From 71a42ab05e4c16f8d2915ddc131ef5892ddf9a24 Mon Sep 17 00:00:00 2001 From: Larry Knox Date: Thu, 26 Nov 2020 06:32:33 -0600 Subject: Merge available RM doxygen from develop to hdf5 1 12 (#131) * Snapshot version 1.12 release 1-3. Update version to 1.12.1-4. * First cut of the H5 public API documentation. (#80) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Full set of current H5F documentation. (#105) * First cut of the H5 public API documentation. * Added H5Z "bonus track." * Applied Quincey's patch. * Added the missing patches from Quincey's original patch. * H5PL (complete) and basic H5VL API documentation. * Added H5I API docs. * Added H5L API docs. * First installment from Elena's H5T batch. * Second installment of Elena's H5T batch. * Final installment of Elena's H5T batch. * Migrated documentation for SWMR functions. * Catching up on MDC functions. * Integrated the H5F MDC function documentation. * Added MDC and parallel H5F functions. * Slightly updated main page. * Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST. * Doxygen - added (mostly) beginner functions (#112) * Doxygen - added (mostly) beginner functions * Removed duplicate H5Pset_szip function * Add src/H5module.h to MANIFEST. Co-authored-by: Gerd Heber Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com> --- MANIFEST | 2 + doxygen/Doxyfile.in | 1 + doxygen/aliases | 16 +- doxygen/dox/H5AC_cache_config_t.dox | 415 +++++ doxygen/dox/mainpage.dox | 70 +- src/H5.c | 36 + src/H5Amodule.h | 17 + src/H5Apublic.h | 341 ++++- src/H5Fpublic.h | 868 ++++++++++- src/H5Imodule.h | 5 + src/H5Ipublic.h | 615 +++++++- src/H5Lmodule.h | 8 + src/H5Lpublic.h | 2035 ++++++++++++++++++++++-- src/H5PLmodule.h | 5 + src/H5PLpublic.h | 176 ++- src/H5Pmodule.h | 43 + src/H5Ppublic.h | 868 ++++++++++- src/H5Smodule.h | 27 + src/H5Spublic.h | 282 +++- src/H5Tmodule.h | 76 + src/H5Tpublic.h | 2896 ++++++++++++++++++++++++++++++++--- src/H5VLconnector.h | 91 +- src/H5VLmodule.h | 15 + src/H5VLnative.h | 6 + src/H5VLpublic.h | 287 +++- src/H5Zmodule.h | 67 + src/H5Zpublic.h | 661 ++++++-- src/H5checksum.c | 3 +- src/H5dbg.c | 1 + src/H5err.txt | 1 + src/H5module.h | 34 + src/H5private.h | 2 - src/H5public.h | 459 +++++- src/H5system.c | 3 +- src/H5timer.c | 1 + src/H5trace.c | 1 + 36 files changed, 9796 insertions(+), 638 deletions(-) create mode 100644 doxygen/dox/H5AC_cache_config_t.dox create mode 100644 src/H5module.h diff --git a/MANIFEST b/MANIFEST index c925f6f..c78280d 100644 --- a/MANIFEST +++ b/MANIFEST @@ -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 - * - * - * - * \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 diff --git a/src/H5.c b/src/H5.c index e7514b4..7efd4f0 100644 --- a/src/H5.c +++ b/src/H5.c @@ -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 + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
int version 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).
hbool_t rpt_fcn_enabled

OUT: Boolean flag indicating whether the adaptive cache resize report function is enabled. This + * field should almost always be set to disabled (0). Since resize algorithm activity is + * reported via stdout, it MUST be set to disabled (0) on Windows machines.

The + * report function is not supported code, and can be expected to change between versions of the + * library. Use it at your own risk.

hbool_t open_trace_file OUT: Boolean field indicating whether the trace_file_name field should be used to open + * a trace file for the cache. This field will always be set to 0 in this context.
hbool_t close_trace_file OUT: Boolean field indicating whether the current trace file (if any) should be closed. This field + * will always be set to 0 in this context.
char*trace_file_name OUT: Full path name of the trace file to be opened if the open_trace_file field is set + * to 1. This field will always be set to the empty string in this context.
hbool_t evictions_enabled OUT: Boolean flag indicating whether metadata cache entry evictions are + * enabled.
hbool_t set_initial_size OUT: Boolean flag indicating whether the cache should be created with a user specified initial + * maximum size.

If the configuration is loaded from the cache, this flag will always be set + * to 0.

size_t initial_size OUT: Initial maximum size of the cache in bytes, if applicable.

If the configuration is loaded + * from the cache, this field will contain the cache maximum size as of the time of the + * call.

double min_clean_fraction OUT: Float value specifying the minimum fraction of the cache that must be kept either clean or + * empty when possible.
size_t max_size OUT: Upper bound (in bytes) on the range of values that the adaptive cache resize code can select + * as the maximum cache size.
size_t min_size OUT: Lower bound (in bytes) on the range of values that the adaptive cache resize code can select + * as the maximum cache size.
long int epoch_length OUT: Number of cache accesses between runs of the adaptive cache resize + * code.
+ * + * \par Increment configuration section + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
enum H5C_cache_incr_mode incr_mode OUT: Enumerated value indicating the operational mode of the automatic cache size increase code. At + * present, only the following values are legal:

\c H5C_incr__off: Automatic cache size increase is + * disabled.

\c H5C_incr__threshold: Automatic cache size increase is enabled using the hit rate + * threshold algorithm.

double lower_hr_threshold OUT: Hit rate threshold used in the hit rate threshold cache size increase algorithm.
double increment 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.
hbool_t apply_max_increment OUT: Boolean flag indicating whether an upper limit will be applied to the size of cache size + * increases.
size_t max_increment OUT: The maximum number of bytes by which the maximum cache size can be increased in a single step + * -- if applicable.
enum H5C_cache_flash_incr_mode flash_incr_mode OUT: Enumerated value indicating the operational mode of the flash cache size increase code. At + * present, only the following values are legal:

\c H5C_flash_incr__off: Flash cache size increase is + * disabled.

\c H5C_flash_incr__add_space: Flash cache size increase is enabled using the add space + * algorithm.

double flash_threshold 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.
double flash_multiple 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 max_size field above.
+ * + * \par Decrement configuration section + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
Decrement configuration + * section:
enum H5C_cache_decr_mode decr_mode OUT: Enumerated value indicating the operational mode of the automatic cache size decrease code. At + * present, the following values are legal:

H5C_decr__off: Automatic cache size decrease is disabled, + * and the remaining decrement fields are ignored.

H5C_decr__threshold: Automatic cache size + * decrease is enabled using the hit rate threshold algorithm.

H5C_decr__age_out: Automatic cache + * size decrease is enabled using the ageout algorithm.

H5C_decr__age_out_with_threshold: + * Automatic cache size decrease is enabled using the ageout with hit rate threshold + * algorithm

double upper_hr_threshold 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.
double decrement 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.
hbool_t apply_max_decrement OUT: Boolean flag indicating whether an upper limit should be applied to the size of cache size + * decreases.
size_t max_decrement OUT: The maximum number of bytes by which cache size can be decreased if any single step, if + * applicable.
int epochs_before_eviction 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.
hbool_t apply_empty_reserve OUT: Boolean flag indicating whether an empty reserve should be maintained under either of the + * ageout cache size reduction algorithms.
double empty_reserve OUT: Empty reserve for use with the ageout cache size reduction algorithms, if applicable.
+ * + * \par Parallel configuration section + * + * + * + * + *
int dirty_bytes_threshold OUT: Threshold number of bytes of dirty metadata generation for triggering synchronizations of the + * metadata caches serving the target file in the parallel case.

Synchronization occurs whenever the + * number of bytes of dirty metadata created since the last synchronization exceeds this limit.

+ * + * \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 + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
int versionIN: 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).
hbool_t rpt_fcn_enabledIN: Boolean flag indicating whether the adaptive cache resize report function is enabled. This + * field should almost always be set to disabled (0). Since resize algorithm activity is reported + * via stdout, it MUST be set to disabled (0) on Windows machines.

The report function is not + * supported code, and can be expected to change between versions of the library. Use it at your own + * risk.

hbool_t open_trace_FileIN: Boolean field indicating whether the trace_file_name field should be used to open + * a trace file for the cache.

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 0, as trace file collection imposes considerable overhead.

This field should only be + * set to 1 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 close_trace_file field is + * also 1.

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.

hbool_t close_trace_fileIN: Boolean field indicating whether the current trace file (if any) should be closed.

See the + * above comments on the open_trace_file field. This field should be set to 0 unless + * there is an open trace file on the cache that you wish to close.

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.

char trace_file_name[]IN: Full path of the trace file to be opened if the open_trace_file field is set + * to 1.

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.

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.

hbool_t evictions_enabledIN: A boolean flag indicating whether evictions from the metadata cache are enabled. This flag is + * initially set to enabled (1).

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 evictions_enabled 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.

The evictions_enabled field may not be set to + * disabled (0) unless all adaptive cache resizing code is disabled via + * the incr_mode, flash_incr_mode, and decr_mode fields.

When + * this flag is set to disabled (0), the metadata cache will not attempt to evict entries to make + * space for new entries, and thus will grow without bound.

Evictions will be re-enabled when this field + * is set back to 1. This should be done as soon as + * possible.

hbool_t set_initial_sizeIN: Boolean flag indicating whether the cache should be forced to the user specified initial + * size.
size_t initial_sizeIN: If set_initial_size is set to 1, then initial_size must + * contain the desired initial size in bytes. This value must lie in the closed interval [min_size, + * max_size]. (see below)
double min_clean_fractionIN: This field specifies the minimum fraction of the cache that must be kept either clean or + * empty.

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 Metadata Caching in HDF5 in the collection + * "Advanced Topics in HDF5."

size_t max_sizeIN: Upper bound (in bytes) on the range of values that the adaptive cache resize code can select as + * the maximum cache size.
size_t min_sizeIN: Lower bound (in bytes) on the range of values that the adaptive cache resize code can select as + * the maximum cache size.
long int epoch_lengthIN: Number of cache accesses between runs of the adaptive cache resize code. 50,000 is a good + * starting number.
+ * + * \par Increment configuration fields + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
enum H5C_cache_incr_mode incr_modeIN: Enumerated value indicating the operational mode of the automatic cache size increase code. At + * present, only two values are legal:

\c H5C_incr__off: Automatic cache size increase is disabled, and the + * remaining increment fields are ignored.

\c H5C_incr__threshold: Automatic cache size increase is enabled + * using the hit rate threshold + * algorithm.

double lower_hr_thresholdIN: Hit rate threshold used by the hit rate threshold cache size increment algorithm.

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.

This field must lie in the interval [0.0, 1.0]. 0.8 or 0.9 is a good starting + * point.

double incrementIN: Factor by which the hit rate threshold cache size increment algorithm multiplies the current + * maximum cache size to obtain a tentative new cache size.

The actual cache size increase will be clipped + * to satisfy the max_size specified in the general configuration, and possibly max_increment below.

The + * parameter must be greater than or equal to 1.0 -- 2.0 is a reasonable value.

If you set it to 1.0, + * you will effectively disable cache size + * increases.

hbool_t apply_max_incrementIN: Boolean flag indicating whether an upper limit should be applied to the size of cache size + * increases.
size_t max_incrementIN: Maximum number of bytes by which cache size can be increased in a single step -- if + * applicable.
enum H5C_cache_flash_incr_mode flash_incr_modeIN: Enumerated value indicating the operational mode of the flash cache size increase code. At + * present, only the following values are legal:

\c H5C_flash_incr__off: Flash cache size increase is + * disabled.

\c H5C_flash_incr__add_space: Flash cache size increase is enabled using the add space + * algorithm.

double flash_thresholdIN: 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.

At present, this value must + * lie in the range [0.1, 1.0].

double flash_multipleIN: 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 max_size field above.

At present, this field must lie in the range [0.1, + * 10.0].

+ * + * \par Decrement configuration fields + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
enum H5C_cache_decr_mode decr_modeIN: Enumerated value indicating the operational mode of the automatic cache size decrease code. At + * present, the following values are legal:

\c H5C_decr__off: Automatic cache size decrease is + * disabled.

\c H5C_decr__threshold: Automatic cache size decrease is enabled using the hit rate threshold + * algorithm.

\c H5C_decr__age_out: Automatic cache size decrease is enabled using the ageout + * algorithm.

\c H5C_decr__age_out_with_threshold: Automatic cache size decrease is enabled using the + * ageout with hit rate threshold + * algorithm

double upper_hr_thresholdIN: Hit rate threshold for the hit rate threshold and ageout with hit rate threshold cache size + * decrement algorithms.

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.

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.

This field must lie in the interval [0.0, 1.0].

For \c H5C_incr__threshold, .9995 or + * .99995 is a good place to start.

For \c H5C_decr__age_out_with_threshold, .999 might be more + * useful.

double decrementIN: 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.

The actual cache + * size decrease will be clipped to satisfy the min_size specified in the general configuration, and possibly + * max_decrement below.

The parameter must be be in the interval [0.0, 1.0].

If you set it to 1.0, + * you will effectively disable cache size decreases. 0.9 is a reasonable starting + * point.

hbool_t apply_max_decrementIN: Boolean flag indicating whether an upper limit should be applied to the size of cache size + * decreases.
size_t max_decrementIN: Maximum number of bytes by which the maximum cache size can be decreased in any single step -- + * if applicable.
int epochs_before_evictionIN: 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.
hbool_t apply_empty_reserveIN: Boolean flag indicating whether the ageout based decrement algorithms will maintain a empty + * reserve when decreasing cache size.
double empty_reserveIN: Empty reserve as a fraction of maximum cache size if applicable.

When so directed, the ageout + * based algorithms will not decrease the maximum cache size unless the empty reserve can be met.

The + * parameter must lie in the interval [0.0, 1.0]. 0.1 or 0.05 is a good place to + * start.

+ * + * \par Parallel configuration fields + * + * + * + * + * + *
int dirty_bytes_thresholdIN: Threshold number of bytes of dirty metadata generation for triggering synchronizations of the + * metadata caches serving the target file in the parallel case.

Synchronization occurs whenever the number + * of bytes of dirty metadata created since the last synchronization exceeds this limit.

This field only + * applies to the parallel case. While it is ignored elsewhere, it can still draw a value out of bounds + * error.

It must be consistant across all caches on any given file.

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.

+ * + * \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[]}: + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
Index for \Code{retries[]}Metadata entries*
0Object header (version 2)
1Object header chunk (version 2)
2B-tree header (version 2)
3B-tree internal node (version 2)
4B-tree leaf node (version 2)
5Fractal heap header
6Fractal heap direct block (optional checksum)
7Fractal heap indirect block
8Free-space header
9Free-space sections
10Shared object header message table
11Shared message record list
12Extensive array header
13Extensive array index block
14Extensive array super block
15Extensive array data block
16Extensive array data block page
17Fixed array super block
18Fixed array data block
19Fixed array data block page
20File's superblock (version 2)
* All entries are of version 0 (zero) unless indicated otherwise.
+ * + * \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: + *
    + *
  1. 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.
    2. + *
  2. 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.
    3. + *
+ * 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. + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
Link class identifier or Value rangeDescriptionLink class or label
0 to 63Reserved range
64 to 255User-definable range
64Minimum user-defined value#H5L_TYPE_UD_MIN
64External link#H5L_TYPE_EXTERNAL
255Maximum user-defined value#H5L_TYPE_UD_MAX
255Maximum value#H5L_TYPE_MAX
-1Error#H5L_TYPE_ERROR
+ * + * 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: + *
    + *
  1. Call H5Lget_info() to get the link type and the size of the + * link value.
  2. + *
  3. Verify that the link is an external link, i.e., that its link + * type is #H5L_TYPE_EXTERNAL.
    4. + *
  4. Call H5Lget_val() to get the link value.
    5. + *
  5. Call H5Lunpack_elink_val() to unpack that value.
    6. + *
+ * + * \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: + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
Class IdentifierClass NameComments
#H5P_ATTRIBUTE_CREATEattribute createProperties for attribute creation
#H5P_DATASET_ACCESSdataset accessProperties for dataset access
#H5P_DATASET_CREATEdataset createProperties for dataset creation
#H5P_DATASET_XFERdata transferProperties for raw data transfer
#H5P_DATATYPE_ACCESSdatatype accessProperties for datatype access
#H5P_DATATYPE_CREATEdatatype createProperties for datatype creation
#H5P_FILE_ACCESSfile accessProperties for file access
#H5P_FILE_CREATEfile createProperties for file creation
#H5P_FILE_MOUNTfile mountProperties for file mounting
#H5P_GROUP_ACCESSgroup accessProperties for group access
#H5P_GROUP_CREATEgroup createProperties for group creation
#H5P_LINK_ACCESSlink accessProperties governing link traversal when accessing objects
#H5P_LINK_CREATElink createProperties governing link creation
#H5P_OBJECT_COPYobject copyProperties governing the object copying process
#H5P_OBJECT_CREATEobject createProperties for object creation
#H5P_STRING_CREATEstring createProperties for character encoding when encoding strings or + * object names
#H5P_VOL_INITIALIZEvol initializeProperties for VOL initialization
+ * + * 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: + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
#H5D_FILL_TIME_IFSETFill 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) + *
#H5D_FILL_TIME_ALLOCFill values are written to the dataset when storage + * space is allocated.
#H5D_FILL_TIME_NEVERFill values are never written to the dataset.
+ * + * \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 232-1 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 232-1, + * 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: + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
#H5D_FILL_TIME_IFSETWrite 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)
#H5D_FILL_TIME_ALLOCWrite fill values to the dataset when storage space is + * allocated.
#H5D_FILL_TIME_NEVERNever write fill values to the dataset.
+ * + * \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. + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
OptionDescription (Mutually exclusive; select one.)
#H5_SZIP_EC_OPTION_MASKSelects entropy coding method
#H5_SZIP_NN_OPTION_MASKSelects nearest neighbor coding method
+ * + * 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: + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
#H5S_SELECT_SETReplaces the existing selection with the + * parameters from this call. Overlapping blocks + * are not supported with this operator.
#H5S_SELECT_ORAdds the new selection to the existing selection. + * (Binary OR)
#H5S_SELECT_ANDRetains only the overlapping portions of the + * new selection and the existing selection. + * (Binary AND)
#H5S_SELECT_XORRetains 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) + *
#H5S_SELECT_NOTBRetains only elements of the existing selection + * that are not in the new selection.
#H5S_SELECT_NOTARetains only elements of the new selection that + * are not in the existing selection.
+ * + * 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); -H5_DLL hid_t H5Tdecode(const void *buf); -H5_DLL herr_t H5Tflush(hid_t type_id); -H5_DLL herr_t H5Trefresh(hid_t type_id); - -/* Operations defined on compound datatypes */ -H5_DLL herr_t H5Tinsert(hid_t parent_id, const char *name, size_t offset, hid_t member_id); +/** + * \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: + * + * + * + * + * + * + * + *
#H5Z_FILTER_DEFLATEThe gzip compression, or + * deflation, filter
#H5Z_FILTER_SZIPThe SZIP compression + * filter
#H5Z_FILTER_NBITThe N-bit compression + * filter
#H5Z_FILTER_SCALEOFFSETThe scale-offset + * compression filter
#H5Z_FILTER_SHUFFLEThe shuffle algorithm + * filter
#H5Z_FILTER_FLETCHER32The Fletcher32 checksum, + * or error checking, filter
+ * 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: + * + * + * + * + * + *
#H5Z_FILTER_CONFIG_ENCODE_ENABLEDEncoding is enabled for this filter
#H5Z_FILTER_CONFIG_DECODE_ENABLEDDecoding is enabled for this filter
+ * + * 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 " 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{\.\.\}\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(): + * + * + * + * + * + * + * + * + * + * + *
\Code{H5resize_memory(buffer, size)}Resizes buffer. Returns pointer to resized buffer.
\Code{H5resize_memory(NULL, size)}Allocates memory using HDF5 Library allocator. + * Returns pointer to new buffer
\Code{H5resize_memory(buffer, 0)}Frees memory using HDF5 Library allocator. + * Returns NULL.
\Code{H5resize_memory(NULL, 0)}Returns NULL (undefined in C standard).
+ * + * 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 */ /***********/ -- cgit v0.12