5_SZIP_NN_OPTION_MASK, preprocesses the data then the + * applies EC method as above. + * + * Other factors may affect results, but the above criteria + * provides a good starting point for optimizing data compression. + * + * SZIP compresses data block by block, with a user-tunable block + * size. This block size is passed in the parameter + * \p pixels_per_block and must be even and not greater than 32, + * with typical values being 8, 10, 16, or 32. This parameter + * affects compression ratio; the more pixel values vary, the + * smaller this number should be to achieve better performance. + * + * In HDF5, compression can be applied only to chunked datasets. + * If \p pixels_per_block is bigger than the total number of + * elements in a dataset chunk, H5Pset_szip() will succeed but + * the subsequent call to H5Dcreate() will fail; the conflict + * can be detected only when the property list is used. + * + * To achieve optimal performance for SZIP compression, it is + * recommended that a chunk's fastest-changing dimension be equal + * to N times \p pixels_per_block where N is the maximum number of + * blocks per scan line allowed by the SZIP library. In the + * current version of SZIP, N is set to 128. + * + * SZIP compression is an optional HDF5 filter. + * + * \b Limitations: + * + * - SZIP compression cannot be applied to compound, array, + * variable-length, enumeration, or any other user-defined + * datatypes. If an SZIP filter is set in a dataset creation + * property list used to create a dataset containing a + * non-allowed datatype, the call to H5Dcreate() will fail; the + * conflict can be detected only when the property list is used. + * - Users should be aware that there are factors that affect one’s + * rights and ability to use SZIP compression by reviewing the + * SZIP copyright notice. + * + * \note \b For \b Users \b Familiar \b with \b SZIP \b in \b Other \b Contexts: + * + * \note The following notes are of interest primarily to those who have + * used SZIP compression outside of the HDF5 context. + * In non-HDF5 applications, SZIP typically requires that the user + * application supply additional parameters: + * - \p pixels_in_object, the number of pixels in the object to + * be compressed + * - \p bits_per_pixel, the number of bits per pixel + * - \p pixels_per_scanline, the number of pixels per scan line + * + * \note These values need not be independently supplied in the HDF5 + * environment as they are derived from the datatype and dataspace, + * which are already known. In particular, HDF5 sets + * \p pixels_in_object to the number of elements in a chunk and + * \p bits_per_pixel to the size of the element or pixel datatype. + * + * \note The following algorithm is used to set \p pixels_per_scanline: + * - If the size of a chunk's fastest-changing dimension, size, + * is greater than 4K, set \p pixels_per_scanline to 128 times + * \p pixels_per_block. + * - If size is less than 4K but greater than \p pixels_per_block, + * set \p pixels_per_scanline to the minimum of size and 128 + * times \p pixels_per_block. + * - If size is less than \p pixels_per_block but greater than the + * number elements in the chunk, set \p pixels_per_scanline to + * the minimum of the number elements in the chunk and 128 times + * \p pixels_per_block. + * + * \note The HDF5 datatype may have precision that is less than the full + * size of the data element, e.g., an 11-bit integer can be defined + * using H5Tset_precision(). To a certain extent, SZIP can take + * advantage of the precision of the datatype to improve compression: + * - If the HDF5 datatype size is 24-bit or less and the offset of + * the bits in the HDF5 datatype is zero (see H5Tset_offset() or + * H5Tget_offset()), the data is the in lowest N bits of the data + * element. In this case, the SZIP \p bits_per_pixel is set to the + * precision of the HDF5 datatype. + * - If the offset is not zero, the SZIP \p bits_per_pixel will be + * set to the number of bits in the full size of the data element. + * - If the HDF5 datatype precision is 25-bit to 32-bit, the SZIP + * \p bits_per_pixel will be set to 32. + * - If the HDF5 datatype precision is 33-bit to 64-bit, the SZIP + * \p bits_per_pixel will be set to 64. + * + * \note HDF5 always modifies the options mask provided by the user to set up + * usage of RAW_OPTION_MASK, ALLOW_K13_OPTION_MASK, and one of + * LSB_OPTION_MASK or MSB_OPTION_MASK, depending on endianness of the + * datatype. + * + * \since 1.6.0 + * + *-------------------------------------------------------------------------- + */ +H5_DLL herr_t H5Pset_szip(hid_t plist_id, unsigned options_mask, unsigned pixels_per_block); H5_DLL herr_t H5Pset_virtual(hid_t dcpl_id, hid_t vspace_id, const char *src_file_name, const char *src_dset_name, hid_t src_space_id); H5_DLL herr_t H5Pget_virtual_count(hid_t dcpl_id, size_t *count /*out*/); @@ -391,22 +1182,14 @@ H5_DLL hid_t H5Pget_virtual_srcspace(hid_t dcpl_id, size_t index); H5_DLL ssize_t H5Pget_virtual_filename(hid_t dcpl_id, size_t index, char *name /*out*/, size_t size); H5_DLL ssize_t H5Pget_virtual_dsetname(hid_t dcpl_id, size_t index, char *name /*out*/, size_t size); H5_DLL herr_t H5Pset_external(hid_t plist_id, const char *name, off_t offset, hsize_t size); -H5_DLL herr_t H5Pset_chunk_opts(hid_t plist_id, unsigned opts); -H5_DLL herr_t H5Pget_chunk_opts(hid_t plist_id, unsigned *opts); H5_DLL int H5Pget_external_count(hid_t plist_id); H5_DLL herr_t H5Pget_external(hid_t plist_id, unsigned idx, size_t name_size, char *name /*out*/, off_t *offset /*out*/, hsize_t *size /*out*/); -H5_DLL herr_t H5Pset_szip(hid_t plist_id, unsigned options_mask, unsigned pixels_per_block); -H5_DLL herr_t H5Pset_shuffle(hid_t plist_id); H5_DLL herr_t H5Pset_nbit(hid_t plist_id); H5_DLL herr_t H5Pset_scaleoffset(hid_t plist_id, H5Z_SO_scale_type_t scale_type, int scale_factor); -H5_DLL herr_t H5Pset_fill_value(hid_t plist_id, hid_t type_id, const void *value); -H5_DLL herr_t H5Pget_fill_value(hid_t plist_id, hid_t type_id, void *value /*out*/); H5_DLL herr_t H5Pfill_value_defined(hid_t plist, H5D_fill_value_t *status); H5_DLL herr_t H5Pset_alloc_time(hid_t plist_id, H5D_alloc_time_t alloc_time); H5_DLL herr_t H5Pget_alloc_time(hid_t plist_id, H5D_alloc_time_t *alloc_time /*out*/); -H5_DLL herr_t H5Pset_fill_time(hid_t plist_id, H5D_fill_time_t fill_time); -H5_DLL herr_t H5Pget_fill_time(hid_t plist_id, H5D_fill_time_t *fill_time /*out*/); H5_DLL herr_t H5Pget_dset_no_attrs_hint(hid_t dcpl_id, hbool_t *minimize); H5_DLL herr_t H5Pset_dset_no_attrs_hint(hid_t dcpl_id, hbool_t minimize); @@ -526,6 +1309,59 @@ H5_DLL herr_t H5Pinsert1(hid_t plist_id, const char *name, size_t size, vo H5P_prp_delete_func_t prp_delete, H5P_prp_copy_func_t prp_copy, H5P_prp_close_func_t prp_close); H5_DLL herr_t H5Pencode1(hid_t plist_id, void *buf, size_t *nalloc); +/** + *------------------------------------------------------------------------- + * \ingroup OCPL + * + * \brief Returns information about a filter in a pipeline (DEPRECATED) + * + * \todo H5Pget_filter1() prototype does not match source in H5Pocpl.c. + * Also, it is not in a deprecated file. Is that okay? + * + * \plist_id{plist_id} + * \param[in] filter Sequence number within the filter pipeline of the filter + * for which information is sought + * \param[out] flags Bit vector specifying certain general properties of + * the filter + * \param[in,out] cd_nelmts Number of elements in \p cd_values + * \param[out] cd_values Auxiliary data for the filter + * \param[in] namelen Anticipated number of characters in \p name + * \param[out] name Name of the filter + * + * \return Returns the filter identifier if successful; Otherwise returns + * a negative value. See: #H5Z_filter_t + * + * \details H5Pget_filter1() returns information about a filter, specified + * by its filter number, in a filter pipeline, specified by the + * property list with which it is associated. + * + * \p plist_id must be a dataset or group creation property list. + * + * \p filter is a value between zero and N-1, as described in + * H5Pget_nfilters(). The function will return a negative value + * if the filter number is out of range. + * + * The structure of the \p flags argument is discussed in + * H5Pset_filter(). + * + * On input, \p cd_nelmts indicates the number of entries in the + * \p cd_values array, as allocated by the caller; on return, + * \p cd_nelmts contains the number of values defined by the filter. + * + * If \p name is a pointer to an array of at least \p namelen + * bytes, the filter name will be copied into that array. The name + * will be null terminated if \p namelen is large enough. The + * filter name returned will be the name appearing in the file, the + * name registered for the filter, or an empty string. + * + * \version 1.8.5 Function extended to work with group creation property + * lists. + * \version 1.8.0 N-bit and scale-offset filters added. + * \version 1.8.0 Function H5Pget_filter() renamed to H5Pget_filter1() and + * deprecated in this release. + * \version 1.6.4 \p filter parameter type changed to unsigned. + * + */ H5_DLL H5Z_filter_t H5Pget_filter1(hid_t plist_id, unsigned filter, unsigned int *flags /*out*/, size_t *cd_nelmts /*out*/, unsigned cd_values[] /*out*/, size_t namelen, char name[]); diff --git a/src/H5Smodule.h b/src/H5Smodule.h index 11494ee..6e8208b 100644 --- a/src/H5Smodule.h +++ b/src/H5Smodule.h @@ -29,4 +29,31 @@ #define H5_MY_PKG_ERR H5E_DATASPACE #define H5_MY_PKG_INIT YES +/**\defgroup H5S H5S + * \brief Dataspace Interface + * + * \details The Dataspace Interface provides functions for creating and + * working with dataspaces. + * + * A dataspace has two roles: + * + * \li It contains the spatial information (logical layout) of a + * dataset stored in a file. + * \li It describes an application’s data buffers and data elements + * participating in I/O. In other words, it can be used to + * select a portion or subset of a dataset. + * + * The spatial information of a dataset in a file includes the + * rank and dimensions of the dataset, which are a permanent part + * of the dataset definition. It can have dimensions that are fixed + * (unchanging) or unlimited, which means they can grow in size + * (or are extendible). + * + * A dataspace can consist of: + * \li no elements (NULL) + * \li a single element (scalar), or + * \li a simple array. + * + */ + #endif /* _H5Smodule_H */ diff --git a/src/H5Spublic.h b/src/H5Spublic.h index f0aa6dc..c16af93 100644 --- a/src/H5Spublic.h +++ b/src/H5Spublic.h @@ -120,17 +120,288 @@ typedef enum { extern "C" { #endif -/* Operations on dataspaces */ +/* Operations on dataspaces and dataspace selections */ + +/** + * \ingroup H5S + * + * \brief Releases and terminates access to a dataspace + * + * \space_id + * + * \return \herr_t + * + * \details H5Sclose() releases a dataspace. Further access through the + * dataspace identifier is illegal. Failure to release a dataspace with this + * call will result in resource leaks. + * + * \version 1.4.0 Fortran subroutine introduced in this release. + * \since 1.0.0 + * + */ +H5_DLL herr_t H5Sclose(hid_t space_id); +/** + * \ingroup H5S + * + * \brief Creates a new dataspace of a specified type + * + * \param[in] type Type of dataspace to be created + * + * \return \hid_t{dataspace} + * + * \details H5Screate() creates a new dataspace of a particular type. Currently + * supported types are #H5S_SCALAR, #H5S_SIMPLE, and #H5S_NULL. + * + * Further dataspace types may be added later. + * + * A scalar dataspace, #H5S_SCALAR, has a single element, though that + * element may be of a complex datatype, such as a compound or array + * datatype. By convention, the rank of a scalar dataspace is always \p 0 + * (zero); think of it geometrically as a single, dimensionless point, + * though that point can be complex. + * + * A simple dataspace, #H5S_SIMPLE, consists of a regular array of elements. + * + * A null dataspace, #H5S_NULL, has no data elements. + * + * The dataspace identifier returned by this function can be released with + * H5Sclose() so that resource leaks will not occur. + * + * \version 1.4.0 Fortran subroutine introduced. + * \since 1.0.0 + * + */ H5_DLL hid_t H5Screate(H5S_class_t type); +/** + * \ingroup H5S + * \brief Creates a new simple dataspace and opens it for access + * + * \param[in] rank Number of dimensions of dataspace + * \param[in] dims Array specifying the size of each dimension + * \param[in] maxdims Array specifying the maximum size of each dimension + * + * \return \hid_t{dataspace} + * + * \details H5Screate_simple() creates a new simple dataspace and opens it + * for access, returning a dataspace identifier. + * + * \p rank is the number of dimensions used in the dataspace. + * + * \p dims is a one-dimensional array of size rank specifying the + * size of each dimension of the dataset. \p maxdims is an array of the + * same size specifying the upper limit on the size of each dimension. + * + * Any element of \p dims can be \p 0 (zero). Note that no data can + * be written to a dataset if the size of any dimension of its current + * dataspace is \p 0. This is sometimes a useful initial state for a dataset. + * + * \p maxdims may be the null pointer, in which case the upper limit is + * the same as \p dims. Otherwise, no element of \p maxdims + * should be smaller than the corresponding element of \p dims. + * + * If an element of \p maxdims is #H5S_UNLIMITED, the maximum size of the + * corresponding dimension is unlimited. + * + * Any dataset with an unlimited dimension must also be chunked; see + * H5Pset_chunk(). Similarly, a dataset must be chunked if \p dims does + * not equal \p maxdims. + * + * The dataspace identifier returned from this function must be released with + * H5Sclose() or resource leaks will occur. + * + * \note Once a dataspace has been created, specific regions or elements in + * the dataspace can be selected and selections can be removed, as well. + * For example, H5Sselect_hyperslab() selects a region in a dataspace and + * H5Sselect_elements() selects array elements in a dataspace. These + * functions are used for subsetting. H5Sselect_none() removes all + * selections from a dataspace and is used in Parallel HDF5 when a process + * does not have or need to write data. + * + * \version 1.4.0 Fortran subroutine introduced. + * + * \since 1.0.0 + * + */ H5_DLL hid_t H5Screate_simple(int rank, const hsize_t dims[], const hsize_t maxdims[]); +/*--------------------------------------------------------------------------*/ +/**\ingroup H5S + * + * \brief Determines the number of elements in a dataspace selection + * + * \space_id{spaceid} + * + * \return Returns the number of elements in the selection if successful; + * otherwise returns a negative value. + * + * \details H5Sget_select_npoints() determines the number of elements in + * the current selection of a dataspace. It works with any + * selection type, and is the correct way to retrieve the number + * of elements in a selection. + * + * \version 1.4.0 Fortran subroutine introduced in this release. + * \since 1.0.0 + * + */ +H5_DLL hssize_t H5Sget_select_npoints(hid_t spaceid); +/*-------------------------------------------------------------------------*/ +/**\ingroup H5S + * + * \brief Retrieves dataspace dimension size and maximum size + * + * \space_id + * \param[out] dims Pointer to array to store the size of each dimension + * \param[out] maxdims Pointer to array to store the maximum size of each + * dimension + * + * \return Returns the number of dimensions in the dataspace if successful; + * otherwise returns a negative value. + * + * \details H5Sget_simple_extent_dims() returns the size and maximum sizes + * of each dimension of a dataspace \p space_id through the \p dims + * and \p maxdims parameters. + * + * Either or both of \p dims and \p maxdims may be NULL. + * + * If a value in the returned array \p maxdims is #H5S_UNLIMITED (-1), + * the maximum size of that dimension is unlimited. + * + * \version 1.4.0 Fortran subroutine introduced. + * \since 1.0.0 + * + */ +H5_DLL int H5Sget_simple_extent_dims(hid_t space_id, hsize_t dims[], + hsize_t maxdims[]); +/*-------------------------------------------------------------------------*/ +/**\ingroup H5S + * + * \brief Determines the dimensionality of a dataspace + * + * \space_id + * + * \return Returns the number of dimensions in the dataspace if successful; + * otherwise returns a negative value. + * + * \details H5Sget_simple_extent_ndims() determines the dimensionality (or + * rank) of a dataspace. + * + * \version 1.4.0 Fortran subroutine introduced. + * \since 1.0.0 + * + */ +H5_DLL int H5Sget_simple_extent_ndims(hid_t space_id); +/*--------------------------------------------------------------------------*/ +/**\ingroup H5S + * + * \brief Selects a hyperslab region to add to the current selected region + * + * \space_id + * \param[in] op Operation to perform on current selection + * \param[in] start Offset of start of hyperslab + * \param[in] stride Hyperslab stride + * \param[in] count Number of blocks included in hyperslab + * \param[in] block Size of block in hyperslab + * + * \return \herr_t + * + * \details H5Sselect_hyperslab() selects a hyperslab region to add to the + * current selected region for the dataspace specified by + * \p space_id. + * + * The \p start, \p stride, \p count, and \p block arrays must be the + * same size as the rank of the dataspace. For example, if the + * dataspace is 4-dimensional, each of these parameters must be a + * 1-dimensional array of size 4. + * + * The selection operator \p op determines how the new selection + * is to be combined with the already existing selection for the + * dataspace. The following operators are supported: + * + * <table> + * <tr> + * <td>#H5S_SELECT_SET</td> + * <td>Replaces the existing selection with the + * parameters from this call. Overlapping blocks + * are not supported with this operator.</td> + * </tr> + * <tr> + * <td>#H5S_SELECT_OR</td> + * <td>Adds the new selection to the existing selection. + * (Binary OR)</td> + * </tr> + * <tr> + * <td>#H5S_SELECT_AND</td> + * <td>Retains only the overlapping portions of the + * new selection and the existing selection. + * (Binary AND)</td> + * </tr> + * <tr> + * <td>#H5S_SELECT_XOR</td> + * <td>Retains only the elements that are members of + * the new selection or the existing selection, + * excluding elements that are members of both + * selections. (Binary exclusive-OR, XOR) + * </td> + * </tr> + * <tr> + * <td>#H5S_SELECT_NOTB</td> + * <td>Retains only elements of the existing selection + * that are not in the new selection.</td> + * </tr> + * <tr> + * <td>#H5S_SELECT_NOTA</td> + * <td>Retains only elements of the new selection that + * are not in the existing selection.</td> + * </tr> + * </table> + * + * The \p start array specifies the offset of the starting element + * of the specified hyperslab. + * + * The \p stride array chooses array locations from the dataspace with + * each value in the \p stride array determining how many elements to + * move in each dimension. Setting a value in the \p stride array to + * \p 1 moves to each element in that dimension of the dataspace; + * setting a value of \p 2 in allocation in the \p stride array moves + * to every other element in that dimension of the dataspace. In + * other words, the \p stride determines the number of elements to + * move from the \p start location in each dimension. Stride values + * of \p 0 are not allowed. If the \p stride parameter is NULL, a + * contiguous hyperslab is selected (as if each value in the \p stride + * array were set to \p 1). + * + * The \p count array determines how many blocks to select from the + * dataspace, in each dimension. + * + * The \p block array determines the size of the element block + * selected from the dataspace. If the \p block parameter is set to + * NULL, the block size defaults to a single element in each dimension + * (as if each value in the \p block array were set to \p 1). + * + * For example, consider a 2-dimensional dataspace with hyperslab + * selection settings as follows: the \p start offset is specified as + * [1,1], \p stride is [4,4], \p count is [3,7], and \p block is [2,2]. + * In C, these settings will specify a hyperslab consisting of 21 + * 2x2 blocks of array elements starting with location (1,1) with the + * selected blocks at locations (1,1), (5,1), (9,1), (1,5), (5,5), etc.; + * in Fortran, they will specify a hyperslab consisting of 21 2x2 + * blocks of array elements starting with location (2,2) with the + * selected blocks at locations (2,2), (6,2), (10,2), (2,6), (6,6), etc. + * + * Regions selected with this function call default to C order + * iteration when I/O is performed. + * + * \version 1.4.0 Fortran subroutine introduced in this release. + * \since 1.0.0 + * + */ +H5_DLL herr_t H5Sselect_hyperslab(hid_t space_id, H5S_seloper_t op, + const hsize_t start[], const hsize_t stride[], const hsize_t count[], + const hsize_t block[]); H5_DLL herr_t H5Sset_extent_simple(hid_t space_id, int rank, const hsize_t dims[], const hsize_t max[]); H5_DLL hid_t H5Scopy(hid_t space_id); -H5_DLL herr_t H5Sclose(hid_t space_id); H5_DLL herr_t H5Sencode2(hid_t obj_id, void *buf, size_t *nalloc, hid_t fapl); H5_DLL hid_t H5Sdecode(const void *buf); H5_DLL hssize_t H5Sget_simple_extent_npoints(hid_t space_id); -H5_DLL int H5Sget_simple_extent_ndims(hid_t space_id); -H5_DLL int H5Sget_simple_extent_dims(hid_t space_id, hsize_t dims[], hsize_t maxdims[]); H5_DLL htri_t H5Sis_simple(hid_t space_id); H5_DLL H5S_class_t H5Sget_simple_extent_type(hid_t space_id); H5_DLL herr_t H5Sset_extent_none(hid_t space_id); @@ -139,7 +410,6 @@ H5_DLL htri_t H5Sextent_equal(hid_t sid1, hid_t sid2); /* Operations on dataspace selections */ H5_DLL H5S_sel_type H5Sget_select_type(hid_t spaceid); -H5_DLL hssize_t H5Sget_select_npoints(hid_t spaceid); H5_DLL herr_t H5Sselect_copy(hid_t dst_id, hid_t src_id); H5_DLL htri_t H5Sselect_valid(hid_t spaceid); H5_DLL herr_t H5Sselect_adjust(hid_t spaceid, const hssize_t *offset); @@ -153,8 +423,6 @@ H5_DLL herr_t H5Sselect_elements(hid_t space_id, H5S_seloper_t op, size_t num_ H5_DLL hssize_t H5Sget_select_elem_npoints(hid_t spaceid); H5_DLL herr_t H5Sget_select_elem_pointlist(hid_t spaceid, hsize_t startpoint, hsize_t numpoints, hsize_t buf[/*numpoints*/]); -H5_DLL herr_t H5Sselect_hyperslab(hid_t space_id, H5S_seloper_t op, const hsize_t start[], - const hsize_t _stride[], const hsize_t count[], const hsize_t _block[]); H5_DLL hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op, const hsize_t start[], const hsize_t _stride[], const hsize_t count[], const hsize_t _block[]); H5_DLL herr_t H5Smodify_select(hid_t space1_id, H5S_seloper_t op, hid_t space2_id); diff --git a/src/H5Tmodule.h b/src/H5Tmodule.h index b508dfd..fd545c2 100644 --- a/src/H5Tmodule.h +++ b/src/H5Tmodule.h @@ -29,4 +29,80 @@ #define H5_MY_PKG_ERR H5E_DATATYPE #define H5_MY_PKG_INIT YES +/** + * \defgroup H5T H5T + * \brief Datatype Interface + * \todo Describe concisely what the functions in this module are about. + * + * \defgroup ARRAY Array Datatypes + * \ingroup H5T + * \defgroup ATOM Atomic Datatypes + * \ingroup H5T + * \defgroup COMPOUND Compound Datatypes + * \ingroup H5T + * \defgroup CONV Conversion Function + * \ingroup H5T + * \defgroup ENUM Enumeration Datatypes + * \ingroup H5T + * \defgroup GTO General Datatype Operations + * \ingroup H5T + * \defgroup OPAQUE Opaque Datatypes + * \ingroup H5T + * \defgroup STRING String Datatypes + * \ingroup H5T + * \defgroup VLEN Variable-length Sequence Datatypes + * \ingroup H5T + * + * \defgroup PDT Predefined Datatypes + * \ingroup H5T + * \details What is a predefined HDF5 datatype? + * \todo Fill in the blanks! + * + * \defgroup PDTCPU By CPU + * \ingroup PDT + * \details CPU-specific datatypes + * \defgroup PDTALPHA DEC Alpha + * \ingroup PDTCPU + * \defgroup PDTX86 AMD & INTEL + * \ingroup PDTCPU + * \defgroup PDTMIPS SGI MIPS + * \ingroup PDTCPU + * + * \defgroup PDTIEEE IEEE + * \ingroup PDT + * \details The IEEE floating point types in big- and little-endian byte orders. + * + * \defgroup PDTSTD Standard Datatypes + * \ingroup PDT + * \details These are "standard" types. For instance, signed (2's complement) + * and unsigned integers of various sizes in big- and little-endian + * byte orders. + * + * \defgroup PDTUNIX UNIX-specific Datatypes + * \ingroup PDT + * \details Types which are particular to Unix. + * \todo Fill in the blanks! + * + * \defgroup PDTNAT Native Datatypes + * \ingroup PDT + * \details These are the datatypes detected during library \Emph{compilation} + * by \c H5detect(). Their names differ from other HDF5 datatype names + * as follows: + * \li Instead of a class name, precision and byte order as the last + * component, they have a C-like type name. + * \li If the type begins with \c U then it is the unsigned version of + * the integer type; other integer types are signed. + * \li The datatype \c LLONG corresponds C's \Code{long long} and + * \c LDOUBLE is \Code{long double}. These types might be the same + * as \c LONG and \c DOUBLE, respectively. + * \defgroup PDTC9x C9x Integer Datatypes + * \ingroup PDTNAT + * \details C9x integer types + * \todo Fill in the blanks! + * + * \defgroup PDTS Strings + * \ingroup PDT + * + */ + #endif /* _H5Tmodule_H */ diff --git a/src/H5Tpublic.h b/src/H5Tpublic.h index 73a00b6..8bebb98 100644 --- a/src/H5Tpublic.h +++ b/src/H5Tpublic.h @@ -23,197 +23,249 @@ #define HOFFSET(S, M) (offsetof(S, M)) -/* These are the various classes of datatypes */ -/* If this goes over 16 types (0-15), the file format will need to change) */ +/** + * These are the various classes of datatypes + * internal If this goes over 16 types (0-15), the file format will need to + * change. + */ +//! [H5T_class_t_snip] typedef enum H5T_class_t { - H5T_NO_CLASS = -1, /*error */ - H5T_INTEGER = 0, /*integer types */ - H5T_FLOAT = 1, /*floating-point types */ - H5T_TIME = 2, /*date and time types */ - H5T_STRING = 3, /*character string types */ - H5T_BITFIELD = 4, /*bit field types */ - H5T_OPAQUE = 5, /*opaque types */ - H5T_COMPOUND = 6, /*compound types */ - H5T_REFERENCE = 7, /*reference types */ - H5T_ENUM = 8, /*enumeration types */ - H5T_VLEN = 9, /*Variable-Length types */ - H5T_ARRAY = 10, /*Array types */ - - H5T_NCLASSES /*this must be last */ + H5T_NO_CLASS = -1, /**< error */ + H5T_INTEGER = 0, /**< integer types */ + H5T_FLOAT = 1, /**< floating-point types */ + H5T_TIME = 2, /**< date and time types */ + H5T_STRING = 3, /**< character string types */ + H5T_BITFIELD = 4, /**< bit field types */ + H5T_OPAQUE = 5, /**< opaque types */ + H5T_COMPOUND = 6, /**< compound types */ + H5T_REFERENCE = 7, /**< reference types */ + H5T_ENUM = 8, /**< enumeration types */ + H5T_VLEN = 9, /**< variable-Length types */ + H5T_ARRAY = 10, /**< array types */ + + H5T_NCLASSES /**< sentinel: this must be last */ } H5T_class_t; +//! [H5T_class_t_snip] -/* Byte orders */ +/** + * Byte orders + */ +//! [H5T_order_t_snip] typedef enum H5T_order_t { - H5T_ORDER_ERROR = -1, /*error */ - H5T_ORDER_LE = 0, /*little endian */ - H5T_ORDER_BE = 1, /*bit endian */ - H5T_ORDER_VAX = 2, /*VAX mixed endian */ - H5T_ORDER_MIXED = 3, /*Compound type with mixed member orders */ - H5T_ORDER_NONE = 4 /*no particular order (strings, bits,..) */ + H5T_ORDER_ERROR = -1, /**< error */ + H5T_ORDER_LE = 0, /**< little endian */ + H5T_ORDER_BE = 1, /**< bit endian */ + H5T_ORDER_VAX = 2, /**< VAX mixed endian */ + H5T_ORDER_MIXED = 3, /**< Compound type with mixed member orders */ + H5T_ORDER_NONE = 4 /**< no particular order (strings, bits,..) */ /*H5T_ORDER_NONE must be last */ } H5T_order_t; +//! [H5T_order_t_snip] -/* Types of integer sign schemes */ +/** + * Types of integer sign schemes + */ +//! [H5T_sign_t_snip] typedef enum H5T_sign_t { - H5T_SGN_ERROR = -1, /*error */ - H5T_SGN_NONE = 0, /*this is an unsigned type */ - H5T_SGN_2 = 1, /*two's complement */ + H5T_SGN_ERROR = -1, /**< error */ + H5T_SGN_NONE = 0, /**< this is an unsigned type */ + H5T_SGN_2 = 1, /**< two's complement */ - H5T_NSGN = 2 /*this must be last! */ + H5T_NSGN = 2 /** sentinel: this must be last! */ } H5T_sign_t; +//! [H5T_sign_t_snip] -/* Floating-point normalization schemes */ +/** + * Floating-point normalization schemes + */ +//! [H5T_norm_t_snip] typedef enum H5T_norm_t { - H5T_NORM_ERROR = -1, /*error */ - H5T_NORM_IMPLIED = 0, /*msb of mantissa isn't stored, always 1 */ - H5T_NORM_MSBSET = 1, /*msb of mantissa is always 1 */ - H5T_NORM_NONE = 2 /*not normalized */ + H5T_NORM_ERROR = -1, /**< error */ + H5T_NORM_IMPLIED = 0, /**< msb of mantissa isn't stored, always 1 */ + H5T_NORM_MSBSET = 1, /**< msb of mantissa is always 1 */ + H5T_NORM_NONE = 2 /**< not normalized */ /*H5T_NORM_NONE must be last */ } H5T_norm_t; +//! [H5T_norm_t_snip] -/* - * Character set to use for text strings. Do not change these values since - * they appear in HDF5 files! +/** + * Character set to use for text strings. + * \internal Do not change these values since they appear in HDF5 files! */ typedef enum H5T_cset_t { - H5T_CSET_ERROR = -1, /*error */ - H5T_CSET_ASCII = 0, /*US ASCII */ - H5T_CSET_UTF8 = 1, /*UTF-8 Unicode encoding */ - H5T_CSET_RESERVED_2 = 2, /*reserved for later use */ - H5T_CSET_RESERVED_3 = 3, /*reserved for later use */ - H5T_CSET_RESERVED_4 = 4, /*reserved for later use */ - H5T_CSET_RESERVED_5 = 5, /*reserved for later use */ - H5T_CSET_RESERVED_6 = 6, /*reserved for later use */ - H5T_CSET_RESERVED_7 = 7, /*reserved for later use */ - H5T_CSET_RESERVED_8 = 8, /*reserved for later use */ - H5T_CSET_RESERVED_9 = 9, /*reserved for later use */ - H5T_CSET_RESERVED_10 = 10, /*reserved for later use */ - H5T_CSET_RESERVED_11 = 11, /*reserved for later use */ - H5T_CSET_RESERVED_12 = 12, /*reserved for later use */ - H5T_CSET_RESERVED_13 = 13, /*reserved for later use */ - H5T_CSET_RESERVED_14 = 14, /*reserved for later use */ - H5T_CSET_RESERVED_15 = 15 /*reserved for later use */ + H5T_CSET_ERROR = -1, /**< error */ + H5T_CSET_ASCII = 0, /**< US ASCII */ + H5T_CSET_UTF8 = 1, /**< UTF-8 Unicode encoding */ + H5T_CSET_RESERVED_2 = 2, /**< reserved for later use */ + H5T_CSET_RESERVED_3 = 3, /**< reserved for later use */ + H5T_CSET_RESERVED_4 = 4, /**< reserved for later use */ + H5T_CSET_RESERVED_5 = 5, /**< reserved for later use */ + H5T_CSET_RESERVED_6 = 6, /**< reserved for later use */ + H5T_CSET_RESERVED_7 = 7, /**< reserved for later use */ + H5T_CSET_RESERVED_8 = 8, /**< reserved for later use */ + H5T_CSET_RESERVED_9 = 9, /**< reserved for later use */ + H5T_CSET_RESERVED_10 = 10, /**< reserved for later use */ + H5T_CSET_RESERVED_11 = 11, /**< reserved for later use */ + H5T_CSET_RESERVED_12 = 12, /**< reserved for later use */ + H5T_CSET_RESERVED_13 = 13, /**< reserved for later use */ + H5T_CSET_RESERVED_14 = 14, /**< reserved for later use */ + H5T_CSET_RESERVED_15 = 15 /**< reserved for later use */ } H5T_cset_t; -#define H5T_NCSET H5T_CSET_RESERVED_2 /*Number of character sets actually defined */ +#define H5T_NCSET H5T_CSET_RESERVED_2 /*Number of character sets actually defined */ -/* - * Type of padding to use in character strings. Do not change these values - * since they appear in HDF5 files! +/** + * Type of padding to use in character strings. + * \internal Do not change these values since they appear in HDF5 files! */ typedef enum H5T_str_t { - H5T_STR_ERROR = -1, /*error */ - H5T_STR_NULLTERM = 0, /*null terminate like in C */ - H5T_STR_NULLPAD = 1, /*pad with nulls */ - H5T_STR_SPACEPAD = 2, /*pad with spaces like in Fortran */ - H5T_STR_RESERVED_3 = 3, /*reserved for later use */ - H5T_STR_RESERVED_4 = 4, /*reserved for later use */ - H5T_STR_RESERVED_5 = 5, /*reserved for later use */ - H5T_STR_RESERVED_6 = 6, /*reserved for later use */ - H5T_STR_RESERVED_7 = 7, /*reserved for later use */ - H5T_STR_RESERVED_8 = 8, /*reserved for later use */ - H5T_STR_RESERVED_9 = 9, /*reserved for later use */ - H5T_STR_RESERVED_10 = 10, /*reserved for later use */ - H5T_STR_RESERVED_11 = 11, /*reserved for later use */ - H5T_STR_RESERVED_12 = 12, /*reserved for later use */ - H5T_STR_RESERVED_13 = 13, /*reserved for later use */ - H5T_STR_RESERVED_14 = 14, /*reserved for later use */ - H5T_STR_RESERVED_15 = 15 /*reserved for later use */ + H5T_STR_ERROR = -1, /**< error */ + H5T_STR_NULLTERM = 0, /**< null terminate like in C */ + H5T_STR_NULLPAD = 1, /**< pad with nulls */ + H5T_STR_SPACEPAD = 2, /**< pad with spaces like in Fortran */ + H5T_STR_RESERVED_3 = 3, /**< reserved for later use */ + H5T_STR_RESERVED_4 = 4, /**< reserved for later use */ + H5T_STR_RESERVED_5 = 5, /**< reserved for later use */ + H5T_STR_RESERVED_6 = 6, /**< reserved for later use */ + H5T_STR_RESERVED_7 = 7, /**< reserved for later use */ + H5T_STR_RESERVED_8 = 8, /**< reserved for later use */ + H5T_STR_RESERVED_9 = 9, /**< reserved for later use */ + H5T_STR_RESERVED_10 = 10, /**< reserved for later use */ + H5T_STR_RESERVED_11 = 11, /**< reserved for later use */ + H5T_STR_RESERVED_12 = 12, /**< reserved for later use */ + H5T_STR_RESERVED_13 = 13, /**< reserved for later use */ + H5T_STR_RESERVED_14 = 14, /**< reserved for later use */ + H5T_STR_RESERVED_15 = 15 /**< reserved for later use */ } H5T_str_t; -#define H5T_NSTR H5T_STR_RESERVED_3 /*num H5T_str_t types actually defined */ +#define H5T_NSTR H5T_STR_RESERVED_3 /*num H5T_str_t types actually defined */ -/* Type of padding to use in other atomic types */ +/** + * Type of padding to use in other atomic types + */ +//! [H5T_pad_t_snip] typedef enum H5T_pad_t { - H5T_PAD_ERROR = -1, /*error */ - H5T_PAD_ZERO = 0, /*always set to zero */ - H5T_PAD_ONE = 1, /*always set to one */ - H5T_PAD_BACKGROUND = 2, /*set to background value */ + H5T_PAD_ERROR = -1, /**< error */ + H5T_PAD_ZERO = 0, /**< always set to zero */ + H5T_PAD_ONE = 1, /**< always set to one */ + H5T_PAD_BACKGROUND = 2, /**< set to background value */ - H5T_NPAD = 3 /*THIS MUST BE LAST */ + H5T_NPAD = 3 /**< sentinal: THIS MUST BE LAST */ } H5T_pad_t; +//! [H5T_pad_t_snip] -/* Commands sent to conversion functions */ +/** + * Commands sent to conversion functions + */ typedef enum H5T_cmd_t { - H5T_CONV_INIT = 0, /*query and/or initialize private data */ - H5T_CONV_CONV = 1, /*convert data from source to dest datatype */ - H5T_CONV_FREE = 2 /*function is being removed from path */ + H5T_CONV_INIT = 0, /**< query and/or initialize private data */ + H5T_CONV_CONV = 1, /**< convert data from source to dest datatype */ + H5T_CONV_FREE = 2 /**< function is being removed from path */ } H5T_cmd_t; -/* How is the `bkg' buffer used by the conversion function? */ +/** + * How is the `bkg' buffer used by the conversion function? + */ typedef enum H5T_bkg_t { - H5T_BKG_NO = 0, /*background buffer is not needed, send NULL */ - H5T_BKG_TEMP = 1, /*bkg buffer used as temp storage only */ - H5T_BKG_YES = 2 /*init bkg buf with data before conversion */ + H5T_BKG_NO = 0, /**< background buffer is not needed, send NULL */ + H5T_BKG_TEMP = 1, /**< bkg buffer used as temp storage only */ + H5T_BKG_YES = 2 /**< init bkg buf with data before conversion */ } H5T_bkg_t; -/* Type conversion client data */ +/** + * Type conversion client data + */ +//! [H5T_cdata_t_snip] typedef struct H5T_cdata_t { - H5T_cmd_t command; /*what should the conversion function do? */ - H5T_bkg_t need_bkg; /*is the background buffer needed? */ - hbool_t recalc; /*recalculate private data */ - void * priv; /*private data */ + H5T_cmd_t command;/**< what should the conversion function do? */ + H5T_bkg_t need_bkg;/**< is the background buffer needed? */ + hbool_t recalc; /**< recalculate private data */ + void *priv; /**< private data */ } H5T_cdata_t; +//! [H5T_cdata_t_snip] -/* Conversion function persistence */ +/** + * Conversion function persistence + */ typedef enum H5T_pers_t { - H5T_PERS_DONTCARE = -1, /*wild card */ - H5T_PERS_HARD = 0, /*hard conversion function */ - H5T_PERS_SOFT = 1 /*soft conversion function */ + H5T_PERS_DONTCARE = -1, /**< wild card */ + H5T_PERS_HARD = 0, /**< hard conversion function */ + H5T_PERS_SOFT = 1 /**< soft conversion function */ } H5T_pers_t; -/* The order to retrieve atomic native datatype */ +/** + * The order to retrieve atomic native datatype + */ +//! [H5T_direction_t_snip] typedef enum H5T_direction_t { - H5T_DIR_DEFAULT = 0, /*default direction is inscendent */ - H5T_DIR_ASCEND = 1, /*in inscendent order */ - H5T_DIR_DESCEND = 2 /*in descendent order */ + H5T_DIR_DEFAULT = 0, /**< default direction is inscendent */ + H5T_DIR_ASCEND = 1, /**< in inscendent order */ + H5T_DIR_DESCEND = 2 /**< in descendent order */ } H5T_direction_t; +//! [H5T_direction_t_snip] -/* The exception type passed into the conversion callback function */ +/** + * The exception type passed into the conversion callback function + */ typedef enum H5T_conv_except_t { - H5T_CONV_EXCEPT_RANGE_HI = 0, /*source value is greater than destination's range */ - H5T_CONV_EXCEPT_RANGE_LOW = 1, /*source value is less than destination's range */ - H5T_CONV_EXCEPT_PRECISION = 2, /*source value loses precision in destination */ - H5T_CONV_EXCEPT_TRUNCATE = 3, /*source value is truncated in destination */ - H5T_CONV_EXCEPT_PINF = 4, /*source value is positive infinity(floating number) */ - H5T_CONV_EXCEPT_NINF = 5, /*source value is negative infinity(floating number) */ - H5T_CONV_EXCEPT_NAN = 6 /*source value is NaN(floating number) */ + H5T_CONV_EXCEPT_RANGE_HI = 0, /**< source value is greater than destination's range */ + H5T_CONV_EXCEPT_RANGE_LOW = 1, /**< source value is less than destination's range */ + H5T_CONV_EXCEPT_PRECISION = 2, /**< source value loses precision in destination */ + H5T_CONV_EXCEPT_TRUNCATE = 3, /**< source value is truncated in destination */ + H5T_CONV_EXCEPT_PINF = 4, /**< source value is positive infinity(floating number) */ + H5T_CONV_EXCEPT_NINF = 5, /**< source value is negative infinity(floating number) */ + H5T_CONV_EXCEPT_NAN = 6 /**< source value is NaN(floating number) */ } H5T_conv_except_t; -/* The return value from conversion callback function H5T_conv_except_func_t */ +/** + * The return value from conversion callback function H5T_conv_except_func_t() + */ typedef enum H5T_conv_ret_t { - H5T_CONV_ABORT = -1, /*abort conversion */ - H5T_CONV_UNHANDLED = 0, /*callback function failed to handle the exception */ - H5T_CONV_HANDLED = 1 /*callback function handled the exception successfully */ + H5T_CONV_ABORT = -1, /**< abort conversion */ + H5T_CONV_UNHANDLED = 0, /**< callback function failed to handle the exception */ + H5T_CONV_HANDLED = 1 /**< callback function handled the exception successfully */ } H5T_conv_ret_t; -/* Variable Length Datatype struct in memory */ -/* (This is only used for VL sequences, not VL strings, which are stored in char *'s) */ +/** + * Variable Length Datatype struct in memory (This is only used for VL + * sequences, not VL strings, which are stored in char *'s) + */ typedef struct { - size_t len; /* Length of VL data (in base type units) */ - void * p; /* Pointer to VL data */ + size_t len; /**< Length of VL data (in base type units) */ + void *p; /**< Pointer to VL data */ } hvl_t; /* Variable Length String information */ -#define H5T_VARIABLE \ - ((size_t)( \ - -1)) /* Indicate that a string is variable length (null-terminated in C, instead of fixed length) */ +/** + * Indicate that a string is variable length (null-terminated in C, instead of + * fixed length) + */ +#define H5T_VARIABLE ((size_t)(-1)) /* Opaque information */ -#define H5T_OPAQUE_TAG_MAX 256 /* Maximum length of an opaque tag */ - /* This could be raised without too much difficulty */ +/** + * Maximum length of an opaque tag + * \internal This could be raised without too much difficulty + */ +#define H5T_OPAQUE_TAG_MAX 256 #ifdef __cplusplus extern "C" { #endif -/* All datatype conversion functions are... */ -typedef herr_t (*H5T_conv_t)(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, size_t buf_stride, - size_t bkg_stride, void *buf, void *bkg, hid_t dset_xfer_plist); +/** + * All datatype conversion functions are... + */ +//! [H5T_conv_t_snip] +typedef herr_t (*H5T_conv_t) (hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, + size_t nelmts, size_t buf_stride, size_t bkg_stride, void *buf, + void *bkg, hid_t dset_xfer_plist); +//! [H5T_conv_t_snip] -/* Exception handler. If an exception like overflow happenes during conversion, - * this function is called if it's registered through H5Pset_type_conv_cb. +/** + * Exception handler. If an exception like overflow happenes during conversion, + * this function is called if it's registered through H5Pset_type_conv_cb(). */ -typedef H5T_conv_ret_t (*H5T_conv_except_func_t)(H5T_conv_except_t except_type, hid_t src_id, hid_t dst_id, - void *src_buf, void *dst_buf, void *user_data); +typedef H5T_conv_ret_t (*H5T_conv_except_func_t)(H5T_conv_except_t except_type, + hid_t src_id, hid_t dst_id, void *src_buf, void *dst_buf, void *user_data); /* When this header is included from a private header, don't make calls to H5open() */ #undef H5OPEN @@ -226,10 +278,26 @@ typedef H5T_conv_ret_t (*H5T_conv_except_func_t)(H5T_conv_except_t except_type, /* * The IEEE floating point types in various byte orders. */ -#define H5T_IEEE_F32BE (H5OPEN H5T_IEEE_F32BE_g) -#define H5T_IEEE_F32LE (H5OPEN H5T_IEEE_F32LE_g) -#define H5T_IEEE_F64BE (H5OPEN H5T_IEEE_F64BE_g) -#define H5T_IEEE_F64LE (H5OPEN H5T_IEEE_F64LE_g) +/** + * \ingroup PDTIEEE + * 32-bit big-endian IEEE floating-point numbers + */ +#define H5T_IEEE_F32BE (H5OPEN H5T_IEEE_F32BE_g) +/** + * \ingroup PDTIEEE + * 32-bit little-endian IEEE floating-point numbers + */ +#define H5T_IEEE_F32LE (H5OPEN H5T_IEEE_F32LE_g) +/** + * \ingroup PDTIEEE + * 64-bit big-endian IEEE floating-point numbers + */ +#define H5T_IEEE_F64BE (H5OPEN H5T_IEEE_F64BE_g) +/** + * \ingroup PDTIEEE + * 64-bit little-endian IEEE floating-point numbers + */ +#define H5T_IEEE_F64LE (H5OPEN H5T_IEEE_F64LE_g) H5_DLLVAR hid_t H5T_IEEE_F32BE_g; H5_DLLVAR hid_t H5T_IEEE_F32LE_g; H5_DLLVAR hid_t H5T_IEEE_F64BE_g; @@ -239,33 +307,141 @@ H5_DLLVAR hid_t H5T_IEEE_F64LE_g; * These are "standard" types. For instance, signed (2's complement) and * unsigned integers of various sizes and byte orders. */ -#define H5T_STD_I8BE (H5OPEN H5T_STD_I8BE_g) -#define H5T_STD_I8LE (H5OPEN H5T_STD_I8LE_g) -#define H5T_STD_I16BE (H5OPEN H5T_STD_I16BE_g) -#define H5T_STD_I16LE (H5OPEN H5T_STD_I16LE_g) -#define H5T_STD_I32BE (H5OPEN H5T_STD_I32BE_g) -#define H5T_STD_I32LE (H5OPEN H5T_STD_I32LE_g) -#define H5T_STD_I64BE (H5OPEN H5T_STD_I64BE_g) -#define H5T_STD_I64LE (H5OPEN H5T_STD_I64LE_g) -#define H5T_STD_U8BE (H5OPEN H5T_STD_U8BE_g) -#define H5T_STD_U8LE (H5OPEN H5T_STD_U8LE_g) -#define H5T_STD_U16BE (H5OPEN H5T_STD_U16BE_g) -#define H5T_STD_U16LE (H5OPEN H5T_STD_U16LE_g) -#define H5T_STD_U32BE (H5OPEN H5T_STD_U32BE_g) -#define H5T_STD_U32LE (H5OPEN H5T_STD_U32LE_g) -#define H5T_STD_U64BE (H5OPEN H5T_STD_U64BE_g) -#define H5T_STD_U64LE (H5OPEN H5T_STD_U64LE_g) -#define H5T_STD_B8BE (H5OPEN H5T_STD_B8BE_g) -#define H5T_STD_B8LE (H5OPEN H5T_STD_B8LE_g) -#define H5T_STD_B16BE (H5OPEN H5T_STD_B16BE_g) -#define H5T_STD_B16LE (H5OPEN H5T_STD_B16LE_g) -#define H5T_STD_B32BE (H5OPEN H5T_STD_B32BE_g) -#define H5T_STD_B32LE (H5OPEN H5T_STD_B32LE_g) -#define H5T_STD_B64BE (H5OPEN H5T_STD_B64BE_g) -#define H5T_STD_B64LE (H5OPEN H5T_STD_B64LE_g) -#define H5T_STD_REF_OBJ (H5OPEN H5T_STD_REF_OBJ_g) -#define H5T_STD_REF_DSETREG (H5OPEN H5T_STD_REF_DSETREG_g) -#define H5T_STD_REF (H5OPEN H5T_STD_REF_g) +/** + * \ingroup PDTSTD + * 8-bit big-endian signed integers + */ +#define H5T_STD_I8BE (H5OPEN H5T_STD_I8BE_g) +/** + * \ingroup PDTSTD + * 8-bit little-endian signed integers + */ +#define H5T_STD_I8LE (H5OPEN H5T_STD_I8LE_g) +/** + * \ingroup PDTSTD + * 16-bit big-endian signed integers + */ +#define H5T_STD_I16BE (H5OPEN H5T_STD_I16BE_g) +/** + * \ingroup PDTSTD + * 16-bit little-endian signed integers + */ +#define H5T_STD_I16LE (H5OPEN H5T_STD_I16LE_g) +/** + * \ingroup PDTSTD + * 32-bit big-endian signed integers + */ +#define H5T_STD_I32BE (H5OPEN H5T_STD_I32BE_g) +/** + * \ingroup PDTSTD + * 32-bit little-endian signed integers + */ +#define H5T_STD_I32LE (H5OPEN H5T_STD_I32LE_g) +/** + * \ingroup PDTSTD + * 64-bit big-endian signed integers + */ +#define H5T_STD_I64BE (H5OPEN H5T_STD_I64BE_g) +/** + * \ingroup PDTSTD + * 64-bit little-endian signed integers + */ +#define H5T_STD_I64LE (H5OPEN H5T_STD_I64LE_g) +/** + * \ingroup PDTSTD + * 8-bit big-endian unsigned integers + */ +#define H5T_STD_U8BE (H5OPEN H5T_STD_U8BE_g) +/** + * \ingroup PDTSTD + * 8-bit little-endian unsigned integers + */ +#define H5T_STD_U8LE (H5OPEN H5T_STD_U8LE_g) +/** + * \ingroup PDTSTD + * 16-bit big-endian unsigned integers + */ +#define H5T_STD_U16BE (H5OPEN H5T_STD_U16BE_g) +/** + * \ingroup PDTSTD + * 16-bit little-endian unsigned integers + */ +#define H5T_STD_U16LE (H5OPEN H5T_STD_U16LE_g) +/** + * \ingroup PDTSTD + * 32-bit big-endian unsigned integers + */ +#define H5T_STD_U32BE (H5OPEN H5T_STD_U32BE_g) +/** + * \ingroup PDTSTD + * 32-bit little-endian unsigned integers + */ +#define H5T_STD_U32LE (H5OPEN H5T_STD_U32LE_g) +/** + * \ingroup PDTSTD + * 64-bit big-endian unsigned integers + */ +#define H5T_STD_U64BE (H5OPEN H5T_STD_U64BE_g) +/** + * \ingroup PDTSTD + * 64-bit little-endian unsigned integers + */ +#define H5T_STD_U64LE (H5OPEN H5T_STD_U64LE_g) +/** + * \ingroup PDTSTD + * 8-bit big-endian bitfield + */ +#define H5T_STD_B8BE (H5OPEN H5T_STD_B8BE_g) +/** + * \ingroup PDTSTD + * 8-bit little-endian bitfield + */ +#define H5T_STD_B8LE (H5OPEN H5T_STD_B8LE_g) +/** + * \ingroup PDTSTD + * 16-bit big-endian bitfield + */ +#define H5T_STD_B16BE (H5OPEN H5T_STD_B16BE_g) +/** + * \ingroup PDTSTD + * 16-bit little-endian bitfield + */ +#define H5T_STD_B16LE (H5OPEN H5T_STD_B16LE_g) +/** + * \ingroup PDTSTD + * 32-bit big-endian bitfield + */ +#define H5T_STD_B32BE (H5OPEN H5T_STD_B32BE_g) +/** + * \ingroup PDTSTD + * 32-bit little-endian bitfield + */ +#define H5T_STD_B32LE (H5OPEN H5T_STD_B32LE_g) +/** + * \ingroup PDTSTD + * 64-bit big-endian bitfield + */ +#define H5T_STD_B64BE (H5OPEN H5T_STD_B64BE_g) +/** + * \ingroup PDTSTD + * 64-bit little-endian bitfield + */ +#define H5T_STD_B64LE (H5OPEN H5T_STD_B64LE_g) +/** + * \ingroup PDTSTD + * Object reference + */ +#define H5T_STD_REF_OBJ (H5OPEN H5T_STD_REF_OBJ_g) +/** + * \ingroup PDTSTD + * Dataset region reference + */ +#define H5T_STD_REF_DSETREG (H5OPEN H5T_STD_REF_DSETREG_g) +/** + * \ingroup PDTSTD + * Generic reference + */ +#define H5T_STD_REF (H5OPEN H5T_STD_REF_g) H5_DLLVAR hid_t H5T_STD_I8BE_g; H5_DLLVAR hid_t H5T_STD_I8LE_g; H5_DLLVAR hid_t H5T_STD_I16BE_g; @@ -297,10 +473,22 @@ H5_DLLVAR hid_t H5T_STD_REF_g; /* * Types which are particular to Unix. */ -#define H5T_UNIX_D32BE (H5OPEN H5T_UNIX_D32BE_g) -#define H5T_UNIX_D32LE (H5OPEN H5T_UNIX_D32LE_g) -#define H5T_UNIX_D64BE (H5OPEN H5T_UNIX_D64BE_g) -#define H5T_UNIX_D64LE (H5OPEN H5T_UNIX_D64LE_g) +/** + * \ingroup PDTUNIX + */ +#define H5T_UNIX_D32BE (H5OPEN H5T_UNIX_D32BE_g) +/** + * \ingroup PDTUNIX + */ +#define H5T_UNIX_D32LE (H5OPEN H5T_UNIX_D32LE_g) +/** + * \ingroup PDTUNIX + */ +#define H5T_UNIX_D64BE (H5OPEN H5T_UNIX_D64BE_g) +/** + * \ingroup PDTUNIX + */ +#define H5T_UNIX_D64LE (H5OPEN H5T_UNIX_D64LE_g) H5_DLLVAR hid_t H5T_UNIX_D32BE_g; H5_DLLVAR hid_t H5T_UNIX_D32LE_g; H5_DLLVAR hid_t H5T_UNIX_D64BE_g; @@ -310,12 +498,20 @@ H5_DLLVAR hid_t H5T_UNIX_D64LE_g; * Types particular to the C language. String types use `bytes' instead * of `bits' as their size. */ +/** + * \ingroup PDTS + * String datatype in C (size defined in bytes rather than in bits) + */ #define H5T_C_S1 (H5OPEN H5T_C_S1_g) H5_DLLVAR hid_t H5T_C_S1_g; /* * Types particular to Fortran. */ +/** + * \ingroup PDTS + * String datatype in Fortran (as defined for the HDF5 C library) + */ #define H5T_FORTRAN_S1 (H5OPEN H5T_FORTRAN_S1_g) H5_DLLVAR hid_t H5T_FORTRAN_S1_g; @@ -323,63 +519,239 @@ H5_DLLVAR hid_t H5T_FORTRAN_S1_g; * These types are for Intel CPU's. They are little endian with IEEE * floating point. */ -#define H5T_INTEL_I8 H5T_STD_I8LE -#define H5T_INTEL_I16 H5T_STD_I16LE -#define H5T_INTEL_I32 H5T_STD_I32LE -#define H5T_INTEL_I64 H5T_STD_I64LE -#define H5T_INTEL_U8 H5T_STD_U8LE -#define H5T_INTEL_U16 H5T_STD_U16LE -#define H5T_INTEL_U32 H5T_STD_U32LE -#define H5T_INTEL_U64 H5T_STD_U64LE -#define H5T_INTEL_B8 H5T_STD_B8LE -#define H5T_INTEL_B16 H5T_STD_B16LE -#define H5T_INTEL_B32 H5T_STD_B32LE -#define H5T_INTEL_B64 H5T_STD_B64LE -#define H5T_INTEL_F32 H5T_IEEE_F32LE -#define H5T_INTEL_F64 H5T_IEEE_F64LE +/** + * \ingroup PDTX86 + * 8-bit little-endian signed (2's complement) integers for Intel CPUs + */ +#define H5T_INTEL_I8 H5T_STD_I8LE +/** + * \ingroup PDTX86 + * 16-bit little-endian signed (2's complement) integers for Intel CPUs + */ +#define H5T_INTEL_I16 H5T_STD_I16LE +/** + * \ingroup PDTX86 + * 32-bit little-endian signed (2's complement) integers for Intel CPUs + */ +#define H5T_INTEL_I32 H5T_STD_I32LE +/** + * \ingroup PDTX86 + * 64-bit little-endian signed (2's complement) integers for Intel CPUs + */ +#define H5T_INTEL_I64 H5T_STD_I64LE +/** + * \ingroup PDTX86 + * 8-bit little-endian unsigned integers for Intel CPUs + */ +#define H5T_INTEL_U8 H5T_STD_U8LE +/** + * \ingroup PDTX86 + * 16-bit little-endian unsigned integers for Intel CPUs + */ +#define H5T_INTEL_U16 H5T_STD_U16LE +/** + * \ingroup PDTX86 + * 32-bit little-endian unsigned integers for Intel CPUs + */ +#define H5T_INTEL_U32 H5T_STD_U32LE +/** + * \ingroup PDTX86 + * 64-bit little-endian unsigned integers for Intel CPUs + */ +#define H5T_INTEL_U64 H5T_STD_U64LE +/** + * \ingroup PDTX86 + * 8-bit little-endian bitfield for Intel CPUs + */ +#define H5T_INTEL_B8 H5T_STD_B8LE +/** + * \ingroup PDTX86 + * 16-bit little-endian bitfield for Intel CPUs + */ +#define H5T_INTEL_B16 H5T_STD_B16LE +/** + * \ingroup PDTX86 + * 32-bit little-endian bitfield for Intel CPUs + */ +#define H5T_INTEL_B32 H5T_STD_B32LE +/** + * \ingroup PDTX86 + * 64-bit little-endian bitfield for Intel CPUs + */ +#define H5T_INTEL_B64 H5T_STD_B64LE +/** + * \ingroup PDTX86 + * 32-bit little-endian IEEE floating-point numbers for Intel CPUs + */ +#define H5T_INTEL_F32 H5T_IEEE_F32LE +/** + * \ingroup PDTX86 + * 64-bit little-endian IEEE floating-point numbers for Intel CPUs + */ +#define H5T_INTEL_F64 H5T_IEEE_F64LE /* * These types are for DEC Alpha CPU's. They are little endian with IEEE * floating point. */ -#define H5T_ALPHA_I8 H5T_STD_I8LE -#define H5T_ALPHA_I16 H5T_STD_I16LE -#define H5T_ALPHA_I32 H5T_STD_I32LE -#define H5T_ALPHA_I64 H5T_STD_I64LE -#define H5T_ALPHA_U8 H5T_STD_U8LE -#define H5T_ALPHA_U16 H5T_STD_U16LE -#define H5T_ALPHA_U32 H5T_STD_U32LE -#define H5T_ALPHA_U64 H5T_STD_U64LE -#define H5T_ALPHA_B8 H5T_STD_B8LE -#define H5T_ALPHA_B16 H5T_STD_B16LE -#define H5T_ALPHA_B32 H5T_STD_B32LE -#define H5T_ALPHA_B64 H5T_STD_B64LE -#define H5T_ALPHA_F32 H5T_IEEE_F32LE -#define H5T_ALPHA_F64 H5T_IEEE_F64LE +/** + * \ingroup PDTALPHA + * 8-bit little-endian signed (2's complement) integers for DEC Alpha CPUs + */ +#define H5T_ALPHA_I8 H5T_STD_I8LE +/** + * \ingroup PDTALPHA + * 16-bit little-endian signed (2's complement) integers for DEC Alpha CPUs + */ +#define H5T_ALPHA_I16 H5T_STD_I16LE +/** + * \ingroup PDTALPHA + * 32-bit little-endian signed (2's complement) integers for DEC Alpha CPUs + */ +#define H5T_ALPHA_I32 H5T_STD_I32LE +/** + * \ingroup PDTALPHA + * 64-bit little-endian signed (2's complement) integers for DEC Alpha CPUs + */ +#define H5T_ALPHA_I64 H5T_STD_I64LE +/** + * \ingroup PDTALPHA + * 8-bit little-endian unsigned integers for DEC Alpha CPUs + */ +#define H5T_ALPHA_U8 H5T_STD_U8LE +/** + * \ingroup PDTALPHA + * 16-bit little-endian unsigned integers for DEC Alpha CPUs + */ +#define H5T_ALPHA_U16 H5T_STD_U16LE +/** + * \ingroup PDTALPHA + * 32-bit little-endian unsigned integers for DEC Alpha CPUs + */ +#define H5T_ALPHA_U32 H5T_STD_U32LE +/** + * \ingroup PDTALPHA + * 64-bit little-endian unsigned integers for DEC Alpha CPUs + */ +#define H5T_ALPHA_U64 H5T_STD_U64LE +/** + * \ingroup PDTALPHA + * 8-bit little-endian bitfield for DEC Alpha CPUs + */ +#define H5T_ALPHA_B8 H5T_STD_B8LE +/** + * \ingroup PDTALPHA + * 16-bit little-endian bitfield for DEC Alpha CPUs + */ +#define H5T_ALPHA_B16 H5T_STD_B16LE +/** + * \ingroup PDTALPHA + * 32-bit little-endian bitfield for DEC Alpha CPUs + */ +#define H5T_ALPHA_B32 H5T_STD_B32LE +/** + * \ingroup PDTALPHA + * 64-bit little-endian bitfield for DEC Alpha CPUs + */ +#define H5T_ALPHA_B64 H5T_STD_B64LE +/** + * \ingroup PDTALPHA + * 32-bit little-endian IEEE floating-point numbers for DEC Alpha CPUs + */ +#define H5T_ALPHA_F32 H5T_IEEE_F32LE +/** + * \ingroup PDTALPHA + * 64-bit little-endian IEEE floating-point numbers for DEC Alpha CPUs + */ +#define H5T_ALPHA_F64 H5T_IEEE_F64LE /* * These types are for MIPS cpu's commonly used in SGI systems. They are big * endian with IEEE floating point. */ -#define H5T_MIPS_I8 H5T_STD_I8BE -#define H5T_MIPS_I16 H5T_STD_I16BE -#define H5T_MIPS_I32 H5T_STD_I32BE -#define H5T_MIPS_I64 H5T_STD_I64BE -#define H5T_MIPS_U8 H5T_STD_U8BE -#define H5T_MIPS_U16 H5T_STD_U16BE -#define H5T_MIPS_U32 H5T_STD_U32BE -#define H5T_MIPS_U64 H5T_STD_U64BE -#define H5T_MIPS_B8 H5T_STD_B8BE -#define H5T_MIPS_B16 H5T_STD_B16BE -#define H5T_MIPS_B32 H5T_STD_B32BE -#define H5T_MIPS_B64 H5T_STD_B64BE -#define H5T_MIPS_F32 H5T_IEEE_F32BE -#define H5T_MIPS_F64 H5T_IEEE_F64BE +/** + * \ingroup PDTMIPS + * 8-bit big-endian signed (2's complement) integers for SGI MIPS CPUs + */ +#define H5T_MIPS_I8 H5T_STD_I8BE +/** + * \ingroup PDTMIPS + * 16-bit big-endian signed (2's complement) integers for SGI MIPS CPUs + */ +#define H5T_MIPS_I16 H5T_STD_I16BE +/** + * \ingroup PDTMIPS + * 32-bit big-endian signed (2's complement) integers for SGI MIPS CPUs + */ +#define H5T_MIPS_I32 H5T_STD_I32BE +/** + * \ingroup PDTMIPS + * 64-bit big-endian signed (2's complement) integers for SGI MIPS CPUs + */ +#define H5T_MIPS_I64 H5T_STD_I64BE +/** + * \ingroup PDTMIPS + * 8-bit big-endian unsigned integers for SGI MIPS CPUs + */ +#define H5T_MIPS_U8 H5T_STD_U8BE +/** + * \ingroup PDTMIPS + * 16-bit big-endian unsigned integers for SGI MIPS CPUs + */ +#define H5T_MIPS_U16 H5T_STD_U16BE +/** + * \ingroup PDTMIPS + * 32-bit big-endian unsigned integers for SGI MIPS CPUs + */ +#define H5T_MIPS_U32 H5T_STD_U32BE +/** + * \ingroup PDTMIPS + * 64-bit big-endian unsigned integers for SGI MIPS CPUs + */ +#define H5T_MIPS_U64 H5T_STD_U64BE +/** + * \ingroup PDTMIPS + * 8-bit big-endian bitfield for SGI MIPS CPUs + */ +#define H5T_MIPS_B8 H5T_STD_B8BE +/** + * \ingroup PDTMIPS + * 16-bit big-endian bitfield for SGI MIPS CPUs + */ +#define H5T_MIPS_B16 H5T_STD_B16BE +/** + * \ingroup PDTMIPS + * 32-bit big-endian bitfield for SGI MIPS CPUs + */ +#define H5T_MIPS_B32 H5T_STD_B32BE +/** + * \ingroup PDTMIPS + * 64-bit big-endian bitfield for SGI MIPS CPUs + */ +#define H5T_MIPS_B64 H5T_STD_B64BE +/** + * \ingroup PDTMIPS + * 32-bit big-endian IEEE floating-point numbers for MIPS CPUs + */ +#define H5T_MIPS_F32 H5T_IEEE_F32BE +/** + * \ingroup PDTMIPS + * 64-bit big-endian IEEE floating-point numbers for MIPS CPUs + */ +#define H5T_MIPS_F64 H5T_IEEE_F64BE /* * The VAX floating point types (i.e. in VAX byte order) */ +/** + * \ingroup PDTALPHA + * 32-bit VAX byte order floating-point numbers for OpenVMS on DEC Alpha CPUs + */ #define H5T_VAX_F32 (H5OPEN H5T_VAX_F32_g) +/** + * \ingroup PDTALPHA + * 64-bit VAX byte order floating-point numbers for OpenVMS on DEC Alpha CPUs + */ #define H5T_VAX_F64 (H5OPEN H5T_VAX_F64_g) H5_DLLVAR hid_t H5T_VAX_F32_g; H5_DLLVAR hid_t H5T_VAX_F64_g; @@ -393,32 +765,128 @@ H5_DLLVAR hid_t H5T_VAX_F64_g; * to C's `long long' and LDOUBLE is `long double' (these types might be the * same as `LONG' and `DOUBLE' respectively). */ -#define H5T_NATIVE_CHAR (CHAR_MIN ? H5T_NATIVE_SCHAR : H5T_NATIVE_UCHAR) +/** + * \ingroup PDTNAT + * C-style \c char + */ +#define H5T_NATIVE_CHAR (CHAR_MIN?H5T_NATIVE_SCHAR:H5T_NATIVE_UCHAR) +/** + * \ingroup PDTNAT + * C-style \Code{signed char} + */ #define H5T_NATIVE_SCHAR (H5OPEN H5T_NATIVE_SCHAR_g) +/** + * \ingroup PDTNAT + * C-style \Code{unsigned char} + */ #define H5T_NATIVE_UCHAR (H5OPEN H5T_NATIVE_UCHAR_g) +/** + * \ingroup PDTNAT + * C-style \Code{short} + */ #define H5T_NATIVE_SHORT (H5OPEN H5T_NATIVE_SHORT_g) +/** + * \ingroup PDTNAT + * C-style \Code{unsigned short} + */ #define H5T_NATIVE_USHORT (H5OPEN H5T_NATIVE_USHORT_g) +/** + * \ingroup PDTNAT + * C-style \Code{int} + */ #define H5T_NATIVE_INT (H5OPEN H5T_NATIVE_INT_g) +/** + * \ingroup PDTNAT + * C-style \Code{unsigned int} + */ #define H5T_NATIVE_UINT (H5OPEN H5T_NATIVE_UINT_g) +/** + * \ingroup PDTNAT + * C-style \Code{long} + */ #define H5T_NATIVE_LONG (H5OPEN H5T_NATIVE_LONG_g) +/** + * \ingroup PDTNAT + * C-style \Code{unsigned long} + */ #define H5T_NATIVE_ULONG (H5OPEN H5T_NATIVE_ULONG_g) +/** + * \ingroup PDTNAT + * C-style \Code{long long} + */ #define H5T_NATIVE_LLONG (H5OPEN H5T_NATIVE_LLONG_g) +/** + * \ingroup PDTNAT + * C-style \Code{unsigned long long} + */ #define H5T_NATIVE_ULLONG (H5OPEN H5T_NATIVE_ULLONG_g) +/** + * \ingroup PDTNAT + * C-style \Code{float} + */ #define H5T_NATIVE_FLOAT (H5OPEN H5T_NATIVE_FLOAT_g) +/** + * \ingroup PDTNAT + * C-style \Code{double} + */ #define H5T_NATIVE_DOUBLE (H5OPEN H5T_NATIVE_DOUBLE_g) -#if H5_SIZEOF_LONG_DOUBLE != 0 +#if H5_SIZEOF_LONG_DOUBLE !=0 +/** + * \ingroup PDTNAT + * C-style \Code{long double} + */ #define H5T_NATIVE_LDOUBLE (H5OPEN H5T_NATIVE_LDOUBLE_g) #endif +/** + * \ingroup PDTNAT + * HDF5 8-bit bitfield based on native types + */ #define H5T_NATIVE_B8 (H5OPEN H5T_NATIVE_B8_g) +/** + * \ingroup PDTNAT + * HDF5 16-bit bitfield based on native types + */ #define H5T_NATIVE_B16 (H5OPEN H5T_NATIVE_B16_g) +/** + * \ingroup PDTNAT + * HDF5 32-bit bitfield based on native types + */ #define H5T_NATIVE_B32 (H5OPEN H5T_NATIVE_B32_g) -#define H5T_NATIVE_B64 (H5OPEN H5T_NATIVE_B64_g) +/** + * \ingroup PDTNAT + * HDF5 64-bit bitfield based on native types + */ +#define H5T_NATIVE_B64 (H5OPEN H5T_NATIVE_B64_g) +/** + * \ingroup PDTNAT + * HDF5 opaque unit based on native types + */ #define H5T_NATIVE_OPAQUE (H5OPEN H5T_NATIVE_OPAQUE_g) +/** + * \ingroup PDTNAT + * HDF5 address type based on native types + */ #define H5T_NATIVE_HADDR (H5OPEN H5T_NATIVE_HADDR_g) +/** + * \ingroup PDTNAT + * HDF5 size type based on native types + */ #define H5T_NATIVE_HSIZE (H5OPEN H5T_NATIVE_HSIZE_g) +/** + * \ingroup PDTNAT + * HDF5 signed size type based on native types + */ #define H5T_NATIVE_HSSIZE (H5OPEN H5T_NATIVE_HSSIZE_g) -#define H5T_NATIVE_HERR (H5OPEN H5T_NATIVE_HERR_g) -#define H5T_NATIVE_HBOOL (H5OPEN H5T_NATIVE_HBOOL_g) +/** + * \ingroup PDTNAT + * HDF5 error code type based on native types + */ +#define H5T_NATIVE_HERR (H5OPEN H5T_NATIVE_HERR_g) +/** + * \ingroup PDTNAT + * HDF5 Boolean type based on native types + */ +#define H5T_NATIVE_HBOOL (H5OPEN H5T_NATIVE_HBOOL_g) H5_DLLVAR hid_t H5T_NATIVE_SCHAR_g; H5_DLLVAR hid_t H5T_NATIVE_UCHAR_g; H5_DLLVAR hid_t H5T_NATIVE_SHORT_g; @@ -446,12 +914,30 @@ H5_DLLVAR hid_t H5T_NATIVE_HERR_g; H5_DLLVAR hid_t H5T_NATIVE_HBOOL_g; /* C9x integer types */ -#define H5T_NATIVE_INT8 (H5OPEN H5T_NATIVE_INT8_g) -#define H5T_NATIVE_UINT8 (H5OPEN H5T_NATIVE_UINT8_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT8 (H5OPEN H5T_NATIVE_INT8_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT8 (H5OPEN H5T_NATIVE_UINT8_g) +/** + * \ingroup PDTC9x + */ #define H5T_NATIVE_INT_LEAST8 (H5OPEN H5T_NATIVE_INT_LEAST8_g) -#define H5T_NATIVE_UINT_LEAST8 (H5OPEN H5T_NATIVE_UINT_LEAST8_g) -#define H5T_NATIVE_INT_FAST8 (H5OPEN H5T_NATIVE_INT_FAST8_g) -#define H5T_NATIVE_UINT_FAST8 (H5OPEN H5T_NATIVE_UINT_FAST8_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT_LEAST8 (H5OPEN H5T_NATIVE_UINT_LEAST8_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT_FAST8 (H5OPEN H5T_NATIVE_INT_FAST8_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT_FAST8 (H5OPEN H5T_NATIVE_UINT_FAST8_g) H5_DLLVAR hid_t H5T_NATIVE_INT8_g; H5_DLLVAR hid_t H5T_NATIVE_UINT8_g; H5_DLLVAR hid_t H5T_NATIVE_INT_LEAST8_g; @@ -459,12 +945,30 @@ H5_DLLVAR hid_t H5T_NATIVE_UINT_LEAST8_g; H5_DLLVAR hid_t H5T_NATIVE_INT_FAST8_g; H5_DLLVAR hid_t H5T_NATIVE_UINT_FAST8_g; -#define H5T_NATIVE_INT16 (H5OPEN H5T_NATIVE_INT16_g) -#define H5T_NATIVE_UINT16 (H5OPEN H5T_NATIVE_UINT16_g) -#define H5T_NATIVE_INT_LEAST16 (H5OPEN H5T_NATIVE_INT_LEAST16_g) -#define H5T_NATIVE_UINT_LEAST16 (H5OPEN H5T_NATIVE_UINT_LEAST16_g) -#define H5T_NATIVE_INT_FAST16 (H5OPEN H5T_NATIVE_INT_FAST16_g) -#define H5T_NATIVE_UINT_FAST16 (H5OPEN H5T_NATIVE_UINT_FAST16_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT16 (H5OPEN H5T_NATIVE_INT16_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT16 (H5OPEN H5T_NATIVE_UINT16_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT_LEAST16 (H5OPEN H5T_NATIVE_INT_LEAST16_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT_LEAST16 (H5OPEN H5T_NATIVE_UINT_LEAST16_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT_FAST16 (H5OPEN H5T_NATIVE_INT_FAST16_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT_FAST16 (H5OPEN H5T_NATIVE_UINT_FAST16_g) H5_DLLVAR hid_t H5T_NATIVE_INT16_g; H5_DLLVAR hid_t H5T_NATIVE_UINT16_g; H5_DLLVAR hid_t H5T_NATIVE_INT_LEAST16_g; @@ -472,12 +976,30 @@ H5_DLLVAR hid_t H5T_NATIVE_UINT_LEAST16_g; H5_DLLVAR hid_t H5T_NATIVE_INT_FAST16_g; H5_DLLVAR hid_t H5T_NATIVE_UINT_FAST16_g; -#define H5T_NATIVE_INT32 (H5OPEN H5T_NATIVE_INT32_g) -#define H5T_NATIVE_UINT32 (H5OPEN H5T_NATIVE_UINT32_g) -#define H5T_NATIVE_INT_LEAST32 (H5OPEN H5T_NATIVE_INT_LEAST32_g) -#define H5T_NATIVE_UINT_LEAST32 (H5OPEN H5T_NATIVE_UINT_LEAST32_g) -#define H5T_NATIVE_INT_FAST32 (H5OPEN H5T_NATIVE_INT_FAST32_g) -#define H5T_NATIVE_UINT_FAST32 (H5OPEN H5T_NATIVE_UINT_FAST32_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT32 (H5OPEN H5T_NATIVE_INT32_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT32 (H5OPEN H5T_NATIVE_UINT32_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT_LEAST32 (H5OPEN H5T_NATIVE_INT_LEAST32_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT_LEAST32 (H5OPEN H5T_NATIVE_UINT_LEAST32_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT_FAST32 (H5OPEN H5T_NATIVE_INT_FAST32_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT_FAST32 (H5OPEN H5T_NATIVE_UINT_FAST32_g) H5_DLLVAR hid_t H5T_NATIVE_INT32_g; H5_DLLVAR hid_t H5T_NATIVE_UINT32_g; H5_DLLVAR hid_t H5T_NATIVE_INT_LEAST32_g; @@ -485,12 +1007,30 @@ H5_DLLVAR hid_t H5T_NATIVE_UINT_LEAST32_g; H5_DLLVAR hid_t H5T_NATIVE_INT_FAST32_g; H5_DLLVAR hid_t H5T_NATIVE_UINT_FAST32_g; -#define H5T_NATIVE_INT64 (H5OPEN H5T_NATIVE_INT64_g) -#define H5T_NATIVE_UINT64 (H5OPEN H5T_NATIVE_UINT64_g) -#define H5T_NATIVE_INT_LEAST64 (H5OPEN H5T_NATIVE_INT_LEAST64_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT64 (H5OPEN H5T_NATIVE_INT64_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT64 (H5OPEN H5T_NATIVE_UINT64_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT_LEAST64 (H5OPEN H5T_NATIVE_INT_LEAST64_g) +/** + * \ingroup PDTC9x + */ #define H5T_NATIVE_UINT_LEAST64 (H5OPEN H5T_NATIVE_UINT_LEAST64_g) -#define H5T_NATIVE_INT_FAST64 (H5OPEN H5T_NATIVE_INT_FAST64_g) -#define H5T_NATIVE_UINT_FAST64 (H5OPEN H5T_NATIVE_UINT_FAST64_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_INT_FAST64 (H5OPEN H5T_NATIVE_INT_FAST64_g) +/** + * \ingroup PDTC9x + */ +#define H5T_NATIVE_UINT_FAST64 (H5OPEN H5T_NATIVE_UINT_FAST64_g) H5_DLLVAR hid_t H5T_NATIVE_INT64_g; H5_DLLVAR hid_t H5T_NATIVE_UINT64_g; H5_DLLVAR hid_t H5T_NATIVE_INT_LEAST64_g; @@ -499,92 +1039,1837 @@ H5_DLLVAR hid_t H5T_NATIVE_INT_FAST64_g; H5_DLLVAR hid_t H5T_NATIVE_UINT_FAST64_g; /* Operations defined on all datatypes */ +/** + * \ingroup H5T + * + * \brief Creates a new datatype. + * + * \param[in] type Class of datatype to create + * \param[in] size Size, in bytes, of the datatype being created + * + * \return \hid_t{datatype} + * + * \details H5Tcreate() creates a new datatype of the specified class with the + * specified number of bytes. This function is used only with the + * following datatype classes: + * - #H5T_COMPOUND + * - #H5T_OPAQUE + * - #H5T_ENUM + * - #H5T_STRING + * + * Other datatypes, including integer and floating-point datatypes, + * are typically created by using H5Tcopy() to copy and modify a + * predefined datatype. + * + * When creating a variable-length string datatype, \p size must + * be #H5T_VARIABLE. + * + * When creating a fixed-length string datatype, \p size will + * be the length of the string in bytes. The length of the + * string in characters will depend on i the encoding used; see + * H5Pset_char_encoding(). + * + * ENUMs created with this function have a signed native integer + * base datatype. Use H5Tenum_create() if a different integer base + * datatype is required. + * + * The datatype identifier returned from this function should be + * released with H5Tclose or resource leaks will result. + * + * \since 1.2.0 + * + * \see H5Tclose() + * + * \todo Original has a reference to “Creating variable-length string + * datatypes”. + * \todo Create an example for H5Tcreate. + * + */ H5_DLL hid_t H5Tcreate(H5T_class_t type, size_t size); +/** + * \ingroup H5T + * + * \brief Copies an existing datatype. + * + * \type_id + * + * \return \hid_t{datatype} + * + * \details H5Tcopy() makes a copy of an existing datatype. The returned type + * is always transient and unlocked. + * + * The \p type_id argument can be either a datatype identifier, + * a predefined datatype (defined in H5Tpublic.h), or a dataset + * identifier. If \p type_id is a dataset identifier, this function + * returns a transient, modifiable datatype which is a copy of the + * dataset's datatype. + * + * The returned datatype identifier should be released with H5Tclose() + * to prevent resource leak. + * + * \todo Create an example for H5Tcopy(). + * + */ H5_DLL hid_t H5Tcopy(hid_t type_id); +/** + * \ingroup H5T + * + * \brief Releases a datatype + * + * \type_id + * + * \return \herr_t + * + * \details H5Tclose() releases the datatype \p dtype_id. Further access + * through this datatype identifier is illegal. Failure to release + * a datatype with this call will result in resource leaks. + * + */ H5_DLL herr_t H5Tclose(hid_t type_id); +/** + * \ingroup H5T + * + * \brief Determines whether two datatype identifiers refer to the same datatype + * + * \type_id{type1_id} + * \type_id{type2_id} + * + * \return \htri_t + * + * \details H5Tequal() determines whether two datatype identifiers refer to + * the same datatype. + * + * \since 1.6 or earlier + * + */ H5_DLL htri_t H5Tequal(hid_t type1_id, hid_t type2_id); +/** + * \ingroup H5T + * + * \brief Locks a datatype + * + * \type_id + * + * \return \herr_t + * + * \details H5Tlock() locks the datatype specified by the dtype_id identifier, + * making it read-only and non-destructible. This is normally done by + * the library for predefined datatypes so the application does not + * inadvertently change or delete a predefined type. Once a datatype + * is locked it can never be unlocked. + * + */ H5_DLL herr_t H5Tlock(hid_t type_id); +/** + * \ingroup H5T + * + * \brief Commits a transient datatype, linking it into the file and creating + * a new committed datatype + * + * \fg_loc_id + * \param[in] name Name given to committed datatype + * \type_id Identifier of datatype to be committed and, upon function’s + * return, identifier for the committed datatype + * \lcpl_id + * \tcpl_id + * \tapl_id + * + * \return \herr_t + * + * \details H5Tcommit2() saves a transient datatype as an immutable committed + * datatype in a file. The datatype specified by \p dtype_id is + * committed to the file with the name name at the location specified + * by \p loc_id and with the datatype creation and access property + * lists \p tcpl_id and \p tapl_id, respectively. + * + * \p loc_id may be a file identifier, or a group identifier within + * that file. \p name may be either an absolute path in the file or + * a relative path from \p loc_id naming the newly-commited datatype. + * + * The link creation property list, \p lcpl_id, governs creation of + * the link(s) by which the new committed datatype is accessed and + * the creation of any intermediate groups that may be missing. + * + * Once commited, this datatype may be used to define the datatype + * of any other dataset or attribute in the file. + * + * This function will not accept a datatype that cannot actually hold + * information. This currently includes compound datatypes with no + * fields and enumerated datatypes with no members. + * + * Committed datatypes are sometimes referred to as named datatypes. + * + * \version 1.8.7 Function modified in this release to reject datatypes that + * will not accomodate actual data, such as a compound datatype + * with no fields or an enumerated datatype with no members. + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Tcommit2(hid_t loc_id, const char *name, hid_t type_id, hid_t lcpl_id, hid_t tcpl_id, hid_t tapl_id); +/** + * -------------------------------------------------------------------------- + * \ingroup H5T + * + * \brief Opens a committed (named) datatype + * + * \fgdta_loc_id + * \param[in] name Name of the datatype to open + * \tapl_id + * + * \return \hid_t{datatype} + * + * \details H5Topen2() opens a committed datatype at the location specified + * by \p loc_id and returns an identifier for the datatype. \p + * loc_id is either a file or group identifier. The identifier should + * eventually be closed by calling H5Tclose() to release resources. + * + * The committed datatype is opened with the datatype access property + * list tapl_id. + * + * \since 1.8.0 + * + */ H5_DLL hid_t H5Topen2(hid_t loc_id, const char *name, hid_t tapl_id); +/** + * \ingroup H5T + * + * \brief Commits a transient datatype to a file, creating a new named + * datatype, but does not link it into the file structure + * + * \fg_loc_id + * \type_id + * \tcpl_id + * \tapl_id + * + * \return \herr_t + * + * \details H5Tcommit_anon() commits a transient datatype (not immutable) + * to a file, turning it into a named datatype with the specified + * creation and property lists. With default property lists, + * #H5P_DEFAULT, H5Tcommit_anon() provides similar functionality to + * that of H5Tcommit(), with the differences described below. + * + * #H5P_DEFAULT can be passed in for the datatype creation property + * list identifier, \p tcpl_id. The datatype access property list + * identifier, \p tapl_id, is provided for future functionality and + * is not used at this time. This parameter should always be passed + * as the value #H5P_DEFAULT. + * + * Note that H5Tcommit_anon() does not link this newly-committed + * datatype into the file. After the H5Tcommit_anon() call, the + * datatype identifier \p type_id must be linked into the HDF5 file + * structure with H5Olink() or it will be deleted from the file when + * the file is closed. + * + * The differences between this function and H5Tcommit() are as follows: + * \li H5Tcommit_anon() explicitly includes property lists, + * which provides for greater control of the creation process + * and of the properties of the new named datatype. H5Tcommit() + * always uses default properties. + * \li H5Tcommit_anon() neither provides the new named datatype’s + * name nor links it into the HDF5 file structure; those actions + * must be performed separately through a call to H5Olink(), + * which offers greater control over linking. + * + * This function will not accept a datatype that cannot actually + * hold data. This currently includes compound datatypes with no + * fields and enumerated datatypes with no members. + * + * \version 1.8.7 Function modified in this release to reject datatypes that + * will not accomodate actual data, such as a compound datatype + * with no fields or an enumerated datatype with no members. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tcommit_anon(hid_t loc_id, hid_t type_id, hid_t tcpl_id, hid_t tapl_id); +/** + * \ingroup H5T + * + * \brief Returns a copy of a datatype's creation property list + * + * \type_id + * + * \return \hid_t{datatype creation property list} + * + * \details H5Tget_create_plist() returns a property list identifier + * for the datatype creation property list associated with the datatype + * specified by \p type_id. + * + * The creation property list identifier should be released with + * H5Pclose() to prevent memory leaks. + * + * \since 1.8.0 + * + */ H5_DLL hid_t H5Tget_create_plist(hid_t type_id); +/** + * \ingroup H5T + * + * \brief Determines whether a datatype is a committed type or a transient type + * + * \type_id + * + * \return \htri_t + * + * \details H5Tcommitted() queries a type to determine whether the type + * specified by the \p dtype_id identifier is a committed (formerly + * known as a \Emph{named}) type or a transient type. If this function returns + * a positive value, then the type is committed (that is, it has been + * committed, perhaps by some other application). Datasets which + * return committed datatypes with H5Dget_type() are able to share + * the datatype with other datasets in the same file. + * + * \version 1.8.0 Fortran API was added + * + * \since 1.6 or earlier + * + */ H5_DLL htri_t H5Tcommitted(hid_t type_id); +/** + * \ingroup H5T + * + * \brief Encodes a datatype object description into a binary buffer + * + * \param[in] obj_id Identifier of the object to be encoded + * \param[in,out] buf Buffer for the object to be encoded into. + * \param[in,out] nalloc IN: The size of the allocated buffer + * OUT: The size of the buffer needed + * + * \return \herr_t + * + * \details H5Tencode() Given datatype identifier, H5Tencode() converts a + * datatype description into binary form in a buffer. Using this + * binary form in the buffer, a datatype object can be reconstructed + * using H5Tdecode() to return a new object handle (\ref hid_t) for + * this datatype. + * + * If the provided buffer is NULL, only the size of buffer needed is + * returned through \p nalloc. + * + * A preliminary H5Tencode() call can be made to find out the size + * of the buffer needed. This value is returned as \p nalloc. That + * value can then be assigned to \p nalloc for a second H5Tencode() + * call, which will retrieve the actual encoded object. + * + * If the library finds that \p nalloc is not big enough for the + * object, it simply returns the size of the buffer needed through + * \p nalloc without encoding the provided buffer. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tencode(hid_t obj_id, void *buf, size_t *nalloc); +/** + * \ingroup H5T + * + * \brief Decodes a binary object description of datatype and return a new + * object handle + * + * \param[in] buf Buffer for the datatype object to be decoded + * + * \return \hid_t{datatype} + * + * \details H5Tdecode() Given an object description of datatype in binary in a + * buffer, H5Tdecode() reconstructs the HDF5 datatype object and + * returns a new object handle for it. The binary description of + * the object is encoded by H5Tencode(). User is responsible for + * passing in the right buffer. + * + * The datatype identifier returned by this function can be released + * with H5Tclose() when the identifier is no longer needed so that + * resource leaks will not develop. + * + */ H5_DLL hid_t H5Tdecode(const void *buf); +/** + * \ingroup H5T + * + * \brief Flushes all buffers associated with a committed datatype to disk + * + * \type_id + * + * \return \herr_t + * + * \details H5Tflush() causes all buffers associated with a committed datatype + * \p type_id to be immediately flushed to disk without removing the + * data from the cache. + * + * HDF5 does not possess full control over buffering. H5Tflush() + * flushes the internal HDF5 buffers and then asks the operating + * system (the OS) to flush the system buffers for the open + * files. After that, the OS is responsible for ensuring that the + * data is actually flushed to disk. + * + * \return \herr_t + * + * \since 1.10.0 C function introduced with this release. + * + * \see H5Dflush() + * H5Drefresh() + * H5Tflush() + * H5Grefresh() + * H5Oflush() + * H5Orefresh() + * H5Tflush() + * H5Trefresh() + * H5Fstart_swmr_write() + * H5Pget_append_flush() + * H5Pget_object_flush_cb() + * H5Pset_append_flush() + * H5Pset_object_flush_cb() + * + */ H5_DLL herr_t H5Tflush(hid_t type_id); +/** + * \ingroup H5T + * + * \brief Refreshes all buffers associated with a committed datatype + * + * \type_id + * + * \return \herr_t + * + * \details H5Trefresh() causes all buffers associated with a committed + * datatype to be cleared and immediately re-loaded with updated + * contents from disk. + * + * This function essentially closes the datatype, evicts all + * metadata associated with it from the cache, and then re-opens the + * datatype. The reopened datatype is automatically re-registered + * with the same identifier. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Trefresh(hid_t type_id); /* Operations defined on compound datatypes */ +/** + * \ingroup COMPOUND + * + * \brief Adds a new member to a compound datatype. + * + * \type_id{parent_id} + * \param[in] name Name of the field to insert + * \param[in] offset Offset in memory structure of the field to insert + * \param[in] member_id Datatype identifier of the field to insert + * + * \return \herr_t + * + * \details H5Tinsert() adds another member to the compound datatype, specified + * \p type_id. + * + * The new member has a \p name which must be unique within the + * compound datatype. The \p offset argument defines the start of the + * member in an instance of the compound datatype, and \p member_id + * is the datatype identifier of the new member. + * + * \note Members of a compound datatype do not have to be atomic + * datatypes; a compound datatype can have a member which is a + * compound datatype. + * + * \since 1.2.0 + * + * \todo Create example for H5Tinsert + * + */ H5_DLL herr_t H5Tinsert(hid_t parent_id, const char *name, size_t offset, hid_t member_id); +/** + * \ingroup COMPOUND + * + * \brief Recursively removes padding from within a compound datatype + * + * \type_id + * + * \return \herr_t + * + * \details H5Tpack() recursively removes padding from within a compound + * datatype to make it more efficient (space-wise) to store that data. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tpack(hid_t type_id); /* Operations defined on enumeration datatypes */ +/** + * \ingroup ENUM + * + * \brief Creates a new enumeration datatype + * + * \param[in] base_id Datatype identifier for the base datatype. Must be an + * integer datatype + * + * \return \hid_t{enumeration datatype} + * + * \details H5Tenum_create() creates a new enumeration datatype based on the + * specified base datatype, dtype_id, which must be an integer datatype. + * + * If a particular architecture datatype is required, a little endian + * or big endian datatype for example, use a native datatype as the + * base datatype and use H5Tconvert() on values as they are read + * from or written to a dataset. + * + * \since 1.2.0 + * + */ H5_DLL hid_t H5Tenum_create(hid_t base_id); +/** + * \ingroup ENUM + * + * \brief Inserts a new enumeration datatype member + * + * \type_id{type} + * \param[in] name Name of the new member + * \param[in] value Pointer to the value of the new member + * + * \return \herr_t + * + * \details H5Tenum_insert() inserts a new enumeration datatype member into an + * enumeration datatype. + * + * \p type_id is the datatype identifier for the enumeration datatype, + * \p name is the name of the new member, and \p value points to the + * value of the new member. + * + * \p name and \p value must both be unique within \p dtype_id. + * + * \p value points to data which must be of the integer base datatype + * used when the enumeration datatype was created. If a particular + * architecture datatype is required, a little endian or big endian + * datatype for example, use a native datatype as the base datatype + * and use H5Tconvert() on values as they are read from or written + * to a dataset. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tenum_insert(hid_t type, const char *name, const void *value); +/** + * \ingroup ENUM + * + * \brief Returns the symbol name corresponding to a specified member of an + * enumeration datatype + * + * \type_id{type} + * \param[in] value Value of the enumeration datatype + * \param[out] name Buffer for output of the symbol name + * \param[in] size Anticipated size of the symbol name, in bytes + * + * \return Returns a non-negative value if successful. Otherwise returns a + * negative value + * + * \details H5Tenum_nameof() finds the symbol name that corresponds to the + * specified \p value of the enumeration datatype \p type. + * + * At most \p size characters of the symbol \p name are copied into + * the \p name buffer. If the entire symbol name and null terminator + * do not fit in the name buffer, then as many characters as possible + * are copied (not null terminated) and the function fails. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tenum_nameof(hid_t type, const void *value, char *name /*out*/, size_t size); +/** + * \ingroup ENUM + * + * \brief Returns the value corresponding to a specified member of an + * enumeration datatype + * + * \type_id{type} + * \param[in] name Symbol name of the enumeration datatype + * \param[out] value Buffer for the value of the enumeration datatype + * + * \return \herr_t + * + * \details H5Tenum_valueof() finds the value that corresponds to the + * specified name of the enumeration datatype \p dtype_id. + * + * Values returned in \p value will be of the enumerated type’s + * base type, that is, the datatype used by H5Tenum_create() when + * the enumerated type was created. + * + * The \p value buffer must be at least large enough to hold a value + * of that base type. If the size is unknown, you can determine it + * with H5Tget_size(). + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tenum_valueof(hid_t type, const char *name, void *value /*out*/); /* Operations defined on variable-length datatypes */ +/** + * \ingroup VLEN + * + * \brief Creates a new variable-length array datatype + * + * \type_id{base_id}, the element type of the datatype to create + * + * \return \hid_t{variable-length datatype} + * + * \details H5Tvlen_create() creates a new one-dimensional array datatype of + * variable-length (VL) with the base datatype \p base_id. + * + * This one-dimensional array often represents a data sequence of the + * base datatype, such as characters for character sequences or vertex + * coordinates for polygon lists. The base type specified for the VL + * datatype can be any HDF5 datatype, including another VL datatype, a + * compound datatype, or an atomic datatype. + * + * When necessary, use H5Tget_super() to determine the base type of + * the VL datatype. + * + * The datatype identifier returned from this function should be + * released with H5Tclose() or resource leaks will result. Under + * certain circumstances, H5Dvlen_reclaim() must also be used. + * + * \attention H5Tvlen_create() cannot be used to create a variable-length + * string datatype. H5Tvlen_create() called with a string or + * character base type creates a variable-length sequence of strings + * (a variable-length, 1-dimensional array), with each element of + * the array being of the string or character base type.\n + * To create a variable-length string datatype, see "Creating + * variable-length string datatypes." + * + * \todo Fix the reference. + * + */ H5_DLL hid_t H5Tvlen_create(hid_t base_id); /* Operations defined on array datatypes */ +/** + * \ingroup ARRAY + * + * \brief Creates an array datatype object + * + * \param[in] base_id Datatype identifier for the array base datatype + * \param[in] ndims Rank of the array + * \param[in] dim Size of each array dimension + * + * \return \hid_t{array datatype} + * + * \details H5Tarray_create2() creates a new array datatype object.\n\n + * \p base_id is the datatype of every element of the array, i.e., + * of the number at each position in the array. + * + * \p ndims is the number of dimensions and the size of each dimension + * is specified in the array \p dim. The value of \p rank is + * currently limited to #H5S_MAX_RANK and must be greater than 0 + * (zero). All dimension sizes specified in \p dim must be greater + * than 0 (zero). + * + * \since 1.8.0 + * + */ H5_DLL hid_t H5Tarray_create2(hid_t base_id, unsigned ndims, const hsize_t dim[/* ndims */]); +/** + * \ingroup ARRAY + * + * \brief Returns the rank of an array datatype + * + * \type_id + * + * \return Returns the rank of the array if successful; otherwise returns a + * negative value. + * + * \details H5Tget_array_ndims() returns the rank, i.e., the number of + * dimensions, of an array datatype object. + * + * \since 1.2.0 + * + */ H5_DLL int H5Tget_array_ndims(hid_t type_id); +/** + * \ingroup ARRAY + * + * \brief Retrieves sizes of array dimensions + * + * \type_id + * \param[out] dims Sizes of array dimensions + * + * \return Returns the non-negative number of dimensions of the array type + * if successful; otherwise returns a negative value. + * + * \details H5Tget_array_dims2() returns the sizes of the dimensions of the + * specified array datatype object in the array \p dims. + * + * \since 1.2.0 + * + */ H5_DLL int H5Tget_array_dims2(hid_t type_id, hsize_t dims[]); /* Operations defined on opaque datatypes */ +/** + * \ingroup OPAQUE + * + * \brief Tags an opaque datatype + * + * \type_id{type} of an opaque datatype + * \param[in] tag Descriptive ASCII string with which the opaque datatype is + * to be tagged + * + * \return \herr_t + * + * \details H5Tset_tag() tags an opaque datatype \p type with a descriptive + * ASCII identifier, \p tag. + * + * \p tag is intended to provide a concise description; the maximum + * size is hard-coded in the HDF5 library as 256 bytes + * (#H5T_OPAQUE_TAG_MAX). + * + * \version 1.6.5 The #H5T_OPAQUE_TAG_MAX macro constant, specifying the + * maximum size of an opaque datatype tag, was added in + * H5Tpublic.h. + * + */ H5_DLL herr_t H5Tset_tag(hid_t type, const char *tag); +/** + * \ingroup OPAQUE + * + * \brief Gets the tag associated with an opaque datatype + * + * \type_id{type} of an opaque datatype + * + * \return Returns a pointer to an allocated string if successful; otherwise + * returns NULL. + * + * \details H5Tget_tag() returns the tag associated with the opaque datatype + * \p type. + * + * \attention The tag is returned via a pointer to an allocated string, which + * the caller must free. + * + */ H5_DLL char * H5Tget_tag(hid_t type); /* Querying property values */ +/** + * \ingroup H5T + * + * \brief Returns the base datatype from which a datatype is derived + * + * \type_id{type} + * + * \return \hid_t{datatype} + * + * \details H5Tget_super() returns the base datatype from which the datatype + * \p type_id is derived. In the case of an enumeration type, the + * return value is an integer type. + * + * The datatype identifier returned by this function must be released + * with H5Tclose() when the identifier is no longer needed so that + * resource leaks will not develop. + * + */ H5_DLL hid_t H5Tget_super(hid_t type); +/** + * \ingroup H5T + * + * \brief Returns a datatype class + * + * \type_id + * + * \return Returns the datatype class if successful; otherwise #H5T_NO_CLASS. + * + * \details H5Tget_class() returns the class of the datatype \p type_id. + * Valid class identifiers, as defined in H5Tpublic.h, are: + * \snippet this H5T_class_t_snip + * + * \note The library returns #H5T_STRING for both fixed-length and + * variable-length strings. + * + * \note Unsupported datatype: The time datatype class, #H5T_TIME, + * is not supported. If #H5T_TIME is used, the resulting data will + * be readable and modifiable only on the originating computing + * platform; it will not be portable to other platforms. + * + */ H5_DLL H5T_class_t H5Tget_class(hid_t type_id); +/** + * \ingroup H5T + * + * \brief Determines whether a datatype contains any datatypes of the given + * datatype class + * + * \type_id + * \param[in] cls Datatype class + * + * \return \htri_t + * + * \details H5Tdetect_class() determines whether the datatype specified in + * \p type_id contains any datatypes of the datatype class specified + * in \p dtype_class. + * + * This function is useful primarily in recursively examining all the + * fields and/or base types of compound, array, and variable-length + * datatypes. + * + * Valid class identifiers, as defined in H5Tpublic.h, are: + * \snippet this H5T_class_t_snip + * + * \since 1.6.0 + * + */ H5_DLL htri_t H5Tdetect_class(hid_t type_id, H5T_class_t cls); +/** + * \ingroup H5T + * + * \brief Returns the size of a datatype + * + * \type_id + * + * \return Returns the size of the datatype in bytes if successful; otherwise, + * returns 0. + * + * \details H5Tget_size() returns the size of a datatype in bytes. + * \li For atomic datatypes, array datatypes, compound datatypes, and + * other datatypes of a constant size, the returned value is the + * size of the actual datatype in bytes. + * \li For variable-length string datatypes the returned value is + * the size of the pointer to the actual string, or \c sizeof(\c + * char \c *). This function does not return the size of actual + * variable-length string data. + * \li For variable-length sequence datatypes (see H5Tvlen_create()), + * the returned value is the size of the \p hvl_t struct, or \c + * sizeof(\p hvl_t). The \p hvl_t struct contains a pointer to the + * actual data and a size value. This function does not return the + * size of actual variable-length sequence data. + * + * \since 1.2.0 + * + * \see H5Tset_size() + * + * \todo Original has a reference to “Creating variable-length string datatypes”. + * \todo Create an example for H5Tget_size(). + * + */ H5_DLL size_t H5Tget_size(hid_t type_id); +/** + * \ingroup ATOM + * + * \brief Returns the byte order of an atomic datatype + * + * \type_id + * + * \return Returns a byte order constant if successful; otherwise returns + * #H5T_ORDER_ERROR (-1) + * + * \details H5Tget_order() returns the byte order of an atomic datatype. + * Possible return values are: + * \snippet this H5T_order_t_snip + * Members of a compound datatype need not have the same byte + * order. If members of a compound datatype have more than one of + * little endian, big endian, or VAX byte order, H5Tget_order() will + * return #H5T_ORDER_MIXED for the compound datatype. A byte order of + * #H5T_ORDER_NONE will, however, be ignored; for example, if one or + * more members of a compound datatype have byte order #H5T_ORDER_NONE + * but all other members have byte order #H5T_ORDER_LE, H5Tget_order() + * will return #H5T_ORDER_LE for the compound datatype. + * + * \since 1.2.0 + * + */ H5_DLL H5T_order_t H5Tget_order(hid_t type_id); +/** + * \ingroup ATOM + * + * \brief Returns the precision of an atomic datatype + * + * \type_id + * + * \return Returns the number of significant bits if successful; otherwise 0 + * + * \details H5Tget_precision() returns the precision of an atomic datatype + * (for example, integer or float) or a datatype whose base (parent) + * type is an atomic type (for example, array, enum and variable + * length). The precision is the number of significant bits which, + * unless padding is present, is 8 times larger than the value + * returned by H5Tget_size(). + * + * \since 1.2.0 + * + */ H5_DLL size_t H5Tget_precision(hid_t type_id); +/** + * \ingroup ATOM + * + * \brief Retrieves the bit offset of the first significant bit + * + * \type_id + * + * \return Returns an offset value if successful; otherwise returns a + * negative value. + * + * \details H5Tget_offset() retrieves the bit offset of the first significant + * bit. The significant bits of an atomic datum can be offset from the + * beginning of the memory for that datum by an amount of padding. The + * 'offset' property specifies the number of bits of padding that + * appear to the "right of" the value. That is, if we have a 32-bit + * datum with 16-bits of precision having the value 0x1122 then it + * will be laid out in memory as (from small byte address toward + * larger byte addresses): + * \code{.unparsed} + * 0: [ pad] [0x11] [0x22] [ pad] + * 1: [ pad] [0x22] [0x11] [ pad] + * 2: [0x11] [ pad] [ pad] [0x22] + * 3: [0x22] [ pad] [ pad] [0x11] + * \endcode + * + * \since 1.2.0 + * + */ H5_DLL int H5Tget_offset(hid_t type_id); +/** + * \ingroup ATOM + * + * \brief Retrieves the padding type of the least and most-significant bit padding + * + * \type_id + * \param[out] lsb Buffer for the least-significant bit padding type + * \param[out] msb Buffer for the most-significant bit padding type + * + * \return \herr_t + * + * \details H5Tget_pad() retrieves the padding type of the least and + * most-significant bit padding. Valid padding types are: + * \snippet this H5T_pad_t_snip + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tget_pad(hid_t type_id, H5T_pad_t *lsb /*out*/, H5T_pad_t *msb /*out*/); -H5_DLL H5T_sign_t H5Tget_sign(hid_t type_id); +/** + * \ingroup ATOM + * + * \brief Retrieves the sign type for an integer type + * + * \type_id + * + * \return Returns a valid sign type if successful; otherwise #H5T_SGN_ERROR (-1) + * + * \details H5Tget_sign() retrieves the sign type for an integer type. + * Valid types are: + * \snippet this H5T_sign_t_snip + * + * \since 1.2.0 + * + */ +H5_DLL H5T_sign_t H5Tget_sign(hid_t type_id); +/** + * \ingroup ATOM + * + * \brief Retrieves floating point datatype bit field information + * + * \type_id + * \param[out] spos Pointer to location to return floating-point sign bit + * \param[out] epos Pointer to location to return exponent bit-position + * \param[out] esize Pointer to location to return size of exponent in bits + * \param[out] mpos Pointer to location to return mantissa bit-position + * \param[out] msize Pointer to location to return size of mantissa in bits + * + * \return \herr_t + * + * \details H5Tget_fields() retrieves information about the locations of + * the various bit fields of a floating point datatype. The field + * positions are bit positions in the significant region of the + * datatype. Bits are numbered with the least significant bit number + * zero. Any (or even all) of the arguments can be null pointers. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tget_fields(hid_t type_id, size_t *spos /*out*/, size_t *epos /*out*/, size_t *esize /*out*/, size_t *mpos /*out*/, size_t *msize /*out*/); +/** + * \ingroup ATOM + * + * \brief Retrieves the exponent bias of a floating-point type + * + * \type_id + * + * \return Returns the bias if successful and 0, otherwise. + * + * \details H5Tget_ebias() retrieves the exponent bias of a floating-point type. + * + * \since 1.2.0 + * + */ H5_DLL size_t H5Tget_ebias(hid_t type_id); +/** + * -------------------------------------------------------------------------- + * \ingroup ATOM + * + * \brief Retrieves mantissa normalization of a floating-point datatype + * + * \type_id + * + * \return Returns a valid normalization type if successful; otherwise + * returns #H5T_NORM_ERROR (-1) + * + * \details H5Tget_norm() retrieves the mantissa normalization of a + * floating-point datatype. Valid normalization types are: + * \snippet this H5T_norm_t_snip + * + * \since 1.2.0 + * + */ H5_DLL H5T_norm_t H5Tget_norm(hid_t type_id); +/** + * \ingroup ATOM + * + * \brief Retrieves the internal padding type for unused bits in floating-point + * datatypes + * + * \type_id + * + * \return Returns a valid padding type if successful; otherwise returns + * #H5T_PAD_ERROR (-1). + * + * \details H5Tget_inpad() retrieves the internal padding type for unused + * bits in floating-point datatypes. Valid padding types are: + * \snippet this H5T_pad_t_snip + * + * \since 1.2.0 + * + */ H5_DLL H5T_pad_t H5Tget_inpad(hid_t type_id); +/** + * \ingroup ATOM + * + * \brief Retrieves the type of padding used for a string datatype + * + * \type_id + * + * \return Returns a valid string of the padding if successful; otherwise + * returns #H5T_STR_ERROR (-1) + * + * \details H5Tget_strpad() retrieves the type of padding used for a string + * datatype. + * + * The string padding type is set with H5Tset_strpad(). Possible + * values returned are: + * \str_pad_type + * + * \since 1.2.0 + * + */ H5_DLL H5T_str_t H5Tget_strpad(hid_t type_id); +/** + * \ingroup COMPOUND + * + * \brief Retrieves the number of elements in a compound or enumeration datatype + * + * \type_id + * + * \return Returns the number of elements if successful; otherwise returns a + * negative value. + * + * \details H5Tget_nmembers() retrieves the number of fields in a compound + * datatype or the number of members of an enumeration datatype. + * + * \since 1.2.0 + * + */ H5_DLL int H5Tget_nmembers(hid_t type_id); +/** + * \ingroup COMPOUND + * + * \brief Retrieves the name of a compound or enumeration datatype member + * + * \type_id + * \param[in] membno Zero-based index of the field or element + * + * \return Returns a valid pointer to a string allocated with malloc() if + * successful; otherwise returns NULL. + * + * \details H5Tget_member_name() retrieves the name of a field of a compound + * datatype or an element of an enumeration datatype. + * + * The index of the target field or element is specified in \p + * member_no. Compound datatype fields and enumeration datatype + * elements are stored in no particular order with index values of + * 0 through N-1, where N is the value returned by H5Tget_nmembers(). + * + * The HDF5 library allocates a buffer to receive the name of + * the field. The caller must subsequently free the buffer with + * H5free_memory(). + * + * \since 1.2.0 + * + */ H5_DLL char * H5Tget_member_name(hid_t type_id, unsigned membno); +/** + * \ingroup COMPOUND + * + * \brief Retrieves the index of a compound or enumeration datatype member + * + * \type_id + * \param[in] name Name of the field or member + * + * \return \herr_t + * + * \details H5Tget_member_index() retrieves the index of a field of a compound + * datatype or an element of an enumeration datatype. + * + * The name of the target field or element is specified by \p name. + * + * Fields are stored in no particular order with index values of 0 + * through N-1, where N is the value returned by H5Tget_nmembers() . + * + * \since 1.2.0 + * + */ H5_DLL int H5Tget_member_index(hid_t type_id, const char *name); +/** + * \ingroup COMPOUND + * + * \brief Retrieves the offset of a field of a compound datatype + * + * \type_id + * \param[in] membno Zero-based index of the field or element + * + * \return Returns the byte offset of the field if successful; otherwise + * returns 0 (zero). + * + * \details H5Tget_member_offset() retrieves the byte offset of the beginning + * of a field within a compound datatype with respect to the beginning + * of the compound datatype datum. + * + * Note that zero is a valid offset and that this function will fail + * only if a call to H5Tget_member_class() fails with the same arguments. + * + * \version 1.6.4 \p member_no parameter type changed to unsigned. + * + * \since 1.2.0 + * + */ H5_DLL size_t H5Tget_member_offset(hid_t type_id, unsigned membno); +/** + * \ingroup COMPOUND + * + * \brief Returns datatype class of compound datatype member + * + * \type_id + * \param[in] membno Zero-based index of the field or element + * + * \return Returns the datatype class, a non-negative value, if successful; + * otherwise returns a negative value. + * + * \details Given a compound datatype, \p dtype_id, H5Tget_member_class() + * returns the datatype class of the member specified by \p member_no. + * + * Valid class identifiers, as defined in H5Tpublic.h, are: + * \snippet this H5T_class_t_snip + * + * \since 1.2.0 + * + */ H5_DLL H5T_class_t H5Tget_member_class(hid_t type_id, unsigned membno); +/** + * \ingroup COMPOUND + * + * \brief Returns the datatype of the specified member + * + * \type_id + * \param[in] membno Zero-based index of the field or element + * + * \return Returns the identifier of a copy of the datatype of the field if + * successful; otherwise returns a negative value. + * + * \details H5Tget_member_type() returns the datatype of the specified member. + * The caller should invoke H5Tclose() to release resources associated + * with the type. + * + * \version 1.6.4 \p membno parameter type changed to unsigned. + * + * \since 1.2.0 + * + */ H5_DLL hid_t H5Tget_member_type(hid_t type_id, unsigned membno); +/** + * \ingroup ENUM + * + * \brief Returns the value of an enumeration datatype member + * + * \type_id + * \param[in] membno Number of the enumeration datatype member + * \param[out] value Buffer for the value of the enumeration datatype member + * + * \return \herr_t + * + * \details H5Tget_member_value() returns the value of the enumeration datatype + * member \p member_no. + * + * The member value is returned in a user-supplied buffer pointed to + * by \p value. Values returned in \p value will be of the enumerated + * type’s base type, that is, the datatype used by H5Tenum_create() + * when the enumerated type was created. + * + * The value buffer must be at least large enough to hold a value + * of that base type. If the size is unknown, you can determine it + * with H5Tget_size(). + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tget_member_value(hid_t type_id, unsigned membno, void *value /*out*/); +/** + * \ingroup ATOM + * + * \brief Retrieves the character set type of a string datatype + * + * \type_id + * + * \return Returns a valid character set type if successful; otherwise + * #H5T_CSET_ERROR (-1). + * + * \details H5Tget_cset() retrieves the character set type of a string datatype. + * Valid character set types are: + * \csets + * + * \since 1.2.0 + * + */ H5_DLL H5T_cset_t H5Tget_cset(hid_t type_id); +/** + * \ingroup ATOM + * + * \brief Determines whether datatype is a variable-length string + * + * \type_id + * + * \return Returns: + * \li a positive value if the specified datatype is a variable-length + * string + * \li 0 if the specified datatype is not a variable-length string + * \li a negative value when the function fails + * + * \details H5Tis_variable_str() determines whether the datatype identified + * by \p dtype_id is a variable-length string. + * + * This function can be used to distinguish between fixed and + * variable-length string datatypes. + * + * \since 1.6.0 + * + */ H5_DLL htri_t H5Tis_variable_str(hid_t type_id); +/** + * \ingroup H5T + * + * \brief Returns the native datatype identifier of a specified datatype + * + * \type_id + * \param[in] direction Direction of search + * + * \return \hid_t{native datatype} + * + * \details H5Tget_native_type() returns the equivalent native datatype + * identifier for the datatype specified by \p type_id. + * + * H5Tget_native_type() is designed primarily to facilitate use of + * the H5Dread() function, for which users otherwise must undertake a + * multi-step process to determine the native datatype of a dataset + * prior to reading it into memory. This function can be used for + * the following purposes: + * + * \li To determine the native datatype of an atomic datatype + * \li To determine the base datatype of an array, enumerated, or + * variable-length datatype + * \li To determine the native atomic datatypes of the individual + * components of a compound datatype + * + * For example, if \p type_id is a compound datatype, the returned + * datatype identifier will be for a similar compound datatype with + * each element converted to the corresponding native datatype; + * nested compound datatypes will be unwound. If \p type_id is an + * array, the returned datatype identifier will be for the native + * datatype of a single array element. + * + * H5Tget_native_type() selects the first matching native datatype + * from the following list: + * + * \li #H5T_NATIVE_CHAR + * \li #H5T_NATIVE_SHORT + * \li #H5T_NATIVE_INT + * \li #H5T_NATIVE_LONG + * \li #H5T_NATIVE_LLONG + * + * \li #H5T_NATIVE_UCHAR + * \li #H5T_NATIVE_USHORT + * \li #H5T_NATIVE_UINT + * \li #H5T_NATIVE_ULONG + * \li #H5T_NATIVE_ULLONG + * + * \li #H5T_NATIVE_FLOAT + * \li #H5T_NATIVE_DOUBLE + * \li #H5T_NATIVE_LDOUBLE + * + * \li #H5T_NATIVE_B8 + * \li #H5T_NATIVE_B16 + * \li #H5T_NATIVE_B32 + * \li #H5T_NATIVE_B64 + * + * The direction parameter indicates the order in which the library + * searches for a native datatype match. Valid values for direction + * are as follows: + * \snippet this H5T_direction_t_snip + * + * H5Tget_native_type() is designed primarily for use with integer, + * floating point, and bitfield datatypes. String, time, opaque, and + * reference datatypes are returned as a copy of dtype_id. See above + * for compound, array, enumerated, and variable-length datatypes. + * + * The identifier returned by H5Tget_native_type() should eventually + * be closed by calling H5Tclose() to release resources. + * + * \note Please note that a datatype is actually an object + * identifier or handle returned from opening the datatype. It + * is not persistent and its value can be different from one HDF5 + * session to the next. + * + * \note H5Tequal() can be used to compare datatypes. + * + * \note HDF5 High Level APIs that may also be of interest are: H5LTdtype_to_text() + * creates a text description of a datatype. H5LTtext_to_dtype() creates an + * HDF5 datatype given a text description. + * + * \since 1.6.0 + * + */ H5_DLL hid_t H5Tget_native_type(hid_t type_id, H5T_direction_t direction); /* Setting property values */ +/** + * \ingroup H5T + * + * \brief Sets size for a datatype. + * + * \type_id + * \param[in] size New datatype size is bytes or #H5T_VARIABLE + * + * \return \herr_t + * + * \details H5Tset_size() sets the total size, \p size, in bytes, for a + * datatype. + * + * \p size must have a positive value, unless it is passed in as + * #H5T_VARIABLE and the datatype is a string datatype. + * + * \li Numeric datatypes: If the datatype is atomic and the size + * is decreased so that significant bits of the datatype extend + * beyond the edge of the new size, then the offset property of the + * datatype is decreased toward zero. If the offset becomes zero + * and the significant bits of the datatype still hang over the edge + * of the new size, then the number of significant bits is decreased. + * + * \li String or character datatypes: The size set for a string + * datatype should include space for the null-terminator character, + * otherwise it will not be stored on (or retrieved from) + * disk. Adjusting the size of a string automatically sets the + * precision to \p 8*size. + * + * \li Variable-length string datatypes: If \p dtype_id is a + * variable-length string, size must normally be set to #H5T_VARIABLE. + * + * \li Compound datatypes: This function may be used to increase or + * decrease the size of a compound datatype, but the function will + * fail if the new size is too small to accommodate all member fields. + * + * \li Ineligible datatypes: This function cannot be used with + * enumerated datatypes (#H5T_ENUM), array datatypes (#H5T_ARRAY), + * variable-length array datatypes (#H5T_VLEN), or reference datatypes + * (#H5T_REFERENCE). + * + * \since 1.2.0 + * + * \see H5Tget_size() + * + *\todo Create an example for H5Tset_size(). + *\todo Original has a reference to “Creating variable-length string datatypes”. + * + */ H5_DLL herr_t H5Tset_size(hid_t type_id, size_t size); +/** + * \ingroup ATOM + * + * \brief Sets the byte order of a datatype + * + * \type_id + * \param[in] order Byte order constant + * + * \return \herr_t + * + * \details H5Tset_order() sets the byte order of a datatype.\n + * Byte order can currently be set to any of the following: + * \snippet this H5T_order_t_snip + * #H5T_ORDER_MIXED (3) is a valid value for order only when + * returned by the function H5Tget_order(); it cannot be set with + * H5Tset_order(). + * + * #H5T_ORDER_NONE (4) is a valid value for order, but it has no + * effect. It is valid only for fixed-length strings and object and + * region references and specifies “no particular order.” + * + * The byte order of a derived datatype is initially the same as + * that of the parent type, but can be changed with H5Tset_order(). + * + * This function cannot be used with a datatype after it has been + * committed. + * + * \note Special considerations: + * \li ENUM datatypes: Byte order must be set before any member on + * an ENUM is defined. + * \li Compound datatypes: Byte order is set individually on each member + * of a compound datatype; members of a compound datatype need not + * have the same byte order. + * \li Opaque datatypes: Byte order can be set but has no effect. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_order(hid_t type_id, H5T_order_t order); +/** + * \ingroup ATOM + * + * \brief Sets the precision of an atomic datatype + * + * \type_id + * \param[in] prec Number of bits of precision for datatype + * + * \return \herr_t + * + * \details H5Tset_precision() sets the precision of an atomic datatype. The + * precision is the number of significant bits which, unless + * padding is present, is 8 times larger than the value returned + * by H5Tget_size(). + * + * If the precision is increased then the offset is decreased and + * then the size is increased to insure that significant bits do not + * "hang over" the edge of the datatype. + * + * Changing the precision of an #H5T_STRING automatically changes + * the size as well. The precision must be a multiple of 8. + * + * When decreasing the precision of a floating point type, set the + * locations and sizes of the sign, mantissa, and exponent fields + * first. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_precision(hid_t type_id, size_t prec); +/** + * \ingroup ATOM + * + * \brief Sets the bit offset of the first significant bit + * + * \type_id + * \param[in] offset Offset of first significant bit + * + * \return \herr_t + * + * \details H5Tset_offset() sets the bit offset of the first significant + * bit. The significant bits of an atomic datum can be offset from + * the beginning of the memory for that datum by an amount of + * padding. The offset property specifies the number of bits of + * padding that appear “to the right of” the value. That is, + * if we have a 32-bit datum with 16-bits of precision having the + * value 0x1122, then it will be laid out in memory as (from small + * byte address toward larger byte addresses): + * \code{.unparsed} + * 0: [ pad] [0x11] [0x22] [ pad] + * 1: [ pad] [0x22] [0x11] [ pad] + * 2: [0x11] [ pad] [ pad] [0x22] + * 3: [0x22] [ pad] [ pad] [0x11] + * \endcode + * If the offset is incremented then the total size is incremented + * also if necessary to prevent significant bits of the value from + * hanging over the edge of the datatype. + * + * The offset of an #H5T_STRING cannot be set to anything but zero. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_offset(hid_t type_id, size_t offset); +/** + * \ingroup ATOM + * + * \brief Sets the least and most-significant bits padding types + * + * \type_id + * \param[in] lsb Padding type for least-significant bits + * \param[in] msb Padding type for most-significant bits + * + * \return \herr_t + * + * \details H5Tset_pad() sets the least and most-significant bits padding types. + * Available values are: + * \padding_type + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_pad(hid_t type_id, H5T_pad_t lsb, H5T_pad_t msb); +/** + * \ingroup ATOM + * + * \brief Sets the sign property for an integer type + * + * \type_id + * \param[in] sign Sign type + * + * \return \herr_t + * + * \details H5Tset_sign() sets the sign property for an integer type: + * \sign_prop + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_sign(hid_t type_id, H5T_sign_t sign); +/** + * \ingroup ATOM + * + * \brief Sets locations and sizes of floating point bit fields + * + * \type_id + * \param[in] spos Sign position, i.e., the bit offset of the floating-point + * sign bit + * \param[in] epos Exponent bit position + * \param[in] esize Size of exponent in bits + * \param[in] mpos Mantissa bit position + * \param[in] msize Size of mantissa in bits + * + * \return \herr_t + * + * \details H5Tset_fields() sets the locations and sizes of the various + * floating-point bit fields. The field positions are bit positions + * in the significant region of the datatype. Bits are numbered with + * the least significant bit number zero. + * + * Fields are not allowed to extend beyond the number of bits of + * precision, nor are they allowed to overlap with one another. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_fields(hid_t type_id, size_t spos, size_t epos, size_t esize, size_t mpos, size_t msize); +/** + * \ingroup ATOM + * + * \brief Sets the exponent bias of a floating-point type + * + * \type_id + * \param[in] ebias Exponent bias value + * + * \return \herr_t + * + * \details H5Tset_ebias() sets the exponent bias of a floating-point type. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_ebias(hid_t type_id, size_t ebias); +/** + * \ingroup ATOM + * + * \brief Sets the mantissa normalization of a floating-point datatype + * + * \type_id + * \param[in] norm Mantissa normalization type + * + * \return \herr_t + * + * \details H5Tset_norm() sets the mantissa normalization of a floating-point + * datatype. Valid normalization types are: + * \snippet this H5T_norm_t_snip + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_norm(hid_t type_id, H5T_norm_t norm); +/** + * \ingroup ATOM + * + * \brief Fills unused internal floating-point bits + * + * \type_id + * \param[in] pad Padding type + * + * \return \herr_t + * + * \details H5Tset_inpad() 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. Valid + * padding types are: + * \snippet this H5T_pad_t_snip + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_inpad(hid_t type_id, H5T_pad_t pad); +/** + * \ingroup ATOM + * + * \brief Sets character set to be used in a string or character datatype + * + * \type_id + * \param[in] cset Character set type + * + * \return \herr_t + * + * \details H5Tset_cset() sets the character set to be used in a dataset with + * a string or character datatype. + * + * Valid values for cset include the following: + * \csets + * For example, if the character set for the datatype \p type_id is set + * to #H5T_CSET_UTF8, string or character data of datatype dtype_id + * will be encoded using the UTF-8 Unicode character set. + * + * ASCII and UTF-8 Unicode are the only currently supported character + * encodings. Extended ASCII encodings (for example, ISO 8859) are + * not supported. This encoding policy is not enforced by the HDF5 + * library. Using encodings other than ASCII and UTF-8 can lead to + * compatibility and usability problems. + * + * Note that H5Tset_cset() sets the character set for a character or + * string datatype while H5Pset_char_encoding() sets the character + * set used for an HDF5 link or attribute name. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_cset(hid_t type_id, H5T_cset_t cset); +/** + * \ingroup ATOM + * + * \brief Defines the type of padding used for character strings + * + * \type_id + * \param[in] strpad String padding type + * + * \return \herr_t + * + * \details H5Tset_strpad() defines the type of padding used for a string + * datatype. + * + * The method used to store character strings differs with the + * programming language. C usually null terminates strings while + * Fortran left-justifies and space-pads strings. + * + * Valid values of \p strpad are as follows: + * \str_pad_type + * When converting from a longer string to a shorter string, the + * behavior is as follows. If the shorter string is #H5T_STR_NULLPAD + * or #H5T_STR_SPACEPAD, then the string is simply truncated. If + * the short string is #H5T_STR_NULLTERM, it is truncated and a null + * terminator is appended. + * + * When converting from a shorter string to a longer string, the + * longer string is padded on the end by appending nulls or spaces. + * + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tset_strpad(hid_t type_id, H5T_str_t strpad); /* Type conversion database */ +/** + * \ingroup CONV + * + * \brief Registers a datatype conversion function + * + * \param[in] pers Conversion function type + * \param[in] name Name displayed in diagnostic output + * \type_id{src_id} of source datatype + * \type_id{dst_id} of destination datatype + * \param[in] func Function to convert between source and destination datatypes + * + * \return \herr_t + * + * \details H5Tregister() registers a hard or soft conversion function for a + * datatype conversion path. The parameter \p pers indicates whether a + * conversion function is hard (#H5T_PERS_HARD) or soft + * (#H5T_PERS_SOFT). User-defined functions employing compiler casting + * are designated as \Emph{hard}; other user-defined conversion + * functions registered with the HDF5 library (with H5Tregister() ) + * are designated as \Emph{soft}. The HDF5 library also has its own + * hard and soft conversion functions. + * + * A conversion path can have only one hard function. When type is + * #H5T_PERS_HARD, \p func replaces any previous hard function. + * + * When type is #H5T_PERS_SOFT, H5Tregister() adds the function to the + * end of the master soft list and replaces the soft function in all + * applicable existing conversion paths. Soft functions are used when + * determining which conversion function is appropriate for this path. + * + * The \p name is used only for debugging and should be a short + * identifier for the function. + * + * The path is specified by the source and destination datatypes \p + * src_id and \p dst_id. For soft conversion functions, only the class + * of these types is important. + * + * The type of the conversion function pointer is declared as: + * \snippet this H5T_conv_t_snip + * + * The \ref H5T_cdata_t \c struct is declared as: + * \snippet this H5T_cdata_t_snip + * + * \since 1.6.3 The following change occurred in the \ref H5T_conv_t function: + * the \c nelmts parameter type changed to size_t. + * + */ H5_DLL herr_t H5Tregister(H5T_pers_t pers, const char *name, hid_t src_id, hid_t dst_id, H5T_conv_t func); +/** + * \ingroup CONV + * + * \brief Removes a conversion function + * + * \param[in] pers Conversion function type + * \param[in] name Name displayed in diagnostic output + * \type_id{src_id} of source datatype + * \type_id{dst_id} of destination datatype + * \param[in] func Function to convert between source and destination datatypes + * + * \return \herr_t + * + * \details H5Tunregister() removes a conversion function matching criteria + * such as soft or hard conversion, source and destination types, and + * the conversion function. + * + * If a user is trying to remove a conversion function he registered, + * all parameters can be used. If he is trying to remove a library’s + * default conversion function, there is no guarantee the \p name and + * \p func parameters will match the user’s chosen values. Passing in + * some values may cause this function to fail. A good practice is to + * pass in NULL as their values. + * + * All parameters are optional. The missing parameters will be used to + * generalize the search criteria. + * + * The conversion function pointer type declaration is described in + * H5Tregister(). + * + * \version 1.6.3 The following change occurred in the \ref H5T_conv_t function: + * the \c nelmts parameter type changed to size_t. + * + */ H5_DLL herr_t H5Tunregister(H5T_pers_t pers, const char *name, hid_t src_id, hid_t dst_id, H5T_conv_t func); +/** + * \ingroup CONV + * + * \brief Finds a conversion function + * + * \type_id{src_id} of source datatype + * \type_id{dst_id} of destination datatype + * \param[out] pcdata Pointer to type conversion data + * + * \return Returns a pointer to a suitable conversion function if successful. + * Otherwise returns NULL. + * + * \details H5Tfind() finds a conversion function that can handle a conversion + * from type \p src_id to type \p dst_id. The \p pcdata argument is a + * pointer to a pointer to type conversion data which was created and + * initialized by the soft type conversion function of this path when + * the conversion function was installed on the path. + * + */ H5_DLL H5T_conv_t H5Tfind(hid_t src_id, hid_t dst_id, H5T_cdata_t **pcdata); +/** + * \ingroup CONV + * + * \brief Check whether the library’s default conversion is hard conversion + * + * \type_id{src_id} of source datatype + * \type_id{dst_id} of destination datatype + * + * \return \htri_t + * + * \details H5Tcompiler_conv() determines whether the library’s conversion + * function from type \p src_id to type \p dst_id is a compiler (hard) + * conversion or not. A compiler conversion uses compiler’s casting; a + * library (soft) conversion uses the library’s own conversion + * function. + * + * \since 1.8.0 + * + */ H5_DLL htri_t H5Tcompiler_conv(hid_t src_id, hid_t dst_id); +/** + * -------------------------------------------------------------------------- + * \ingroup CONV + * + * \brief Converts data from one specified datatype to another + * + * \type_id{src_id} of source datatype + * \type_id{dst_id} of destination datatype + * \param[in] nelmts Size of array \p buf + * \param[in,out] buf Array containing pre- and post-conversion values + * \param[in] background Optional background buffer + * \dxpl_id{plist_id} + * + * \return \herr_t + * + * \details H5Tconvert() converts \p nelmts elements from a source datatype, + * specified by \p src_id, to a destination datatype, \p dst_id. The + * source elements are packed in \p buf and on return the destination + * elements will be packed in \p buf. That is, the conversion is + * performed in place. + * + * The optional background buffer is for use with compound datatypes. + * It is an array of \p nelmts values for the destination datatype + * which can then be merged with the converted values to recreate the + * compound datatype. For instance, background might be an array of + * structs with the \c a and \c b fields already initialized and the + * conversion of buf supplies the \c c and \c d field values. + * + * The parameter \p plist_id contains the dataset transfer property list + * identifier which is passed to the conversion functions. As of + * Release 1.2, this parameter is only used to pass along the + * variable-length datatype custom allocation information. + * + * \note H5Tconvert() will not resize the buffer \p buf; it must be large + * enough to hold the larger of the input and output data. + * + * \version 1.6.3 \p nelmts parameter type changed to size_t. + * \version 1.4.0 \p nelmts parameter type changed to \ref hsize_t. + * + */ H5_DLL herr_t H5Tconvert(hid_t src_id, hid_t dst_id, size_t nelmts, void *buf, void *background, hid_t plist_id); +/** + * \ingroup VLEN + * + * \brief Reclaims the variable length (VL) datatype memory buffers + * + * \type_id + * \space_id + * \dxpl_id{plist_id} used to create the buffer + * \param[in] buf Pointer to the buffer to be reclaimed + * + * \return \herr_t + * + * \details H5Treclaim() reclaims memory buffers created to store VL datatypes. + * It only frees the variable length data in the selection defined in + * the dataspace specified by \p space_id. The dataset transfer + * property list \p plist_id is required to find the correct + * allocation and/or free methods for the variable-length data in the + * buffer. + * + * \since 1.12.0 + * + */ H5_DLL herr_t H5Treclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf); /* Symbols defined for compatibility with previous versions of the HDF5 API. @@ -598,10 +2883,139 @@ H5_DLL herr_t H5Treclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void /* Typedefs */ /* Function prototypes */ +/** + * \ingroup H5T + * + * \brief Commits a transient datatype to a file, creating a new named datatype + * + * \fg_loc_id + * \param[in] name Name given to committed datatype + * \param[in] type_id Identifier of datatype to be committed + * + * \return \herr_t + * + * \deprecated This function has been renamed from H5Tcommit() and is + * deprecated in favor of the macro #H5Tcommit or the function + * H5Tcommit2(). + * + * \details H5Tcommit1() commits the transient datatype (not immutable) to + * a file, turning it into a named datatype. + * + * The datatype \p dtype_id is committed as a named datatype at the + * location \p loc_id, which is either a file or group identifier, + * with the name \p name. + * + * \p name can be a relative path based at \p loc_id or an absolute + * path from the root of the file. Use of this function requires + * that any intermediate groups specified in the path already exist. + * + * As is the case for any object in a group, the length of the name + * of a named datatype is not limited. + * + * See H5Tcommit_anon() for a discussion of the differences between + * H5Tcommit() and H5Tcommit_anon(). + * + * This function will not accept a datatype that cannot actually + * hold data. This currently includes compound datatypes with no + * fields and enumerated datatypes with no members. + * + * \version 1.8.7 Function modified in this release to reject datatypes that + * will not accommodate actual data, such as a compound datatype with + * no fields or an enumerated datatype with no members. + * \version 1.8.0 C function H5Tcommit() renamed to H5Tcommit1() and deprecated + * in this release. + * \since 1.2.0 + * + */ H5_DLL herr_t H5Tcommit1(hid_t loc_id, const char *name, hid_t type_id); +/** + * \ingroup H5T + * + * \brief Opens a named datatype + * + * \fg_loc_id + * \param[in] name A datatype name, defined within the specified file or group + * + * \return \herr_t + * + * \deprecated This function has been renamed from H5Topen() and is + * deprecated in favor of the macro #H5Topen or the function + * H5Topen2(). + * + * \details H5Topen1() opens a named datatype at the location specified by + * \p loc_id and returns an identifier for the datatype. \p loc_id + * can be either a file or group identifier. The identifier should + * eventually be closed by calling H5Tclose() to release resources. + * + * \version 1.8.0 Function H5Topen() renamed to H5Topen1() and deprecated in + * this release. + * + * \since 1.2.0 + * + */ H5_DLL hid_t H5Topen1(hid_t loc_id, const char *name); +/** + * \ingroup ARRAY + * + * \brief Creates an array datatype object + * + * \param[in] base_id Datatype identifier for the array base datatype + * \param[in] ndims Rank of the array + * \param[in] dim Size of each array dimension + * \param[in] perm Dimension permutation (Currently not implemented.) + * + * \return \hid_t{array datatype} + * + * \deprecated This function has been renamed from H5Tarray_create() and is + * deprecated in favor of the macro #H5Tarray_create or the function + * H5Tarray_create2(). + * + * \details H5Tarray_create1() creates a new array datatype object.\n\n + * \p base_id is the datatype of every element of the array, i.e., + * of the number at each position in the array. + * + * \p rank is the number of dimensions and the size of each dimension + * is specified in the array dims. The value of rank is currently + * limited to #H5S_MAX_RANK and must be greater than 0 (zero). All + * dimension sizes specified in dims must be greater than 0 (zero). + * + * The array \p perm is designed to contain the dimension permutation, + * i.e. C versus FORTRAN array order. (The parameter perm is + * currently unused and is not yet implemented.) + * + * \version 1.8.0 Function H5Tarray_create() renamed to H5Tarray_create1() + * and deprecated in this release. + * \since 1.4.0 + * + */ H5_DLL hid_t H5Tarray_create1(hid_t base_id, int ndims, const hsize_t dim[/* ndims */], const int perm[/* ndims */]); +/** + * \ingroup ARRAY + * + * \brief Retrieves sizes of array dimensions + * + * \type_id + * \param[out] dims Sizes of array dimensions + * \param[out] perm Dimension permutations (This parameter is not used.) + * + * \return Returns the non-negative number of dimensions of the array type + * if successful; otherwise, returns a negative value. + * + * \deprecated This function has been renamed from H5Tget_array_dims() and is + * deprecated in favor of the macro #H5Tget_array_dims or the + * function H5Tget_array_dims2(). + * + * \details H5Tget_array_dims1() returns the sizes of the dimensions and + * the dimension permutations of the specified array datatype object. + * + * The sizes of the dimensions are returned in the array \p dims. + * + * \version 1.8.0 Function H5Tarray_create() renamed to H5Tarray_create1() + * and deprecated in this release. + * \since 1.2.0 + * + */ H5_DLL int H5Tget_array_dims1(hid_t type_id, hsize_t dims[], int perm[]); #endif /* H5_NO_DEPRECATED_SYMBOLS */ diff --git a/src/H5VLconnector.h b/src/H5VLconnector.h index 63ac910..2abdca3 100644 --- a/src/H5VLconnector.h +++ b/src/H5VLconnector.h @@ -438,39 +438,44 @@ typedef struct H5VL_token_class_t { herr_t (*from_str)(void *obj, H5I_type_t obj_type, const char *token_str, H5O_token_t *token); } H5VL_token_class_t; -/* Class information for each VOL connector */ +/** + * \ingroup H5VLDEV + * Class information for each VOL connector + */ +//! [H5VL_class_t_snip] typedef struct H5VL_class_t { /* Overall connector fields & callbacks */ - unsigned int version; /* VOL connector class struct version # */ - H5VL_class_value_t value; /* Value to identify connector */ - const char * name; /* Connector name (MUST be unique!) */ - unsigned cap_flags; /* Capability flags for connector */ - herr_t (*initialize)(hid_t vipl_id); /* Connector initialization callback */ - herr_t (*terminate)(void); /* Connector termination callback */ + unsigned int version; /**< VOL connector class struct version # */ + H5VL_class_value_t value; /**< Value to identify connector */ + const char * name; /**< Connector name (MUST be unique!) */ + unsigned cap_flags; /**< Capability flags for connector */ + herr_t (*initialize)(hid_t vipl_id); /**< Connector initialization callback */ + herr_t (*terminate)(void); /**< Connector termination callback */ /* VOL framework */ - H5VL_info_class_t info_cls; /* VOL info fields & callbacks */ - H5VL_wrap_class_t wrap_cls; /* VOL object wrap / retrieval callbacks */ + H5VL_info_class_t info_cls; /**< VOL info fields & callbacks */ + H5VL_wrap_class_t wrap_cls; /**< VOL object wrap / retrieval callbacks */ /* Data Model */ - H5VL_attr_class_t attr_cls; /* Attribute (H5A*) class callbacks */ - H5VL_dataset_class_t dataset_cls; /* Dataset (H5D*) class callbacks */ - H5VL_datatype_class_t datatype_cls; /* Datatype (H5T*) class callbacks */ - H5VL_file_class_t file_cls; /* File (H5F*) class callbacks */ - H5VL_group_class_t group_cls; /* Group (H5G*) class callbacks */ - H5VL_link_class_t link_cls; /* Link (H5L*) class callbacks */ - H5VL_object_class_t object_cls; /* Object (H5O*) class callbacks */ + H5VL_attr_class_t attr_cls; /**< Attribute (H5A*) class callbacks */ + H5VL_dataset_class_t dataset_cls; /**< Dataset (H5D*) class callbacks */ + H5VL_datatype_class_t datatype_cls; /**< Datatype (H5T*) class callbacks */ + H5VL_file_class_t file_cls; /**< File (H5F*) class callbacks */ + H5VL_group_class_t group_cls; /**< Group (H5G*) class callbacks */ + H5VL_link_class_t link_cls; /**< Link (H5L*) class callbacks */ + H5VL_object_class_t object_cls; /**< Object (H5O*) class callbacks */ /* Infrastructure / Services */ - H5VL_introspect_class_t introspect_cls; /* Container/connector introspection class callbacks */ - H5VL_request_class_t request_cls; /* Asynchronous request class callbacks */ - H5VL_blob_class_t blob_cls; /* 'Blob' class callbacks */ - H5VL_token_class_t token_cls; /* VOL connector object token class callbacks */ + H5VL_introspect_class_t introspect_cls; /**< Container/connector introspection class callbacks */ + H5VL_request_class_t request_cls; /**< Asynchronous request class callbacks */ + H5VL_blob_class_t blob_cls; /**< 'Blob' class callbacks */ + H5VL_token_class_t token_cls; /**< VOL connector object token class callbacks */ /* Catch-all */ herr_t (*optional)(void *obj, int op_type, hid_t dxpl_id, void **req, - va_list arguments); /* Optional callback */ + va_list arguments); /**< Optional callback */ } H5VL_class_t; +//! [H5VL_class_t_snip] /********************/ /* Public Variables */ @@ -485,10 +490,54 @@ extern "C" { #endif /* Helper routines for VOL connector authors */ +/** + * \ingroup H5VLDEV + * \brief Registers a new VOL connector + * + * \param[in] cls A pointer to the plugin structure to register + * \vipl_id + * \return \hid_t{VOL connector} + * + * \details H5VLregister_connector() registers a new VOL connector as a member + * of the virtual object layer class. This VOL connector identifier is + * good until the library is closed or the connector is unregistered. + * + * \p vipl_id is either #H5P_DEFAULT or the identifier of a VOL + * initialization property list of class #H5P_VOL_INITIALIZE created + * with H5Pcreate(). When created, this property list contains no + * library properties. If a VOL connector author decides that + * initialization-specific data are needed, they can be added to the + * empty list and retrieved by the connector in the VOL connector's + * initialize callback. Use of the VOL initialization property list is + * uncommon, as most VOL-specific properties are added to the file + * access property list via the connector's API calls which set the + * VOL connector for the file open/create. For more information, see + * the VOL documentation. + * + * H5VL_class_t is defined in H5VLconnector.h in the source code. It + * contains class information for each VOL connector: + * \snippet this H5VL_class_t_snip + * + * \todo Fix the reference to VOL documentation. + * + * \since 1.12.0 + */ H5_DLL hid_t H5VLregister_connector(const H5VL_class_t *cls, hid_t vipl_id); +/** + * \ingroup H5VLDEV + */ H5_DLL void *H5VLobject(hid_t obj_id); +/** + * \ingroup H5VLDEV + */ H5_DLL hid_t H5VLget_file_type(void *file_obj, hid_t connector_id, hid_t dtype_id); +/** + * \ingroup H5VLDEV + */ H5_DLL hid_t H5VLpeek_connector_id_by_name(const char *name); +/** + * \ingroup H5VLDEV + */ H5_DLL hid_t H5VLpeek_connector_id_by_value(H5VL_class_value_t value); #ifdef __cplusplus diff --git a/src/H5VLmodule.h b/src/H5VLmodule.h index 1ff9137..91d61c9 100644 --- a/src/H5VLmodule.h +++ b/src/H5VLmodule.h @@ -27,4 +27,19 @@ #define H5_MY_PKG_ERR H5E_VOL #define H5_MY_PKG_INIT YES +/** + * \defgroup H5VL H5VL + * \brief Virtual Object Layer Interface + * \todo Describe concisely what the functions in this module are about. + * + * \defgroup H5VLDEF Definitions + * \ingroup H5VL + * \defgroup H5VLDEV VOL Developer + * \ingroup H5VL + * \defgroup H5VLNAT Native VOL + * \ingroup H5VL + * \defgroup H5VLPT Pass-through VOL + * \ingroup H5VL + */ + #endif /* _H5VLmodule_H */ diff --git a/src/H5VLnative.h b/src/H5VLnative.h index b703c4f..b81f9c1 100644 --- a/src/H5VLnative.h +++ b/src/H5VLnative.h @@ -123,7 +123,13 @@ extern "C" { #endif /* Token <--> address converters */ +/** + * \ingroup H5VLNAT + */ H5_DLL herr_t H5VLnative_addr_to_token(hid_t loc_id, haddr_t addr, H5O_token_t *token); +/** + * \ingroup H5VLNAT + */ H5_DLL herr_t H5VLnative_token_to_addr(hid_t loc_id, H5O_token_t token, haddr_t *addr); /* Not really public but must be included here */ diff --git a/src/H5VLpublic.h b/src/H5VLpublic.h index 919a4b8..19cd2b9 100644 --- a/src/H5VLpublic.h +++ b/src/H5VLpublic.h @@ -28,39 +28,64 @@ /* VOL connector identifier values * These are H5VL_class_value_t values, NOT hid_t values! */ -#define H5_VOL_INVALID (-1) /* Invalid ID for VOL connector ID */ -#define H5_VOL_NATIVE 0 /* Native HDF5 file format VOL connector */ -#define H5_VOL_RESERVED 256 /* VOL connector IDs below this value are reserved for library use */ -#define H5_VOL_MAX 65535 /* Maximum VOL connector ID */ +/** + * \ingroup H5VLDEF + * Invalid ID for VOL connector ID + */ +#define H5_VOL_INVALID (-1) +/** + * \ingroup H5VLDEF + * Native HDF5 file format VOL connector + */ +#define H5_VOL_NATIVE 0 +/** + * \ingroup H5VLDEF + * VOL connector IDs below this value are reserved for library use + */ +#define H5_VOL_RESERVED 256 +/** + * \ingroup H5VLDEF + * Maximum VOL connector ID + */ +#define H5_VOL_MAX 65535 /*******************/ /* Public Typedefs */ /*******************/ -/* - * VOL connector identifiers. Values 0 through 255 are for connectors defined - * by the HDF5 library. Values 256 through 511 are available for testing new - * connectors. Subsequent values should be obtained from the HDF5 development - * team at help@hdfgroup.org. +/** + * \ingroup H5VLDEF + * + * \brief VOL connector identifiers. + * + * \details Values 0 through 255 are for connectors defined by the HDF5 + * library. Values 256 through 511 are available for testing new + * connectors. Subsequent values should be obtained from the HDF5 + * development team at mailto:help@hdfgroup.org. */ +//! [H5VL_class_value_t_snip] typedef int H5VL_class_value_t; +//! [H5VL_class_value_t_snip] -/* Enum type for each VOL subclass */ -/* (Used for various queries, etc) */ +/** + * \ingroup H5VLDEF + * \details Enum type for each VOL subclass + * (Used for various queries, etc) + */ typedef enum H5VL_subclass_t { - H5VL_SUBCLS_NONE, /* Operations outside of a subclass */ - H5VL_SUBCLS_INFO, /* 'Info' subclass */ - H5VL_SUBCLS_WRAP, /* 'Wrap' subclass */ - H5VL_SUBCLS_ATTR, /* 'Attribute' subclass */ - H5VL_SUBCLS_DATASET, /* 'Dataset' subclass */ - H5VL_SUBCLS_DATATYPE, /* 'Named datatype' subclass */ - H5VL_SUBCLS_FILE, /* 'File' subclass */ - H5VL_SUBCLS_GROUP, /* 'Group' subclass */ - H5VL_SUBCLS_LINK, /* 'Link' subclass */ - H5VL_SUBCLS_OBJECT, /* 'Object' subclass */ - H5VL_SUBCLS_REQUEST, /* 'Request' subclass */ - H5VL_SUBCLS_BLOB, /* 'Blob' subclass */ - H5VL_SUBCLS_TOKEN /* 'Token' subclass */ + H5VL_SUBCLS_NONE, /**< Operations outside of a subclass */ + H5VL_SUBCLS_INFO, /**< 'Info' subclass */ + H5VL_SUBCLS_WRAP, /**< 'Wrap' subclass */ + H5VL_SUBCLS_ATTR, /**< 'Attribute' subclass */ + H5VL_SUBCLS_DATASET, /**< 'Dataset' subclass */ + H5VL_SUBCLS_DATATYPE, /**< 'Named datatype' subclass */ + H5VL_SUBCLS_FILE, /**< 'File' subclass */ + H5VL_SUBCLS_GROUP, /**< 'Group' subclass */ + H5VL_SUBCLS_LINK, /**< 'Link' subclass */ + H5VL_SUBCLS_OBJECT, /**< 'Object' subclass */ + H5VL_SUBCLS_REQUEST, /**< 'Request' subclass */ + H5VL_SUBCLS_BLOB, /**< 'Blob' subclass */ + H5VL_SUBCLS_TOKEN /**< 'Token' subclass */ } H5VL_subclass_t; /********************/ @@ -75,16 +100,230 @@ typedef enum H5VL_subclass_t { extern "C" { #endif +/** + * \ingroup H5VL + * \brief Registers a new VOL connector by name + * + * \param[in] connector_name Connector name + * \vipl_id + * \return \hid_t{VOL connector} + * + * \details H5VLregister_connector_by_name() registers a new VOL connector with + * the name \p connector_name as a member of the virtual object layer + * class. This VOL connector identifier is good until the library is + * closed or the connector is unregistered. + * + * \p vipl_id is either #H5P_DEFAULT or the identifier of a VOL + * initialization property list of class #H5P_VOL_INITIALIZE created + * with H5Pcreate(). When created, this property list contains no + * library properties. If a VOL connector author decides that + * initialization-specific data are needed, they can be added to the + * empty list and retrieved by the connector in the VOL connector's + * initialize callback. Use of the VOL initialization property list is + * uncommon, as most VOL-specific properties are added to the file + * access property list via the connector's API calls which set the + * VOL connector for the file open/create. For more information, see + * the VOL documentation. + * + * \todo Fix the reference to VOL documentation. + * + * \since 1.12.0 + */ H5_DLL hid_t H5VLregister_connector_by_name(const char *connector_name, hid_t vipl_id); +/** + * \ingroup H5VL + * \brief Registers a new VOL connector by value + * + * \param[in] connector_value Connector value + * \vipl_id + * \return \hid_t{VOL connector} + * + * \details H5VLregister_connector_by_value() registers a new VOL connector + * with value connector_value as a member of the virtual object layer + * class. This VOL connector identifier is good until the library is + * closed or the connector is unregistered. + * + * \p connector_value has a type of H5VL_class_value_t, which is + * defined in H5VLpublic.h as follows: + * \snippet this H5VL_class_value_t_snip + * + * Valid VOL connector identifiers can have values from 0 through 255 + * for connectors defined by the HDF5 library. Values 256 through 511 + * are available for testing new connectors. Subsequent values should + * be obtained by contacting the The HDF Help Desk. + * + * \p vipl_id is either #H5P_DEFAULT or the identifier of a VOL + * initialization property list of class #H5P_VOL_INITIALIZE created + * with H5Pcreate(). When created, this property list contains no + * library properties. If a VOL connector author decides that + * initialization-specific data are needed, they can be added to the + * empty list and retrieved by the connector in the VOL connector's + * initialize callback. Use of the VOL initialization property list is + * uncommon, as most VOL-specific properties are added to the file + * access property list via the connector's API calls which set the + * VOL connector for the file open/create. For more information, see + * the VOL documentation. + * + * \todo Fix the reference to VOL documentation. + * + * \since 1.12.0 + */ H5_DLL hid_t H5VLregister_connector_by_value(H5VL_class_value_t connector_value, hid_t vipl_id); +/** + * \ingroup H5VL + * \brief Tests whether a VOL class has been registered under a certain name + * + * \param[in] name Alleged name of connector + * \return \htri_t + * + * \details H5VLis_connector_registered_by_name() tests whether a VOL class has + * been registered or not, according to the supplied connector name + * \p name. + * + * \since 1.12.0 + */ H5_DLL htri_t H5VLis_connector_registered_by_name(const char *name); +/** + * \ingroup H5VL + * \brief Tests whether a VOL class has been registered for a given value + * + * \param[in] connector_value Connector value + * \return \htri_t + * + * \details H5VLis_connector_registered_by_value() tests whether a VOL class + * has been registered, according to the supplied connector value \p + * connector_value. + * + * \p connector_value has a type of H5VL_class_value_t, which is + * defined in H5VLpublic.h as follows: + * \snippet this H5VL_class_value_t_snip + * + * Valid VOL connector identifiers can have values from 0 through 255 + * for connectors defined by the HDF5 library. Values 256 through 511 + * are available for testing new connectors. Subsequent values should + * be obtained by contacting the The HDF Help Desk. + * + * \since 1.12.0 + */ H5_DLL htri_t H5VLis_connector_registered_by_value(H5VL_class_value_t connector_value); +/** + * \ingroup H5VL + * \brief Retrieves the VOL connector identifier for a given object identifier + * + * \obj_id + * \return \hid_t{VOL connector} + * + * \details H5VLget_connector_id() retrieves the registered VOL connector + * identifier for the specified object identifier \p obj_id. The VOL + * connector identifier must be closed with H5VLclose() when no longer + * in use. + * + * \since 1.12.0 + */ H5_DLL hid_t H5VLget_connector_id(hid_t obj_id); +/** + * \ingroup H5VL + * \brief Retrieves the identifier for a registered VOL connector name + * + * \param[in] name Connector name + * \return \hid_t{VOL connector} + * + * \details H5VLget_connector_id_by_name() retrieves the identifier for a + * registered VOL connector with the name \p name. The identifier must + * be closed with H5VLclose() when no longer in use. + * + * \since 1.12.0 + */ H5_DLL hid_t H5VLget_connector_id_by_name(const char *name); +/** + * \ingroup H5VL + * \brief Retrieves the identifier for a registered VOL connector value + * + * \param[in] connector_value Connector value + * \return \hid_t{VOL connector} + * + * \details H5VLget_connector_id_by_value() retrieves the identifier for a + * registered VOL connector with the value \p connector_value. The + * identifier will need to be closed by H5VLclose(). + * + * \p connector_value has a type of H5VL_class_value_t, which is + * defined in H5VLpublic.h as follows: + * \snippet this H5VL_class_value_t_snip + * + * Valid VOL connector identifiers can have values from 0 through 255 + * for connectors defined by the HDF5 library. Values 256 through 511 + * are available for testing new connectors. Subsequent values should + * be obtained by contacting the The HDF Help Desk. + * + * \since 1.12.0 + */ H5_DLL hid_t H5VLget_connector_id_by_value(H5VL_class_value_t connector_value); +/** + * \ingroup H5VL + * \brief Retrieves a connector name for a VOL + * + * \obj_id{id} or file identifier + * \param[out] name Connector name + * \param[in] size Maximum length of the name to retrieve + * \return Returns the length of the connector name on success, and a negative value on failure. + * + * \details H5VLget_connector_name() retrieves up to \p size elements of the + * VOL name \p name associated with the object or file identifier \p + * id. + * + * Passing in a NULL pointer for size will return the size of the + * connector name. This can be used to determine the size of the + * buffer to allocate for the name. + * + * \since 1.12.0 + */ H5_DLL ssize_t H5VLget_connector_name(hid_t id, char *name /*out*/, size_t size); +/** + * \ingroup H5VL + * \brief Closes a VOL connector identifier + * + * \param[in] connector_id Connector identifier + * \return \herr_t + * + * \details H5VLclose() closes a VOL connector identifier. This does not affect + * the file access property lists which have been defined to use this + * VOL connector or files which are already opened under this + * connector. + * + * \since 1.12.0 + */ H5_DLL herr_t H5VLclose(hid_t connector_id); +/** + * \ingroup H5VL + * \brief Removes a VOL connector identifier from the library + * + * \param[in] connector_id Connector identifier + * \return \herr_t + * + * \details H5VLunregister_connector() removes a VOL connector identifier from + * the library. This does not affect the file access property lists + * which have been defined to use the VOL connector or any files which + * are already opened with this connector. + * + * \attention H5VLunregister_connector() will fail if attempting to unregister + * the native VOL connector. + * + * \since 1.12.0 + */ H5_DLL herr_t H5VLunregister_connector(hid_t connector_id); +/** + * \ingroup H5VL + * \brief Determine if a VOL connector supports a particular + * optional callback operation. + * + * \obj_id + * \param[in] subcls VOL subclass + * \param[in] opt_type Option type + * \param[out] supported Flag + * \return \herr_t + * + * \since 1.12.0 + */ H5_DLL herr_t H5VLquery_optional(hid_t obj_id, H5VL_subclass_t subcls, int opt_type, hbool_t *supported); #ifdef __cplusplus diff --git a/src/H5Zmodule.h b/src/H5Zmodule.h index d83f338..3be2629 100644 --- a/src/H5Zmodule.h +++ b/src/H5Zmodule.h @@ -29,4 +29,71 @@ #define H5_MY_PKG_ERR H5E_PLINE #define H5_MY_PKG_INIT YES +/** + * \defgroup H5Z H5Z + * + * + * \brief Filter and Compression Interface + * + * \details The functions in this module let you configure filters that process + * data during I/O operation. + * + * HDF5 supports a filter pipeline that provides the capability for + * standard and customized raw data processing during I/O operations. + * HDF5 is distributed with a small set of standard filters such as + * compression (gzip, SZIP, and a shuffling algorithm) and error + * checking (Fletcher32 checksum). For further flexibility, the + * library allows a user application to extend the pipeline through + * the creation and registration of customized filters. + * + * The flexibility of the filter pipeline implementation enables the + * definition of additional filters by a user application. A filter + * \li is associated with a dataset when the dataset is created, + * \li can be used only with chunked data (i.e., datasets stored in + * the #H5D_CHUNKED storage layout), and + * \li is applied independently to each chunk of the dataset. + * + * The HDF5 library does not support filters for contiguous datasets + * because of the difficulty of implementing random access for partial + * I/O. Compact dataset filters are not supported because it would not + * produce significant results. + * + * Filter identifiers for the filters distributed with the HDF5 + * Library are as follows: + * <table> + * <tr><td>#H5Z_FILTER_DEFLATE</td><td>The gzip compression, or + * deflation, filter</td></tr> + * <tr><td>#H5Z_FILTER_SZIP</td><td>The SZIP compression + * filter</td></tr> + * <tr><td>#H5Z_FILTER_NBIT</td><td>The N-bit compression + * filter</td></tr> + * <tr><td>#H5Z_FILTER_SCALEOFFSET</td><td>The scale-offset + * compression filter</td></tr> + * <tr><td>#H5Z_FILTER_SHUFFLE</td><td>The shuffle algorithm + * filter</td></tr> + * <tr><td>#H5Z_FILTER_FLETCHER32</td><td>The Fletcher32 checksum, + * or error checking, filter</td></tr> + * </table> + * Custom filters that have been registered with the library will have + * additional unique identifiers. + * + * See \Emph{HDF5 Dynamically Loaded Filters} for more information on + * how an HDF5 application can apply a filter that is not registered + * with the HDF5 library. + * + * \todo Fix the reference. + * + * \defgroup H5ZPRE Predefined Filters + * \ingroup H5Z + * \defgroup FLETCHER32 Checksum Filter + * \ingroup H5ZPRE + * \defgroup SCALEOFFSET Scale-Offset Filter + * \ingroup H5ZPRE + * \defgroup SHUFFLE Shuffle Filter + * \ingroup H5ZPRE + * \defgroup SZIP Szip Filter + * \ingroup H5ZPRE + * + */ + #endif /* _H5Zmodule_H */ diff --git a/src/H5Zpublic.h b/src/H5Zpublic.h index 97da13c..709e5fd 100644 --- a/src/H5Zpublic.h +++ b/src/H5Zpublic.h @@ -21,201 +21,610 @@ /* Public headers needed by this file */ #include "H5public.h" -/* - * Filter identifiers. Values 0 through 255 are for filters defined by the - * HDF5 library. Values 256 through 511 are available for testing new - * filters. Subsequent values should be obtained from the HDF5 development - * team at help@hdfgroup.org. These values will never change because they - * appear in the HDF5 files. +/** + * \brief Filter identifiers + * + * \details Values 0 through 255 are for filters defined by the HDF5 library. + * Values 256 through 511 are available for testing new filters. + * Subsequent values should be obtained from the HDF5 development team + * at mailto:help@hdfgroup.org. These values will never change because + * they appear in the HDF5 files. */ typedef int H5Z_filter_t; /* Filter IDs */ -#define H5Z_FILTER_ERROR (-1) /*no filter */ -#define H5Z_FILTER_NONE 0 /*reserved indefinitely */ -#define H5Z_FILTER_DEFLATE 1 /*deflation like gzip */ -#define H5Z_FILTER_SHUFFLE 2 /*shuffle the data */ -#define H5Z_FILTER_FLETCHER32 3 /*fletcher32 checksum of EDC */ -#define H5Z_FILTER_SZIP 4 /*szip compression */ -#define H5Z_FILTER_NBIT 5 /*nbit compression */ -#define H5Z_FILTER_SCALEOFFSET 6 /*scale+offset compression */ -#define H5Z_FILTER_RESERVED 256 /*filter ids below this value are reserved for library use */ - -#define H5Z_FILTER_MAX 65535 /*maximum filter id */ +/** + * no filter + */ +#define H5Z_FILTER_ERROR (-1) +/** + * reserved indefinitely +*/ +#define H5Z_FILTER_NONE 0 +/** + * deflation like gzip + */ +#define H5Z_FILTER_DEFLATE 1 +/** + * shuffle the data + */ +#define H5Z_FILTER_SHUFFLE 2 +/** + * fletcher32 checksum of EDC +*/ +#define H5Z_FILTER_FLETCHER32 3 +/** + * szip compression + */ +#define H5Z_FILTER_SZIP 4 +/** + * nbit compression + */ +#define H5Z_FILTER_NBIT 5 +/** + * scale+offset compression + */ +#define H5Z_FILTER_SCALEOFFSET 6 +/** + * filter ids below this value are reserved for library use + */ +#define H5Z_FILTER_RESERVED 256 +/** + * maximum filter id + */ +#define H5Z_FILTER_MAX 65535 /* General macros */ -#define H5Z_FILTER_ALL 0 /* Symbol to remove all filters in H5Premove_filter */ -#define H5Z_MAX_NFILTERS 32 /* Maximum number of filters allowed in a pipeline */ - /* (should probably be allowed to be an - * unlimited amount, but currently each - * filter uses a bit in a 32-bit field, - * so the format would have to be - * changed to accommodate that) - */ +/** + * Symbol to remove all filters in H5Premove_filter() + */ +#define H5Z_FILTER_ALL 0 +/** + * Maximum number of filters allowed in a pipeline + * + * \internal (should probably be allowed to be an unlimited amount, but + * currently each filter uses a bit in a 32-bit field, so the format + * would have to be changed to accommodate that) + */ +#define H5Z_MAX_NFILTERS 32 /* Flags for filter definition (stored) */ -#define H5Z_FLAG_DEFMASK 0x00ff /*definition flag mask */ -#define H5Z_FLAG_MANDATORY 0x0000 /*filter is mandatory */ -#define H5Z_FLAG_OPTIONAL 0x0001 /*filter is optional */ +/** + * definition flag mask + */ +#define H5Z_FLAG_DEFMASK 0x00ff +/** + * filter is mandatory + */ +#define H5Z_FLAG_MANDATORY 0x0000 +/** + * filter is optional + */ +#define H5Z_FLAG_OPTIONAL 0x0001 /* Additional flags for filter invocation (not stored) */ -#define H5Z_FLAG_INVMASK 0xff00 /*invocation flag mask */ -#define H5Z_FLAG_REVERSE 0x0100 /*reverse direction; read */ -#define H5Z_FLAG_SKIP_EDC 0x0200 /*skip EDC filters for read */ +/** + * invocation flag mask + */ +#define H5Z_FLAG_INVMASK 0xff00 +/** + * reverse direction; read + */ +#define H5Z_FLAG_REVERSE 0x0100 +/** + * skip EDC filters for read + */ +#define H5Z_FLAG_SKIP_EDC 0x0200 /* Special parameters for szip compression */ /* [These are aliases for the similar definitions in szlib.h, which we can't * include directly due to the duplication of various symbols with the zlib.h * header file] */ -#define H5_SZIP_ALLOW_K13_OPTION_MASK 1 -#define H5_SZIP_CHIP_OPTION_MASK 2 -#define H5_SZIP_EC_OPTION_MASK 4 -#define H5_SZIP_NN_OPTION_MASK 32 -#define H5_SZIP_MAX_PIXELS_PER_BLOCK 32 +/** + * \ingroup SZIP */ +#define H5_SZIP_ALLOW_K13_OPTION_MASK 1 +/** + * \ingroup SZIP */ +#define H5_SZIP_CHIP_OPTION_MASK 2 +/** + * \ingroup SZIP */ +#define H5_SZIP_EC_OPTION_MASK 4 +/** + * \ingroup SZIP */ +#define H5_SZIP_NN_OPTION_MASK 32 +/** + * \ingroup SZIP */ +#define H5_SZIP_MAX_PIXELS_PER_BLOCK 32 /* Macros for the shuffle filter */ -#define H5Z_SHUFFLE_USER_NPARMS 0 /* Number of parameters that users can set */ -#define H5Z_SHUFFLE_TOTAL_NPARMS 1 /* Total number of parameters for filter */ +/** + * \ingroup SHUFFLE + * Number of parameters that users can set for the shuffle filter +*/ +#define H5Z_SHUFFLE_USER_NPARMS 0 +/** + * \ingroup SHUFFLE + * Total number of parameters for the shuffle filter + */ +#define H5Z_SHUFFLE_TOTAL_NPARMS 1 /* Macros for the szip filter */ -#define H5Z_SZIP_USER_NPARMS 2 /* Number of parameters that users can set */ -#define H5Z_SZIP_TOTAL_NPARMS 4 /* Total number of parameters for filter */ -#define H5Z_SZIP_PARM_MASK 0 /* "User" parameter for option mask */ -#define H5Z_SZIP_PARM_PPB 1 /* "User" parameter for pixels-per-block */ -#define H5Z_SZIP_PARM_BPP 2 /* "Local" parameter for bits-per-pixel */ -#define H5Z_SZIP_PARM_PPS 3 /* "Local" parameter for pixels-per-scanline */ +/** + * \ingroup SZIP + * Number of parameters that users can set for SZIP + */ +#define H5Z_SZIP_USER_NPARMS 2 +/** + * \ingroup SZIP + * Total number of parameters for SZIP filter + */ +#define H5Z_SZIP_TOTAL_NPARMS 4 +/** + * \ingroup SZIP + * "User" parameter for option mask + */ +#define H5Z_SZIP_PARM_MASK 0 +/** + * \ingroup SZIP + * "User" parameter for pixels-per-block + */ +#define H5Z_SZIP_PARM_PPB 1 +/** + * \ingroup SZIP + * "Local" parameter for bits-per-pixel + */ +#define H5Z_SZIP_PARM_BPP 2 +/** + * \ingroup SZIP + * "Local" parameter for pixels-per-scanline + */ +#define H5Z_SZIP_PARM_PPS 3 /* Macros for the nbit filter */ -#define H5Z_NBIT_USER_NPARMS 0 /* Number of parameters that users can set */ +/** + * \ingroup NBIT + * Number of parameters that users can set for the N-bit filter + */ +#define H5Z_NBIT_USER_NPARMS 0 /* Number of parameters that users can set */ /* Macros for the scale offset filter */ -#define H5Z_SCALEOFFSET_USER_NPARMS 2 /* Number of parameters that users can set */ +/** + * \ingroup SCALEOFFSET + * Number of parameters that users can set for the scale-offset filter + */ +#define H5Z_SCALEOFFSET_USER_NPARMS 2 + /* Special parameters for ScaleOffset filter*/ +/** + * \ingroup SCALEOFFSET */ #define H5Z_SO_INT_MINBITS_DEFAULT 0 +/** + * \ingroup SCALEOFFSET */ typedef enum H5Z_SO_scale_type_t { H5Z_SO_FLOAT_DSCALE = 0, H5Z_SO_FLOAT_ESCALE = 1, H5Z_SO_INT = 2 } H5Z_SO_scale_type_t; -/* Current version of the H5Z_class_t struct */ +/** + * Current version of the H5Z_class_t struct + */ #define H5Z_CLASS_T_VERS (1) -/* Values to decide if EDC is enabled for reading data */ +/** + * \ingroup FLETCHER32 + * Values to decide if EDC is enabled for reading data + */ typedef enum H5Z_EDC_t { - H5Z_ERROR_EDC = -1, /* error value */ - H5Z_DISABLE_EDC = 0, - H5Z_ENABLE_EDC = 1, - H5Z_NO_EDC = 2 /* must be the last */ + H5Z_ERROR_EDC = -1, /**< error value */ + H5Z_DISABLE_EDC = 0, + H5Z_ENABLE_EDC = 1, + H5Z_NO_EDC = 2 /**< sentinel */ } H5Z_EDC_t; /* Bit flags for H5Zget_filter_info */ #define H5Z_FILTER_CONFIG_ENCODE_ENABLED (0x0001) #define H5Z_FILTER_CONFIG_DECODE_ENABLED (0x0002) -/* Return values for filter callback function */ +/** + * Return values for filter callback function + */ typedef enum H5Z_cb_return_t { - H5Z_CB_ERROR = -1, - H5Z_CB_FAIL = 0, /* I/O should fail if filter fails. */ - H5Z_CB_CONT = 1, /* I/O continues if filter fails. */ - H5Z_CB_NO = 2 + H5Z_CB_ERROR = -1, + H5Z_CB_FAIL = 0, /**< I/O should fail if filter fails. */ + H5Z_CB_CONT = 1, /**< I/O continues if filter fails. */ + H5Z_CB_NO = 2 } H5Z_cb_return_t; -/* Filter callback function definition */ -typedef H5Z_cb_return_t (*H5Z_filter_func_t)(H5Z_filter_t filter, void *buf, size_t buf_size, void *op_data); +/** + * Filter callback function definition + */ +typedef H5Z_cb_return_t (*H5Z_filter_func_t)(H5Z_filter_t filter, void* buf, + size_t buf_size, void* op_data); -/* Structure for filter callback property */ +/** + * Structure for filter callback property + */ typedef struct H5Z_cb_t { - H5Z_filter_func_t func; - void * op_data; + H5Z_filter_func_t func; + void *op_data; } H5Z_cb_t; #ifdef __cplusplus extern "C" { #endif -/* - * Before a dataset gets created, the "can_apply" callbacks for any filters used - * in the dataset creation property list are called - * with the dataset's dataset creation property list, the dataset's datatype and - * a dataspace describing a chunk (for chunked dataset storage). +/** + * \details Before a dataset gets created, the \c can_apply callbacks for any + * filters used in the dataset creation property list are called with + * the dataset's dataset creation property list, the dataset's + * datatype and a dataspace describing a chunk (for chunked dataset + * storage). * - * The "can_apply" callback must determine if the combination of the dataset - * creation property list setting, the datatype and the dataspace represent a - * valid combination to apply this filter to. For example, some cases of - * invalid combinations may involve the filter not operating correctly on - * certain datatypes (or certain datatype sizes), or certain sizes of the chunk - * dataspace. + * The \c can_apply callback must determine if the combination of the + * dataset creation property list setting, the datatype and the + * dataspace represent a valid combination to apply this filter to. + * For example, some cases of invalid combinations may involve the + * filter not operating correctly on certain datatypes (or certain + * datatype sizes), or certain sizes of the chunk dataspace. * - * The "can_apply" callback can be the NULL pointer, in which case, the library - * will assume that it can apply to any combination of dataset creation - * property list values, datatypes and dataspaces. + * The \c can_apply callback can be the NULL pointer, in which case, + * the library will assume that it can apply to any combination of + * dataset creation property list values, datatypes and dataspaces. * - * The "can_apply" callback returns positive a valid combination, zero for an - * invalid combination and negative for an error. + * The \c can_apply callback returns positive a valid combination, + * zero for an invalid combination and negative for an error. */ +//! [H5Z_can_apply_func_t_snip] typedef htri_t (*H5Z_can_apply_func_t)(hid_t dcpl_id, hid_t type_id, hid_t space_id); - -/* - * After the "can_apply" callbacks are checked for new datasets, the "set_local" - * callbacks for any filters used in the dataset creation property list are - * called. These callbacks receive the dataset's private copy of the dataset - * creation property list passed in to H5Dcreate (i.e. not the actual property - * list passed in to H5Dcreate) and the datatype ID passed in to H5Dcreate - * (which is not copied and should not be modified) and a dataspace describing - * the chunk (for chunked dataset storage) (which should also not be modified). +//! [H5Z_can_apply_func_t_snip] +/** + * \details After the "can_apply" callbacks are checked for new datasets, the + * \c set_local callbacks for any filters used in the dataset creation + * property list are called. These callbacks receive the dataset's + * private copy of the dataset creation property list passed in to + * H5Dcreate() (i.e. not the actual property list passed in to + * H5Dcreate()) and the datatype ID passed in to H5Dcreate() (which is + * not copied and should not be modified) and a dataspace describing + * the chunk (for chunked dataset storage) (which should also not be + * modified). * - * The "set_local" callback must set any parameters that are specific to this - * dataset, based on the combination of the dataset creation property list - * values, the datatype and the dataspace. For example, some filters perform - * different actions based on different datatypes (or datatype sizes) or - * different number of dimensions or dataspace sizes. + * The \c set_local callback must set any parameters that are specific + * to this dataset, based on the combination of the dataset creation + * property list values, the datatype and the dataspace. For example, + * some filters perform different actions based on different datatypes + * (or datatype sizes) or different number of dimensions or dataspace + * sizes. * - * The "set_local" callback can be the NULL pointer, in which case, the library - * will assume that there are no dataset-specific settings for this filter. + * The \c set_local callback can be the NULL pointer, in which case, + * the library will assume that there are no dataset-specific settings + * for this filter. * - * The "set_local" callback must return non-negative on success and negative - * for an error. + * The \c set_local callback must return non-negative on success and + * negative for an error. */ +//! [H5Z_set_local_func_t_snip] typedef herr_t (*H5Z_set_local_func_t)(hid_t dcpl_id, hid_t type_id, hid_t space_id); - -/* - * A filter gets definition flags and invocation flags (defined above), the - * client data array and size defined when the filter was added to the - * pipeline, the size in bytes of the data on which to operate, and pointers - * to a buffer and its allocated size. +//! [H5Z_set_local_func_t_snip] +/** + * \details A filter gets definition flags and invocation flags (defined + * above), the client data array and size defined when the filter was + * added to the pipeline, the size in bytes of the data on which to + * operate, and pointers to a buffer and its allocated size. * - * The filter should store the result in the supplied buffer if possible, - * otherwise it can allocate a new buffer, freeing the original. The - * allocated size of the new buffer should be returned through the BUF_SIZE - * pointer and the new buffer through the BUF pointer. + * The filter should store the result in the supplied buffer if + * possible, otherwise it can allocate a new buffer, freeing the + * original. The allocated size of the new buffer should be returned + * through the \p buf_size pointer and the new buffer through the \p + * buf pointer. * - * The return value from the filter is the number of bytes in the output - * buffer. If an error occurs then the function should return zero and leave - * all pointer arguments unchanged. + * The return value from the filter is the number of bytes in the + * output buffer. If an error occurs then the function should return + * zero and leave all pointer arguments unchanged. */ +//! [H5Z_func_t_snip] typedef size_t (*H5Z_func_t)(unsigned int flags, size_t cd_nelmts, const unsigned int cd_values[], size_t nbytes, size_t *buf_size, void **buf); - -/* +//! [H5Z_func_t_snip] +/** * The filter table maps filter identification numbers to structs that * contain a pointers to the filter function and timing statistics. */ +//! [H5Z_class2_t_snip] typedef struct H5Z_class2_t { - int version; /* Version number of the H5Z_class_t struct */ - H5Z_filter_t id; /* Filter ID number */ - unsigned encoder_present; /* Does this filter have an encoder? */ - unsigned decoder_present; /* Does this filter have a decoder? */ - const char * name; /* Comment for debugging */ - H5Z_can_apply_func_t can_apply; /* The "can apply" callback for a filter */ - H5Z_set_local_func_t set_local; /* The "set local" callback for a filter */ - H5Z_func_t filter; /* The actual filter function */ + int version; /**< Version number of the H5Z_class_t struct */ + H5Z_filter_t id; /**< Filter ID number */ + unsigned encoder_present; /**< Does this filter have an encoder? */ + unsigned decoder_present; /**< Does this filter have a decoder? */ + const char *name; /**< Comment for debugging */ + H5Z_can_apply_func_t can_apply; /**< The "can apply" callback for a filter */ + H5Z_set_local_func_t set_local; /**< The "set local" callback for a filter */ + H5Z_func_t filter; /**< The actual filter function */ } H5Z_class2_t; +//! [H5Z_class2_t_snip] +/** + * \ingroup H5Z + * + * \brief Registers a new filter with the HDF5 library + * + * \param[in] cls A pointer to a buffer for the struct containing the + * filter-definition + * + * \return \herr_t + * + * \details H5Zregister() registers a new filter with the HDF5 library. + * + * \details Making a new filter available to an application is a two-step + * process. The first step is to write the three filter callback + * functions described below: \c can_apply, \c set_local, and \c + * filter. This call to H5Zregister(), registering the filter with the + * library, is the second step. The can_apply and set_local fields can + * be set to NULL if they are not required for the filter being + * registered. + * + * H5Zregister() accepts a single parameter, a pointer to a buffer for + * the \p cls data structure. That data structure must conform to one + * of the following definitions: + * \snippet this H5Z_class1_t_snip + * or + * \snippet this H5Z_class2_t_snip + * + * \c version is a library-defined value reporting the version number + * of the #H5Z_class_t struct. This currently must be set to + * #H5Z_CLASS_T_VERS. + * + * \c id is the identifier for the new filter. This is a user-defined + * value between #H5Z_FILTER_RESERVED and #H5Z_FILTER_MAX. These + * values are defined in the HDF5 source file H5Zpublic.h, but the + * symbols #H5Z_FILTER_RESERVED and #H5Z_FILTER_MAX should always be + * used instead of the literal values. + * + * \c encoder_present is a library-defined value indicating whether + * the filter’s encoding capability is available to the application. + * + * \c decoder_present is a library-defined value indicating whether + * the filter’s encoding capability is available to the application. + * + * \c name is a descriptive comment used for debugging, may contain a + * descriptive name for the filter, and may be the null pointer. + * + * \c can_apply, described in detail below, is a user-defined callback + * function which determines whether the combination of the dataset + * creation property list values, the datatype, and the dataspace + * represent a valid combination to apply this filter to. + * + * \c set_local, described in detail below, is a user-defined callback + * function which sets any parameters that are specific to this + * dataset, based on the combination of the dataset creation property + * list values, the datatype, and the dataspace. + * + * \c filter, described in detail below, is a user-defined callback + * function which performs the action of the filter. + * + * The statistics associated with a filter are not reset by this + * function; they accumulate over the life of the library. + * + * #H5Z_class_t is a macro which maps to either H5Z_class1_t or + * H5Z_class2_t, depending on the needs of the application. To affect + * only this macro, H5Z_class_t_vers may be defined to either 1 or 2. + * Otherwise, it will behave in the same manner as other API + * compatibility macros. See API Compatibility Macros in HDF5 for more + * information. H5Z_class1_t matches the #H5Z_class_t structure that is + * used in the 1.6.x versions of the HDF5 library. + * + * H5Zregister() will automatically detect which structure type has + * been passed in, regardless of the mapping of the #H5Z_class_t macro. + * However, the application must make sure that the fields are filled + * in according to the correct structure definition if the macro is + * used to declare the structure. + * + * \Bold{The callback functions:}\n Before H5Zregister() can link a + * filter into an application, three callback functions must be + * defined as described in the HDF5 library header file H5Zpublic.h. + * + * When a filter is applied to the fractal heap for a group (e.g., + * when compressing group metadata) and if the can apply and set local + * callback functions have been defined for that filter, HDF5 passes + * the value -1 for all parameters for those callback functions. This + * is done to ensure that the filter will not be applied to groups if + * it relies on these parameters, as they are not applicable to group + * fractal heaps; to operate on group fractal heaps, a filter must be + * capable of operating on an opaque block of binary data. + * + * The \Emph{can apply} callback function must return a positive value + * for a valid combination, zero for an invalid combination, and a + * negative value for an error. + * \snippet this H5Z_can_apply_func_t_snip + * + * Before a dataset is created, the \Emph{can apply} callbacks for any + * filters used in the dataset creation property list are called with + * the dataset's dataset creation property list, \c dcpl_id, the + * dataset's datatype, \p type_id, and a dataspace describing a chunk, + * \p space_id, (for chunked dataset storage). + * + * This callback must determine whether the combination of the dataset + * creation property list settings, the datatype, and the dataspace + * represent a valid combination to which to apply this filter. For + * example, an invalid combination may involve the filter not + * operating correctly on certain datatypes, on certain datatype + * sizes, or on certain sizes of the chunk dataspace. If this filter + * is enabled through H5Pset_filter() as optional and the can apply + * function returns 0, the library will skip the filter in the filter + * pipeline. + * + * This callback can be the NULL pointer, in which case the library + * will assume that the filter can be applied to a dataset with any + * combination of dataset creation property list values, datatypes, + * and dataspaces. + * + * The \Emph{set local} callback function is defined as follows: + * \snippet this H5Z_set_local_func_t_snip + * + * After the can apply callbacks are checked for a new dataset, the + * \Emph{set local} callback functions for any filters used in the + * dataset creation property list are called. These callbacks receive + * \c dcpl_id, the dataset's private copy of the dataset creation + * property list passed in to H5Dcreate() (i.e. not the actual + * property list passed in to H5Dcreate()); \c type_id, the datatype + * identifier passed in to H5Dcreate(), which is not copied and should + * not be modified; and \c space_id, a dataspace describing the chunk + * (for chunked dataset storage), which should also not be modified. + * + * The set local callback must set any filter parameters that are + * specific to this dataset, based on the combination of the dataset + * creation property list values, the datatype, and the dataspace. For + * example, some filters perform different actions based on different + * datatypes, datatype sizes, numbers of dimensions, or dataspace + * sizes. + * + * The \Emph{set local} callback may be the NULL pointer, in which + * case, the library will assume that there are no dataset-specific + * settings for this filter. + * + * The \Emph{set local} callback function must return a non-negative + * value on success and a negative value for an error. + * + * The \Emph{filter operation} callback function, defining the + * filter's operation on the data, is defined as follows: + * \snippet this H5Z_func_t_snip + * + * The parameters \c flags, \c cd_nelmts, and \c cd_values are the + * same as for the function H5Pset_filter(). The one exception is that + * an additional flag, #H5Z_FLAG_REVERSE, is set when the filter is + * called as part of the input pipeline. + * + * The parameter \c buf points to the input buffer which has a size of + * \c buf_size bytes, \c nbytes of which are valid data. + * + * The filter should perform the transformation in place if possible. + * If the transformation cannot be done in place, then the filter + * should allocate a new buffer with malloc() and assign it to \c buf, + * assigning the allocated size of that buffer to \c buf_size. The old + * buffer should be freed by calling free(). + * + * If successful, the \Emph{filter operation} callback function + * returns the number of valid bytes of data contained in \c buf. In + * the case of failure, the return value is 0 (zero) and all pointer + * arguments are left unchanged. + * + * \version 1.8.6 Return type for the \Emph{can apply} callback function, + * \ref H5Z_can_apply_func_t, changed to \ref htri_t. + * \version 1.8.5 Semantics of the \Emph{can apply} and \Emph{set local} + * callback functions changed to accommodate the use of filters + * with group fractal heaps. + * \version 1.8.3 #H5Z_class_t renamed to H5Z_class2_t, H5Z_class1_t structure + * introduced for backwards compatibility with release 1.6.x, + * and #H5Z_class_t macro introduced in this release. Function + * modified to accept either structure type. + * \version 1.8.0 The fields \c version, \c encoder_present, and + * \c decoder_present were added to the #H5Z_class_t \c struct + * in this release. + * \version 1.6.0 This function was substantially revised in Release 1.6.0 with + * a new #H5Z_class_t struct and new set local and can apply + * callback functions. + * + */ H5_DLL herr_t H5Zregister(const void *cls); +/** + * \ingroup H5Z + * + * \brief Unregisters a filter. + * + * \param[in] id Identifier of the filter to be unregistered. + * \return \herr_t + * + * \details H5Zunregister() unregisters the filter specified in \p id. + * + * \details This function first iterates through all opened datasets and + * groups. If an open object that uses this filter is found, the + * function will fail with a message indicating that an object using + * the filter is still open. All open files are then flushed to make + * sure that all cached data that may use this filter are written out. + * + * If the application is a parallel program, all processes that + * participate in collective data write should call this function to + * ensure that all data is flushed. + * + * After a call to H5Zunregister(), the filter specified in filter + * will no longer be available to the application. + * + * \version 1.8.12 Function modified to check for open objects using the + * filter. + * \since 1.6.0 + */ H5_DLL herr_t H5Zunregister(H5Z_filter_t id); +/** + * \ingroup H5Z + * + * \brief Determines whether a filter is available + * + * \param[in] id Filter identifier + * \return \htri_t + * + * \details H5Zfilter_avail() determines whether the filter specified in \p id + * is available to the application. + * + * \since 1.6.0 + */ H5_DLL htri_t H5Zfilter_avail(H5Z_filter_t id); +/** + * \ingroup H5Z + * + * \brief Retrieves information about a filter + * + * \param[in] filter Filter identifier + * \param[out] filter_config_flags A bit field encoding the returned filter + * information + * \return \herr_t + * + * \details H5Zget_filter_info() retrieves information about a filter. At + * present, this means that the function retrieves a filter's + * configuration flags, indicating whether the filter is configured to + * decode data, to encode data, neither, or both. + * + * If \p filter_config_flags is not set to NULL prior to the function + * call, the returned parameter contains a bit field specifying the + * available filter configuration. The configuration flag values can + * then be determined through a series of bitwise AND operations, as + * described below. + * + * Valid filter configuration flags include the following: + * <table> + * <tr><td>#H5Z_FILTER_CONFIG_ENCODE_ENABLED</td> + * <td>Encoding is enabled for this filter</td></tr> + * <tr><td>#H5Z_FILTER_CONFIG_DECODE_ENABLED</td> + * <td>Decoding is enabled for this filter</td></tr> + * </table> + * + * A bitwise AND of the returned \p filter_config_flags and a valid + * filter configuration flag will reveal whether the related + * configuration option is available. For example, if the value of + * \code + * H5Z_FILTER_CONFIG_ENCODE_ENABLED & filter_config_flags + * \endcode + * is true, i.e., greater than 0 (zero), the queried filter + * is configured to encode data; if the value is \c FALSE, i.e., equal to + * 0 (zero), the filter is not so configured. + * + * If a filter is not encode-enabled, the corresponding \c H5Pset_* + * function will return an error if the filter is added to a dataset + * creation property list (which is required if the filter is to be + * used to encode that dataset). For example, if the + * #H5Z_FILTER_CONFIG_ENCODE_ENABLED flag is not returned for the SZIP + * filter, #H5Z_FILTER_SZIP, a call to H5Pset_szip() will fail. + * + * If a filter is not decode-enabled, the application will not be able + * to read an existing file encoded with that filter. + * + * This function should be called, and the returned \p + * filter_config_flags analyzed, before calling any other function, + * such as H5Pset_szip() , that might require a particular filter + * configuration. + * + * \since 1.6.3 + */ H5_DLL herr_t H5Zget_filter_info(H5Z_filter_t filter, unsigned int *filter_config_flags); /* Symbols defined for compatibility with previous versions of the HDF5 API. @@ -224,17 +633,19 @@ H5_DLL herr_t H5Zget_filter_info(H5Z_filter_t filter, unsigned int *filter_confi */ #ifndef H5_NO_DEPRECATED_SYMBOLS -/* +/** * The filter table maps filter identification numbers to structs that * contain a pointers to the filter function and timing statistics. */ +//! [H5Z_class1_t_snip] typedef struct H5Z_class1_t { - H5Z_filter_t id; /* Filter ID number */ - const char * name; /* Comment for debugging */ - H5Z_can_apply_func_t can_apply; /* The "can apply" callback for a filter */ - H5Z_set_local_func_t set_local; /* The "set local" callback for a filter */ - H5Z_func_t filter; /* The actual filter function */ + H5Z_filter_t id; /**< Filter ID number */ + const char *name; /**< Comment for debugging */ + H5Z_can_apply_func_t can_apply; /**< The "can apply" callback for a filter */ + H5Z_set_local_func_t set_local; /**< The "set local" callback for a filter */ + H5Z_func_t filter; /**< The actual filter function */ } H5Z_class1_t; +//! [H5Z_class1_t_snip] #endif /* H5_NO_DEPRECATED_SYMBOLS */ diff --git a/src/H5checksum.c b/src/H5checksum.c index bc36bb9..82964d9 100644 --- a/src/H5checksum.c +++ b/src/H5checksum.c @@ -25,6 +25,7 @@ /****************/ /* Module Setup */ /****************/ +#include "H5module.h" /* This source code file is part of the H5 module */ /***********/ /* Headers */ @@ -379,7 +380,7 @@ uint32_t H5_checksum_lookup3(const void *key, size_t length, uint32_t initval) { const uint8_t *k = (const uint8_t *)key; - uint32_t a, b, c; /* internal state */ + uint32_t a, b, c = 0; /* internal state */ FUNC_ENTER_NOAPI_NOINIT_NOERR diff --git a/src/H5dbg.c b/src/H5dbg.c index 1b64d2c..5d38efc 100644 --- a/src/H5dbg.c +++ b/src/H5dbg.c @@ -25,6 +25,7 @@ /****************/ /* Module Setup */ /****************/ +#include "H5module.h" /* This source code file is part of the H5 module */ /***********/ /* Headers */ diff --git a/src/H5err.txt b/src/H5err.txt index 24ac2ac..05476e5 100644 --- a/src/H5err.txt +++ b/src/H5err.txt @@ -46,6 +46,7 @@ MAJOR, H5E_ARGS, Invalid arguments to routine MAJOR, H5E_RESOURCE, Resource unavailable MAJOR, H5E_INTERNAL, Internal error (too specific to document in detail) +MAJOR, H5E_LIB, General library infrastructure MAJOR, H5E_FILE, File accessibility MAJOR, H5E_IO, Low-level I/O MAJOR, H5E_FUNC, Function entry/exit diff --git a/src/H5module.h b/src/H5module.h new file mode 100644 index 0000000..f6884b1 --- /dev/null +++ b/src/H5module.h @@ -0,0 +1,34 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by The HDF Group. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the COPYING file, which can be found at the root of the source code * + * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * If you do not have access to either file, you may request a copy from * + * help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +/* + * Purpose: This file contains declarations which define macros for the + * H5 package. Including this header means that the source file + * is part of the H5 package. + */ +#ifndef _H5module_H +#define _H5module_H + +/* Define the proper control macros for the generic FUNC_ENTER/LEAVE and error + * reporting macros. + */ +#define H5_MODULE +#define H5_MY_PKG H5 +#define H5_MY_PKG_ERR H5E_LIB +#define H5_MY_PKG_INIT YES + +/**\defgroup H5 H5 + * \brief General Library Functions + * \todo Describe concisely what the functions in this module are about. + */ + +#endif /* _H5module_H */ diff --git a/src/H5private.h b/src/H5private.h index 1390b3f..600089d 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -2160,7 +2160,6 @@ H5_DLL herr_t H5CX_pop(void); #define FUNC_ENTER_API_INIT(err) \ /* Initialize the library */ \ if (!H5_INIT_GLOBAL && !H5_TERM_GLOBAL) { \ - H5_INIT_GLOBAL = TRUE; \ if (H5_init_library() < 0) \ HGOTO_ERROR(H5E_FUNC, H5E_CANTINIT, err, "library initialization failed") \ } /* end if */ \ @@ -2603,7 +2602,6 @@ extern hbool_t H5_api_entered_g; /* Has library already been entered through API \ /* Initialize the library or bust */ \ if (!H5_INIT_GLOBAL && !H5_TERM_GLOBAL) { \ - H5_INIT_GLOBAL = TRUE; \ if (H5_init_library() < 0) { \ /* (Can't use H5E_THROW here) */ \ H5E_PRINTF(H5E_CANTINIT, "interface initialization failed"); \ diff --git a/src/H5public.h b/src/H5public.h index 9202be4..44e0d94 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -304,15 +304,21 @@ typedef unsigned long uint32_t; #error "nothing appropriate for uint32_t" #endif -/* Common iteration orders */ +//! [H5_iter_order_t_snip] + +/** + * Common iteration orders + */ typedef enum { - H5_ITER_UNKNOWN = -1, /* Unknown order */ - H5_ITER_INC, /* Increasing order */ - H5_ITER_DEC, /* Decreasing order */ - H5_ITER_NATIVE, /* No particular order, whatever is fastest */ - H5_ITER_N /* Number of iteration orders */ + H5_ITER_UNKNOWN = -1, /**< Unknown order */ + H5_ITER_INC, /**< Increasing order */ + H5_ITER_DEC, /**< Decreasing order */ + H5_ITER_NATIVE, /**< No particular order, whatever is fastest */ + H5_ITER_N /**< Number of iteration orders */ } H5_iter_order_t; +//! [H5_iter_order_t_snip] + /* Iteration callback values */ /* (Actually, any positive value will cause the iterator to stop and pass back * that positive value to the function that called the iterator) @@ -321,18 +327,22 @@ typedef enum { #define H5_ITER_CONT (0) #define H5_ITER_STOP (1) -/* +//! [H5_index_t_snip] + +/** * The types of indices on links in groups/attributes on objects. * Primarily used for "<do> <foo> by index" routines and for iterating over * links in groups/attributes on objects. */ typedef enum H5_index_t { - H5_INDEX_UNKNOWN = -1, /* Unknown index type */ - H5_INDEX_NAME, /* Index on names */ - H5_INDEX_CRT_ORDER, /* Index on creation order */ - H5_INDEX_N /* Number of indices defined */ + H5_INDEX_UNKNOWN = -1, /**< Unknown index type */ + H5_INDEX_NAME, /**< Index on names */ + H5_INDEX_CRT_ORDER, /**< Index on creation order */ + H5_INDEX_N /**< Number of indices defined */ } H5_index_t; +//! [H5_index_t_snip] + /** * Storage info struct used by H5O_info_t and H5F_info_t */ @@ -343,45 +353,446 @@ typedef struct H5_ih_info_t { } H5_ih_info_t; //! [H5_ih_info_t_snip] -/* Tokens are unique and permanent identifiers that are - * used to reference HDF5 objects in a container. */ +/** + * The maximum size allowed for tokens + * \details Tokens are unique and permanent identifiers that are + * used to reference HDF5 objects in a container. This allows + * for 128-bit tokens + */ +#define H5O_MAX_TOKEN_SIZE (16) -/* The maximum size allowed for tokens */ -#define H5O_MAX_TOKEN_SIZE (16) /* Allows for 128-bit tokens */ +//! [H5O_token_t_snip] +/** + * \internal (Hoisted here, since it's used by both the + * H5Lpublic.h and H5Opublic.h headers) */ /* Type for object tokens */ -/* (Hoisted here, since it's used by both the H5Lpublic.h and H5Opublic.h headers) */ typedef struct H5O_token_t { uint8_t __data[H5O_MAX_TOKEN_SIZE]; } H5O_token_t; -/* +//! [H5O_token_t_snip] + +/** * Allocation statistics info struct */ typedef struct H5_alloc_stats_t { - unsigned long long total_alloc_bytes; /* Running count of total # of bytes allocated */ - size_t curr_alloc_bytes; /* Current # of bytes allocated */ - size_t peak_alloc_bytes; /* Peak # of bytes allocated */ - size_t max_block_size; /* Largest block allocated */ - size_t total_alloc_blocks_count; /* Running count of total # of blocks allocated */ - size_t curr_alloc_blocks_count; /* Current # of blocks allocated */ - size_t peak_alloc_blocks_count; /* Peak # of blocks allocated */ + unsigned long long total_alloc_bytes; /**< Running count of total # of bytes allocated */ + size_t curr_alloc_bytes; /**< Current # of bytes allocated */ + size_t peak_alloc_bytes; /**< Peak # of bytes allocated */ + size_t max_block_size; /**< Largest block allocated */ + size_t total_alloc_blocks_count; /**< Running count of total # of blocks allocated */ + size_t curr_alloc_blocks_count; /**< Current # of blocks allocated */ + size_t peak_alloc_blocks_count; /**< Peak # of blocks allocated */ } H5_alloc_stats_t; /* Functions in H5.c */ +/** + * \ingroup H5 + * \brief Initializes the HDF5 library + * \return \herr_t + * + * \details H5open() initializes the HDF5 library. + * + * \details When the HDF5 library is used in a C application, the library is + * automatically initialized when the first HDf5 function call is + * issued. If one finds that an HDF5 library function is failing + * inexplicably, H5open() can be called first. It is safe to call + * H5open() before an application issues any other function calls to + * the HDF5 library as there are no damaging side effects in calling + * it more than once. + */ H5_DLL herr_t H5open(void); +/** + * \ingroup H5 + * \brief Flushes all data to disk, closes all open objects, and releases memory + * \return \herr_t + * + * \details H5close() flushes all data to disk, closes all open HDF5 objects, + * and cleans up all memory used by the HDF5 library. This function is + * generally called when the application calls exit(), but may be + * called earlier in the event of an emergency shutdown or out of a + * desire to free all resources used by the HDF5 library. + */ H5_DLL herr_t H5close(void); +/** + * \ingroup H5 + * \brief Instructs library not to install atexit() cleanup routine + * \return \herr_t + * + * \details H5dont_atexit() indicates to the library that an atexit() cleanup + * routine should not be installed. The major purpose for using this + * function is in situations where the library is dynamically linked + * into an application and is un-linked from the application before + * exit() gets called. In those situations, a routine installed with + * atexit() would jump to a routine which was no longer in memory, + * causing errors. + * + * \attention In order to be effective, this routine \Emph{must} be called + * before any other HDF5 function calls, and must be called each + * time the library is loaded/linked into the application (the first + * time and after it's been un-loaded). + */ H5_DLL herr_t H5dont_atexit(void); +/** + * \ingroup H5 + * \brief Garbage collects on all free-lists of all types + * \return \herr_t + * + * \details H5garbage_collect() walks through all garbage collection routines + * of the library, freeing any unused memory. + * + * It is not required that H5garbage_collect() be called at any + * particular time; it is only necessary in certain situations where + * the application has performed actions that cause the library to + * allocate many objects. The application should call + * H5garbage_collect() if it eventually releases those objects and + * wants to reduce the memory used by the library from the peak usage + * required. + * + * \note The library automatically garbage collects all the free lists when the + * application ends. + */ H5_DLL herr_t H5garbage_collect(void); +/** + * \ingroup H5 + * \brief Sets free-list size limits + * + * \param[in] reg_global_lim The cumulative limit, in bytes, on memory used for + * all regular free lists (Default: 1MB) + * \param[in] reg_list_lim The limit, in bytes, on memory used for each regular + * free list (Default: 64KB) + * \param[in] arr_global_lim The cumulative limit, in bytes, on memory used for + * all array free lists (Default: 4MB) + * \param[in] arr_list_lim The limit, in bytes, on memory used for each array + * free list (Default: 256KB) + * \param[in] blk_global_lim The cumulative limit, in bytes, on memory used for + * all block free lists and, separately, for all + * factory free lists (Default: 16MB) + * \param[in] blk_list_lim The limit, in bytes, on memory used for each block + * or factory free list (Default: 1MB) + * \return \herr_t + * + * \details H5set_free_list_limits() sets size limits on all types of free + * lists. The HDF5 library uses free lists internally to manage + * memory. The types of free lists used are as follows: + * \li Regular free lists manage memory for single internal data + * structures. + * \li Array free lists manage memory for arrays of internal + * data structures. + * \li Block free lists manage memory for arbitrarily-sized blocks + * of bytes. + * \li Factory free lists manage memory for fixed-size blocks of + * bytes. + * + * The parameters specify global and per-list limits; for example, \p + * reg_global_limit and \p reg_list_limit limit the accumulated size + * of all regular free lists and the size of each individual regular + * free list, respectively. Therefore, if an application sets a 1Mb + * limit on each of the global lists, up to 4Mb of total storage might + * be allocated, 1Mb for each of the regular, array, block, and + * factory type lists. + * + * The settings specified for block free lists are duplicated for + * factory free lists. Therefore, increasing the global limit on block + * free lists by x bytes will increase the potential free list memory + * usage by 2x bytes. + * + * Using a value of -1 for a limit means that no limit is set for the + * specified type of free list. + * + * \version 1.8.3 Function changed in this release to set factory free list + * memory limits. + * + * \since 1.6.0 + */ H5_DLL herr_t 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); +/** + * \ingroup H5 + * \brief Gets the current size of the free lists used to manage memory + * + * \param[out] reg_size The current size of all "regular" free list memory used + * \param[out] arr_size The current size of all "array" free list memory used + * \param[out] blk_size The current size of all "block" free list memory used + * \param[out] fac_size The current size of all "factory" free list memory used + * \return \herr_t + * + * \details H5get_free_list_sizes() obtains the current size of the different + * kinds of free lists that the library uses to manage memory. The + * free list sizes can be set with H5set_free_list_limits() and + * garbage collected with H5garbage_collect(). These lists are global + * for the entire library. + * + * \since 1.12.1 + */ H5_DLL herr_t H5get_free_list_sizes(size_t *reg_size, size_t *arr_size, size_t *blk_size, size_t *fac_size); +/** + * \ingroup H5 + * \brief Gets the memory allocation statistics for the library + * + * \param[out] stats Memory allocation statistics + * \return \herr_t + * + * \details H5get_alloc_stats() gets the memory allocation statistics for the + * library, if the \c --enable-memory-alloc-sanity-check option was + * given when building the library. Applications can check whether + * this option was enabled detecting if the + * \c H5_MEMORY_ALLOC_SANITY_CHECK macro is defined. This option is + * enabled by default for debug builds of the library and disabled by + * default for non-debug builds. If the option is not enabled, all the + * values returned with be 0. These statistics are global for the + * entire library, but do not include allocations from chunked dataset + * I/O filters or non-native VOL connectors. + * + * \since 1.12.1 + */ H5_DLL herr_t H5get_alloc_stats(H5_alloc_stats_t *stats); +/** + * \ingroup H5 + * \brief Returns the HDF library release number + * + * \param[out] majnum The major version number of the library + * \param[out] minnum The minor version number of the library + * \param[out] relnum The release version number of the library + * \return \herr_t + * + * \details H5get_libversion() retrieves the major, minor, and release numbers + * of the version of the HDF5 library which is linked to the + * application. + * + */ H5_DLL herr_t H5get_libversion(unsigned *majnum, unsigned *minnum, unsigned *relnum); +/** + * \ingroup H5 + * \brief Verifies that HDF5 library versions are consistent + * + * \param[in] majnum HDF5 library major version number + * \param[in] minnum HDF5 library minor version number + * \param[in] relnum HDF5 library release number + * \return \herr_t + * + * \details H5check_version() verifies that the version of the HDF5 library + * with which an application was compiled, as indicated by the passed + * parameters, matches the version of the HDF5 library against which + * the application is currently linked. + * + * \p majnum is the major version number of the HDF library with which + * the application was compiled, \p minnum is the minor version + * number, and \p relnum is the release number. Consider the following + * example: + * + * An official HDF5 release is labelled as follows: + * HDF5 Release \Code{\<majnum\>.\<minnum\>.\<relnum\>}\n + * For example, in HDF5 Release 1.8.5: + * \li 1 is the major version number, \p majnum. + * \li 8 is the minor version number, \p minnum. + * \li 5 is the release number, \p relnum. + * + * As stated above, H5check_version() first verifies that the version + * of the HDF5 library with which an application was compiled matches + * the version of the HDF5 library against which the application is + * currently linked. If this check fails, H5check_version() causes the + * application to abort (by means of a standard C abort() call) and + * prints information that is usually useful for debugging. This + * precaution is is taken to avoid the risks of data corruption or + * segmentation faults. + * + * The most common cause of this failure is that an application was + * compiled with one version of HDF5 and is dynamically linked with a + * different version different version. + * + * If the above test passes, H5check_version() proceeds to verify the + * consistency of additional library version information. This is + * designed to catch source code inconsistencies that do not normally + * cause failures; if this check reveals an inconsistency, an + * informational warning is printed but the application is allowed to + * run. + * + */ H5_DLL herr_t H5check_version(unsigned majnum, unsigned minnum, unsigned relnum); +/** + * \ingroup H5 + * \brief Determines whether the HDF5 library was built with the thread-safety + * feature enabled + * + * \param[out] is_ts Boolean value indicating whether the library was built + * with thread-safety enabled + * \return \herr_t + * + * \details The HDF5 library, although not internally multi-threaded, can be + * built with a thread-safety feature enabled that protects internal + * data structures with a mutex. In certain circumstances, it may be + * useful to determine, at run-time, whether the linked HDF5 library + * was built with the thread-safety feature enabled. + */ H5_DLL herr_t H5is_library_threadsafe(hbool_t *is_ts); +/** + * \ingroup H5 + * \brief Frees memory allocated by the HDF5 library + * + * \param[in] mem Buffer to be freed. Can be NULL + * \return \herr_t + * + * \details H5free_memory() frees memory that has been allocated by the caller + * with H5allocate_memory() or by the HDF5 library on behalf of the + * caller. + * + * H5Tget_member_name() provides an example of memory allocation on + * behalf of the caller: The function returns a buffer containing the + * name of a compound datatype member. It is the caller’s + * responsibility to eventually free that buffer with H5free_memory(). + * + * \attention It is especially important to use this function to free memory + * allocated by the library on Windows. The C standard library is + * implemented in dynamic link libraries (DLLs) known as the C + * run-time (CRT). Each version of Visual Studio comes with two CRT + * DLLs (debug and release) and allocating and freeing across DLL + * boundaries can cause resource leaks and subtle bugs due to heap + * corruption.\n + * Only use this function to free memory allocated by the HDF5 + * Library. It will generally not be safe to use this function to + * free memory allocated by any other means.\n + * Even when using this function, it is still best to ensure that + * all components of a C application are built with the same version + * of Visual Studio and build (debug or release) and thus linked + * against the same CRT. + * + * \see H5allocate_memory(), H5resize_memory() + * + * \since 1.8.13 + * + */ H5_DLL herr_t H5free_memory(void *mem); +/** + * \ingroup H5 + * \brief Frees memory allocated by the HDF5 library + * + * \param[in] size The size in bytes of the buffer to be allocated + * \param[in] clear Flag whether the new buffer is to be initialized with 0 + * + * \return On success, returns pointer to newly allocated buffer or returns + * NULL if size is 0 (zero).\n + * Returns NULL on failure. + * + * \details H5allocate_memory() allocates a memory buffer of size bytes that + * will later be freed internally by the HDF5 library. + * + * The boolean \p clear parameter specifies whether the buffer should + * be initialized. If clear is \c TRUE, all bits in the buffer are to be + * set to 0 (zero); if clear is \c FALSE, the buffer will not be + * initialized. + * + * This function is intended to have the semantics of malloc() and + * calloc(). However, unlike malloc() and calloc() which allow for a + * "special" pointer to be returned instead of NULL, this function + * always returns NULL on failure or when size is set to 0 (zero). + * + * \note At this time, the only intended use for this function is to allocate + * memory that will be returned to the library as a data buffer from a + * third-party filter. + * + * \attention To avoid heap corruption, allocated memory should be freed using + * the same library that initially allocated it. In most cases, the + * HDF5 API uses resources that are allocated and freed either + * entirely by the user or entirely by the library, so this is not a + * problem. In rare cases, however, HDF5 API calls will free memory + * that the user allocated. This function allows the user to safely + * allocate this memory.\n + * It is particularly important to use this function to allocate + * memory in Microsoft Windows environments. In Windows, the C + * standard library is implemented in dynamic link libraries (DLLs) + * known as the C run-time (CRT). Each version of Visual Studio + * comes with multiple versions of the CRT DLLs (debug, release, et + * cetera) and allocating and freeing memory across DLL boundaries + * can cause resource leaks and subtle bugs due to heap corruption.\n + * Even when using this function, it is best where possible to + * ensure that all components of a C application are built with the + * same version of Visual Studio and configuration (Debug or + * Release), and thus linked against the same CRT.\n + * Use this function only to allocate memory inside third-party HDF5 + * filters. It will generally not be safe to use this function to + * allocate memory for any other purpose. + * + * \see H5free_memory(), H5resize_memory() + * + * \since 1.8.15 + * + */ H5_DLL void * H5allocate_memory(size_t size, hbool_t clear); +/** + * \ingroup H5 + * \brief Resizes and, if required, re-allocates memory that will later be + * freed internally by the HDF5 library + * + * \param[in] mem Pointer to a buffer to be resized. May be NULL + * \param[in] size New size of the buffer, in bytes + + * + * \return On success, returns pointer to resized or reallocated buffer + * or returns NULL if size is 0 (zero).\n + * Returns NULL on failure. + * + * \details H5resize_memory() takes a pointer to an existing buffer and resizes + * the buffer to match the value in \p size. If necessary, the buffer + * is reallocated. If \p size is 0, the buffer is released. + * + * The input buffer must either be NULL or have been allocated by + * H5allocate_memory() since the input buffer may be freed by the + * library. + * + * For certain behaviors, the pointer \p mem may be passed in as NULL. + * + * This function is intended to have the semantics of realloc(): + * + * <table> + * <tr><td>\Code{H5resize_memory(buffer, size)}</td> + * <td>Resizes buffer. Returns pointer to resized buffer.</td></tr> + * <tr><td>\Code{H5resize_memory(NULL, size)}</td> + * <td>Allocates memory using HDF5 Library allocator. + * Returns pointer to new buffer</td></tr> + * <tr><td>\Code{H5resize_memory(buffer, 0)}</td> + * <td>Frees memory using HDF5 Library allocator. + * Returns NULL.</td></tr> + * <tr><td>\Code{H5resize_memory(NULL, 0)}</td> + * <td>Returns NULL (undefined in C standard).</td></tr> + * </table> + * + * Unlike realloc(), which allows for a "special pointer to be + * returned instead of NULL, this function always returns NULL on + * failure or when size is 0 (zero). + * + * \note At this time, the only intended use for this function is to resize or + * reallocate memory that will be returned to the library (and eventually + * to the user) as a data buffer from a third-party HDF5 filter. + * + * \attention To avoid heap corruption, allocated memory should be freed using + * the same library that initially allocated it. In most cases, the + * HDF5 API uses resources that are allocated and freed either + * entirely by the user or entirely by the library, so this is not a + * problem. In rare cases, however, HDF5 API calls will free memory + * that the user allocated. This function allows the user to safely + * allocate this memory.\n + * It is particularly important to use this function to resize + * memory on Microsoft Windows systems. In Windows, the C standard + * library is implemented in dynamic link libraries (DLLs) known as + * the C run-time (CRT). Each version of Visual Studio comes with + * multiple versions of the CRT DLLs (debug, release, et cetera) and + * allocating and freeing memory across DLL boundaries can cause + * resource leaks and subtle bugs due to heap corruption.\n + * Even when using this function, it is still best to ensure that + * all components of a C application are built with the same version + * of Visual Studio and the same configuration (Debug or Release), + * and thus linked against the same CRT.\n + * Only use this function to resize memory inside third-party HDF5 + * filters. It will generally not be safe to use this function to + * resize memory for any other purpose. + * + * \see H5allocate_memory(), H5free_memory() + * + * \since 1.8.15 + * + */ H5_DLL void * H5resize_memory(void *mem, size_t size); #ifdef __cplusplus diff --git a/src/H5system.c b/src/H5system.c index b2a2668..a817b7c 100644 --- a/src/H5system.c +++ b/src/H5system.c @@ -25,6 +25,7 @@ /****************/ /* Module Setup */ /****************/ +#include "H5module.h" /* This source code file is part of the H5 module */ /***********/ /* Headers */ @@ -347,7 +348,7 @@ H5_make_time(struct tm *tm) */ long timezone = 0; #endif /* defined(H5_HAVE_VISUAL_STUDIO) && (_MSC_VER >= 1900) */ - time_t ret_value; /* Return value */ + time_t ret_value = 0; /* Return value */ FUNC_ENTER_NOAPI_NOINIT diff --git a/src/H5timer.c b/src/H5timer.c index 1df2d8d..b53c302 100644 --- a/src/H5timer.c +++ b/src/H5timer.c @@ -24,6 +24,7 @@ /****************/ /* Module Setup */ /****************/ +#include "H5module.h" /* This source code file is part of the H5 module */ /***********/ /* Headers */ diff --git a/src/H5trace.c b/src/H5trace.c index 18c7f7e..0ffa0aa 100644 --- a/src/H5trace.c +++ b/src/H5trace.c @@ -25,6 +25,7 @@ /****************/ /* Module Setup */ /****************/ +#include "H5module.h" /* This source code file is part of the H5 module */ #define H5I_FRIEND /*suppress error about including H5Ipkg */ /***********/ |