diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5Dmodule.h | 11 | ||||
| -rw-r--r-- | src/H5Dpublic.h | 1261 | ||||
| -rw-r--r-- | src/H5Gmodule.h | 7 | ||||
| -rw-r--r-- | src/H5Gpublic.h | 337 |
4 files changed, 1598 insertions, 18 deletions
diff --git a/src/H5Dmodule.h b/src/H5Dmodule.h index 178e50f..fd155b1 100644 --- a/src/H5Dmodule.h +++ b/src/H5Dmodule.h @@ -29,4 +29,15 @@ #define H5_MY_PKG_ERR H5E_DATASET #define H5_MY_PKG_INIT YES +/** + * \defgroup H5D H5D + * \brief Group Interface + * \details The HDF5 Dataset Interface, H5D, provides a mechanism for managing + * HDF5 datasets, including the transfer of data between memory and + * disk and the description of dataset properties. + * + * A Dataset is used by other HDF5 APIs, either by name or by a handle, + * which is obtained by either creating or opening the dataset. + */ + #endif /* _H5Dmodule_H */ diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h index 507f75b..00948f9 100644 --- a/src/H5Dpublic.h +++ b/src/H5Dpublic.h @@ -105,16 +105,22 @@ typedef enum H5D_vds_view_t { /* Callback for H5Pset_append_flush() in a dataset access property list */ typedef herr_t (*H5D_append_cb_t)(hid_t dataset_id, hsize_t *cur_dims, void *op_data); -/* Define the operator function pointer for H5Diterate() */ +/** Define the operator function pointer for H5Diterate() */ +//! [H5D_operator_t_snip] typedef herr_t (*H5D_operator_t)(void *elem, hid_t type_id, unsigned ndim, const hsize_t *point, void *operator_data); +//! [H5D_operator_t_snip] -/* Define the operator function pointer for H5Dscatter() */ +/** Define the operator function pointer for H5Dscatter() */ +//! [H5D_scatter_func_t_snip] typedef herr_t (*H5D_scatter_func_t)(const void **src_buf /*out*/, size_t *src_buf_bytes_used /*out*/, void *op_data); +//! [H5D_scatter_func_t_snip] -/* Define the operator function pointer for H5Dgather() */ +/** Define the operator function pointer for H5Dgather() */ +//! [H5D_gather_func_t_snip] typedef herr_t (*H5D_gather_func_t)(const void *dst_buf, size_t dst_buf_bytes_used, void *op_data); +//! [H5D_gather_func_t_snip] /********************/ /* Public Variables */ @@ -127,57 +133,1280 @@ typedef herr_t (*H5D_gather_func_t)(const void *dst_buf, size_t dst_buf_bytes_us extern "C" { #endif +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Creates a new dataset and links it into the file + * + * \fgdta_loc_id + * \param[in] name Name of the dataset to open + * \type_id + * \space_id + * \lcpl_id + * \dcpl_id + * \dapl_id + * + * \return \hid_t{dataset} + * + * + * \details H5Dcreate2() creates a new dataset named \p name at + * the location specified by \p loc_id, and associates constant + * and initial persistent properties with that dataset, including + * the datatype \p dtype_id, the dataspace \p space_id, and + * other properties as specified by the dataset creation property + * list \p dcpl_id and the access property list \p dapl_id, + * respectively. Once created, the dataset is opened for access. + * + * \p loc_id may specify a file, group, dataset, named datatype, + * or attribute. If an attribute, dataset, or named datatype is + * specified then the dataset will be created at the location + * where the attribute, dataset, or named datatype is attached. + * + * \p name may be either an absolute path in the file or a relative + * path from \p loc_id naming the dataset. + * + * \p dtype_id specifies the datatype of each data element as stored + * in the file. If \p dtype_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. + * + * If \p dtype_id is a committed datatype, and if the file location + * associated with the committed datatype is different from the + * file location where the dataset will be created, the datatype + * is copied and converted to a transient type. + * + * The link creation property list, \p lcpl_id, governs creation + * of the link(s) by which the new dataset is accessed and the + * creation of any * intermediate groups that may be missing. + * + * The datatype and dataspace properties and the dataset creation + * and access property lists are attached to the dataset, so the + * caller may derive new datatypes, dataspaces, and creation and + * access properties from the old ones and reuse them in calls to + * create additional datasets. Once created, the dataset can be + * read from or written to. Reading data from a datatset that was + * not previously written, the HDF5 library will return default + * or user-defined fill values. + * + * To conserve and release resources, the dataset should be closed + * when access is no longer required. + * + * \since 1.8.0 + * + * \see H5Dopen2(), H5Dclose(), H5Tset_size() + * + */ H5_DLL hid_t H5Dcreate2(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id); H5_DLL hid_t H5Dcreate_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t lcpl_id, hid_t dcpl_id, hid_t dapl_id, hid_t es_id); -H5_DLL hid_t H5Dcreate_anon(hid_t file_id, hid_t type_id, hid_t space_id, hid_t plist_id, hid_t dapl_id); -H5_DLL hid_t H5Dopen2(hid_t file_id, const char *name, hid_t dapl_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Creates a dataset in a file without linking it into the file + * structure + * + * \fgdta_loc_id + * \type_id + * \space_id + * \dcpl_id + * \dapl_id + * + * \return \hid_t{dataset} + * + * \details H5Dcreate_anon() creates a dataset in the file specified + * by \p loc_id. + * + * \p loc_id may specify a file, group, dataset, named datatype, + * or attribute. If an attribute, dataset, or named datatype is + * specified then the dataset will be created at the location + * where the attribute, dataset, or named datatype is attached. + * + * The dataset’s datatype and dataspace are specified by + * \p type_id and \p space_id, respectively. These are the + * datatype and dataspace of the dataset as it will exist in + * the file, which may differ from the datatype and dataspace + * in application memory. + * + * Dataset creation property list and dataset access creation + * property list are specified by \p dcpl_id and \p dapl_id. + * + * H5Dcreate_anon() returns a new dataset identifier. Using + * this identifier, the new dataset must be linked into the + * HDF5 file structure with H5Olink() or it will be deleted + * from the file when the file is closed. + * + * See H5Dcreate2() for further details and considerations on + * the use of H5Dcreate2() and H5Dcreate_anon(). + * + * The differences between this function and H5Dcreate2() are + * as follows: + * \li H5Dcreate_anon() explicitly includes a dataset access property + * list. H5Dcreate() always uses default dataset access properties. + * + * \li H5Dcreate_anon() neither provides the new dataset’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. + * + * A dataset created with this function should be closed with + * H5Dclose() when the dataset is no longer needed so that resource + * leaks will not develop. + * + * \since 1.8.0 + * + * \see H5Olink(), H5Dcreate(), Using Identifiers + * + */ +H5_DLL hid_t H5Dcreate_anon(hid_t loc_id, hid_t type_id, hid_t space_id, hid_t dcpl_id, hid_t dapl_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Creates a new dataset and links it into the file + * + * \fgdta_loc_id + * \param[in] name Name of the dataset to open + * \dapl_id + * + * \return \hid_t{dataset} + * + * \details H5Dopen2() opens the existing dataset specified + * by a location identifier and name, \p loc_id and \p name, + * respectively. + * + * \p loc_id may specify a file, group, dataset, named datatype, + * or attribute. If an attribute, dataset, or named datatype is + * specified then the dataset will be opened at the location + * where the attribute, dataset, or named datatype is attached. + * + * The dataset access property list, \p dapl_id, provides + * information regarding access to the dataset. + * + * To conserve and release resources, the dataset should be closed + * when access is no longer required. + * + * \since 1.8.0 + * + * \see H5Dcreate2(), H5Dclose() + * + */ +H5_DLL hid_t H5Dopen2(hid_t loc_id, const char *name, hid_t dapl_id); H5_DLL hid_t H5Dopen_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id, const char *name, hid_t dapl_id, hid_t es_id); + +/** + * -------------------------------------------------------------------------- + *\ingroup H5D + * + * \brief Returns an identifier for a copy of the dataspace for a dataset + * + * \dset_id + * + * \return \hid_t{dataspace} + * + * \details H5Dget_space() makes a copy of the dataspace of + * the dataset specified by \p dset_id. The function returns an + * identifier for the new copy of the dataspace. + * + * A dataspace identifier returned from this function should + * be released with H5Sclose() when the identifier is no longer + * needed so that resource leaks will not occur. + * + * \see H5Sclose() + * + */ H5_DLL hid_t H5Dget_space(hid_t dset_id); H5_DLL hid_t H5Dget_space_async(const char *app_file, const char *app_func, unsigned app_line, hid_t dset_id, hid_t es_id); + H5_DLL herr_t H5Dget_space_status(hid_t dset_id, H5D_space_status_t *allocation); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Returns an identifier for a copy of the datatype for a dataset + * + * \dset_id + * + * \return \hid_t{datatype} + * + * \details H5Dget_type() returns an identifier of a copy of + * the datatype for a dataset. + * + * If a dataset has a named datatype, then an identifier to the + * opened datatype is returned. Otherwise, the returned datatype + * is read-only. If atomization of the datatype fails, then the + * datatype is closed. + * + * A datatype identifier returned from this function should be + * released with H5Tclose() when the identifier is no longer + * needed to prevent resource leaks. + * + * \note Datatype Identifiers + * + * Please note that the datatype identifier is actually an object + * identifier or a handle returned from opening the datatype. It + * is not persistent and its value can be different from one HDF5 + * session to the next. + * + * H5Tequal() can be used to compare datatypes. + * + * 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. + * + */ H5_DLL hid_t H5Dget_type(hid_t dset_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Returns an identifier for a copy of the dataset creation + * property list for a dataset + * + * \dset_id + * + * \return \hid_t{dataset creation property list} + * + * \details H5Dget_create_plist() returns an identifier for + * a copy of the dataset creation property list associated with + * the dataset specified by \p dset_id. + * + * The creation property list identifier should be released + * with H5Pclose() to prevent resource leaks. + * + */ H5_DLL hid_t H5Dget_create_plist(hid_t dset_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Returns the dataset access property list associated with + * a dataset + * + * \dset_id + * + * \return \hid_t{dataset access property list} + * + * \details H5Dget_access_plist() returns a copy of the + * dataset access property list used to open the specified + * dataset, \p dset_id. Modifications to the returned property + * list will have no effect on the dataset it was retrieved from. + * + * The chunk cache parameters in the returned property lists will + * be those used by the dataset. If the properties in the file + * access property list were used to determine the dataset's + * chunk cache configuration, then those properties will be + * present in the returned dataset access property list. If + * the dataset does not use a chunked layout, then the chunk + * cache properties will be set to the default. The chunk cache + * properties in the returned list are considered to be “set”, + * and any use of this list will override the corresponding + * properties in the file’s file access property list. + * + * All link access properties in the returned list will be set + * to the default values. + * + * The access property list identifier should be released with + * H5Pclose() when the identifier is no longer needed so that + * resource leaks will not develop. + * + * \since 1.8.3 + * + */ H5_DLL hid_t H5Dget_access_plist(hid_t dset_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Returns the amount of storage allocated for a dataset + * + * \dset_id + * + * \return Returns the amount of storage space, in bytes, or 0 (zero). + * + * \details H5Dget_storage_size() returns the amount of storage, + * in bytes, that is allocated in the file for the raw data of + * the dataset specified by \p dset_id. + * + * \note The amount of storage in this case is the storage + * allocated in the written file, which will typically differ + * from the space required to hold a dataset in working memory. + * + * \li For contiguous datasets, the returned size equals the current + * allocated size of the raw data. + * \li For unfiltered chunked datasets, the returned size is the + * number of allocated chunks times the chunk size. + * \li For filtered chunked datasets, the returned size is the + * space required to store the filtered data. For example, if a + * compression filter is in use, H5Dget_storage_size() will return + * the total space required to store the compressed chunks. + * + * H5Dget_storage_size() reports only the space required to store + * the data, not including that of any metadata. + * + * \attention H5Dget_storage_size() does not differentiate between 0 (zero), + * the value returned for the storage size of a dataset + * with no stored values, and 0 (zero), the value returned to + * indicate an error. + * + * \note Note that H5Dget_storage_size() is not generally an + * appropriate function to use when determining the amount + * of memory required to work with a dataset. In such + * circumstances, you must determine the number of data + * points in a dataset and the size of an individual data + * element. H5Sget_simple_extent_npoints() and H5Tget_size() + * can be used to get that information. + * + */ H5_DLL hsize_t H5Dget_storage_size(hid_t dset_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Returns the amount of storage allocated within the file for a + * raw data chunk in a dataset + * + * \dset_id + * \param[in] offset Logical offset in the dataset for the chunk to query + * \param[out] chunk_bytes The size in bytes for the chunk + * + * \return \herr_t + * + * \details H5Dget_chunk_storage_size() returns the size in bytes + * allocated in the file for a raw data chunk as specified by + * its logical \p offset in the dataset \p dset_id. The size is + * returned in \p chunk_nbytes. It is the size of the compressed + * data if the chunk is filtered and the size may be zero if no + * storage is allocated yet for the dataset. + * + * \since 1.10.2 + * + */ H5_DLL herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Retrieves number of chunks that have nonempty intersection with a + * specified selection + * + * \dset_id + * \param[in] fspace_id File dataspace selection identifier + * \param[out] nchunks Number of chunks in the selection + * + * \return \herr_t + * + * \details H5Dget_num_chunks() retrieves the number of chunks + * nchunks in a set of selected elements specified by \p fspace_id + * for a dataset specified by the identifier \p dset_id. If \p + * fspace_id is #H5S_ALL, the function will retrieve the total + * number of chunks stored for the dataset. + * + * \p fspace_id specifies the file dataspace selection. It is + * intended to take #H5S_ALL for specifying the current selection. + * + * \note Please be aware that this function currently does not + * support non-trivial selections, thus \p fspace_id has no + * effect. Also, the implementation does not handle the #H5S_ALL + * macro correctly. As a workaround, application can get + * the dataspace for the dataset using H5Dget_space() and pass that + * in for \p fspace_id. This will be fixed in coming releases. + * + * \since 1.10.5 + * + */ H5_DLL herr_t H5Dget_num_chunks(hid_t dset_id, hid_t fspace_id, hsize_t *nchunks); -H5_DLL herr_t H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *coord, unsigned *filter_mask, + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Retrieves information about a chunk specified by its coordinates + * + * \dset_id + * \param[in] offset Logical position of the chunk’s first element + * \param[out] filter_mask Indicating filters used with the chunk when written + * \param[out] addr Chunk address in the file + * \param[out] size Chunk size in bytes, 0 if chunk doesn’t exist + * + * \return \herr_t + * + * \details H5Dget_chunk_info_by_coord() retrieves the \p filter_mask, \p size, + * and \p addr for a chunk in the dataset specified by \p dset_id, + * using the coordinates specified by \p offset. + * + * If the queried chunk does not exist in the file, \p size will + * be set to 0, \p addr to #HADDR_UNDEF, and the buffer \p + * filter_mask will not be modified. + * + * \p offset is a pointer to a one-dimensional array with a size + * equal to the dataset’s rank. Each element is the logical + * position of the chunk’s first element in a dimension. + * + * \since 1.10.5 + * + */ +H5_DLL herr_t H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *offset, unsigned *filter_mask, haddr_t *addr, hsize_t *size); -H5_DLL herr_t H5Dget_chunk_info(hid_t dset_id, hid_t fspace_id, hsize_t chk_idx, hsize_t *coord, + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Retrieves information about a chunk specified by its index + * + * \dset_id + * \param[in] fspace_id File dataspace selection identifier (See Note below) + * \param[in] chk_idx Index of the chunk + * \param[out] offset Logical position of the chunk’s first element + * \param[out] filter_mask Indicating filters used with the chunk when written + * \param[out] addr Chunk address in the file + * \param[out] size Chunk size in bytes, 0 if chunk doesn’t exist + * + * \return \herr_t + * + * \details H5Dget_chunk_info() retrieves the offset coordinates + * offset, filter mask filter_mask, size size and address addr for + * the dataset specified by the identifier dset_id and the chunk + * specified by the index index. The chunk belongs to a set of + * chunks in the selection specified by fspace_id. If the queried + * chunk does not exist in the file, the size will be set to 0 and + * address to #HADDR_UNDEF. The value pointed to by filter_mask will + * not be modified. NULL can be passed in for any \p out parameters. + * + * \p chk_idx is the chunk index in the selection. Index value + * may have a value of 0 up to the number of chunks stored in + * the file that have a nonempty intersection with the file + * dataspace selection + * + * \note As of 1.10.5, the dataspace intersection is not yet + * supported, hence, the index is of all the written chunks. + * + * \p fspace_id specifies the file dataspace selection. It is + * intended to take #H5S_ALL for specifying the current selection. + * + * \note Please be aware that this function currently does not + * support non-trivial selections, thus \p fspace_id has no + * effect. Also, the implementation does not handle the #H5S_ALL + * macro correctly. As a workaround, application can get + * the dataspace for the dataset using H5Dget_space() and pass that + * in for \p fspace_id. This will be fixed in coming releases. + * + * \since 1.10.5 + * + */ +H5_DLL herr_t H5Dget_chunk_info(hid_t dset_id, hid_t fspace_id, hsize_t chk_idx, hsize_t *offset, unsigned *filter_mask, haddr_t *addr, hsize_t *size); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Returns dataset address in file + * + * \dset_id + * + * \return Returns the offset in bytes; otherwise, returns #HADDR_UNDEF, + * a negative value. + * + * \details H5Dget_offset() returns the address in the file of + * the dataset, \p dset_id. That address is expressed as the + * offset in bytes from the beginning of the file. + * + * \since 1.6.0 + * + */ H5_DLL haddr_t H5Dget_offset(hid_t dset_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Reads raw data from a dataset into a provided buffer + * + * \dset_id Identifier of the dataset to read from + * \param[in] mem_type_id Identifier of the memory datatype + * \param[in] mem_space_id Identifier of the memory dataspace + * \param[in] file_space_id Identifier of the dataset's dataspace in the file + * \param[in] dxpl_id Identifier of a transfer property list + * \param[out] buf Buffer to receive data read from file + * + * \return \herr_t + * + * \details H5Dread() reads a dataset, specified by its identifier + * \p dset_id, from the file into an application memory buffer \p + * buf. Data transfer properties are defined by the argument \p + * dxpl_id. The memory datatype of the (partial) dataset + * is identified by the identifier \p mem_type_id. The part + * of the dataset to read is defined by \p mem_space_id and \p + * file_space_id. + * + * \p file_space_id is used to specify only the selection within + * the file dataset's dataspace. Any dataspace specified in \p + * file_space_id is ignored by the library and the dataset's + * dataspace is always used. \p file_space_id can be the constant + * #H5S_ALL, which indicates that the entire file dataspace, + * as defined by the current dimensions of the dataset, is to + * be selected. + * + * \p mem_space_id is used to specify both the memory dataspace + * and the selection within that dataspace. \p mem_space_id can + * be the constant #H5S_ALL, in which case the file dataspace is + * used for the memory dataspace and the selection defined with \p + * file_space_id is used for the selection within that dataspace. + * + * If raw data storage space has not been allocated for the dataset + * and a fill value has been defined, the returned buffer \p buf + * is filled with the fill value. + * + * The behavior of the library for the various combinations of + * valid dataspace identifiers and #H5S_ALL for the \p mem_space_id + * and the \p file_space_id parameters is described below: + * + * <table> + * <tr> + * <th>mem_space_id</th> + * <th>file_space_id</th> + * <th>Behavior</th> + * </tr> + * <tr> + * <td>valid dataspace ID</td> + * <td>valid dataspace ID</td> + * <td>\p mem_space_id specifies the memory dataspace and the + * selection within it. \p file_space_id specifies the + * selection within the file dataset's dataspace.</td> + * </tr> + * <tr> + * <td>#H5S_ALL</td> + * <td>valid dataspace ID</td> + * <td>The file dataset's dataspace is used for the memory + * dataspace and the selection specified with \p file_space_id + * specifies the selection within it. The combination of the + * file dataset's dataspace and the selection from + * \p file_space_id is used for memory also.</td> + * </tr> + * <tr> + * <td>valid dataspace ID</td> + * <td>#H5S_ALL</td> + * <td>\p mem_space_id specifies the memory dataspace and the + * selection within it. The selection within the file + * dataset's dataspace is set to the "all" selection.</td> + * </tr> + * <tr> + * <td>#H5S_ALL</td> + * <td>#H5S_ALL</td> + * <td>The file dataset's dataspace is used for the memory + * dataspace and the selection within the memory dataspace + * is set to the "all" selection. The selection within the + * file dataset's dataspace is set to the "all" selection.</td> + * </tr> + * </table> + * + * \details Setting an #H5S_ALL selection indicates that the entire + * dataspace, as defined by the current dimensions of a dataspace, + * will be selected. The number of elements selected in the memory + * dataspace must match the number of elements selected in the + * file dataspace. + * + * \p dxpl_id can be the constant #H5P_DEFAULT, in which case the + * default data transfer properties are used. + * + */ H5_DLL herr_t H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, - hid_t plist_id, void *buf /*out*/); + hid_t dxpl_id, void *buf /*out*/); + H5_DLL herr_t H5Dread_async(const char *app_file, const char *app_func, unsigned app_line, hid_t dset_id, - hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, + hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id, void *buf /*out*/, hid_t es_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Writes raw data from a buffer to a dataset + * + * \param[in] dset_id Identifier of the dataset to read from + * \param[in] mem_type_id Identifier of the memory datatype + * \param[in] mem_space_id Identifier of the memory dataspace + * \param[in] file_space_id Identifier of the dataset's dataspace in the file + * \dxpl_id + * \param[out] buf Buffer with data to be written to the file + * + * \return \herr_t + * + * \details H5Dwrite() writes a (partial) dataset, specified by + * its identifier \p dset_id, from the application memory buffer \p + * buf into the file. Data transfer properties are defined by the + * argument \p dxpl_id. The memory datatype of the (partial) + * dataset is identified by the identifier \p mem_type_id. The + * part of the dataset to write is defined by \p mem_space_id + * and \p file_space_id. + * + * If \p mem_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. + * + * \p file_space_id is used to specify only the selection within + * the file dataset's dataspace. Any dataspace specified in \p + * file_space_id is ignored by the library and the dataset's + * dataspace is always used. \p file_space_id can be the constant + * #H5S_ALL, which indicates that the entire file dataspace, + * as defined by the current dimensions of the dataset, is to + * be selected. + * + * \p mem_space_id is used to specify both the memory dataspace + * and the selection within that dataspace. mem_space_id can be + * the constant #H5S_ALL, in which case the file dataspace is + * used for the memory dataspace and the selection defined with \p + * file_space_id is used for the selection within that dataspace. + * + * The behavior of the library for the various combinations of + * valid dataspace IDs and #H5S_ALL for the mem_space_id and + * thefile_space_id parameters is described below: + * + * <table> + * <tr><th>\c mem_space_id</th> + * <th>\c file_space_id</th> + * <th>Behavior</th></tr> + * <tr><td>valid dataspace ID</td> + * <td>valid dataspace ID</td> + * <td>\p mem_space_id specifies the memory dataspace and the + * selection within it. \p file_space_id specifies the + * selection within the file dataset's dataspace.</td></tr> + * <tr><td>#H5S_ALL</td> + * <td>valid dataspace ID</td> + * <td>The file dataset's dataspace is used for the memory + * dataspace and the selection specified with \p file_space_id + * specifies the selection within it. The combination of the + * file dataset's dataspace and the selection from \p + * file_space_id is used for memory also. valid dataspace + * ID</td></tr> + * <tr><td>valid dataspace ID</td> + * <td>#H5S_ALL</td> + * <td>\p mem_space_id specifies the memory dataspace and the + * selection within it. The selection within the file + * dataset's dataspace is set to "all" selection.</td></tr> + * <tr><td>#H5S_ALL</td> + * <td>#H5S_ALL</td> + * <td>The file dataset's dataspace is used for the memory + * dataspace and the selection within the memory dataspace is + * set to the "all" selection. The selection within the file + * dataset's dataspace is set to the "all" + * selection.</td></tr> + * </table> + * Setting an "all" selection indicates that the entire dataspace, + * as defined by the current dimensions of a dataspace, will + * be selected. The number of elements selected in the memory + * dataspace must match the number of elements selected in the + * file dataspace. + * + * \p dxpl_id can be the constant #H5P_DEFAULT, in which + * case the default data transfer properties are used. + * + * Writing to a dataset will fail if the HDF5 file was not opened + * with write access permissions. + * + * If the dataset's space allocation time is set to + * #H5D_ALLOC_TIME_LATE or #H5D_ALLOC_TIME_INCR and the space for + * the dataset has not yet been allocated, that space is allocated + * when the first raw data is written to the dataset. Unused space + * in the dataset will be written with fill values at the same + * time if the dataset's fill time is set to #H5D_FILL_TIME_IFSET + * or #H5D_FILL_TIME_ALLOC. + * + * \attention If a dataset's storage layout is 'compact', care must be + * taken when writing data to the dataset in parallel. A compact + * dataset's raw data is cached in memory and may be flushed + * to the file from any of the parallel processes, so parallel + * applications should always attempt to write identical data to + * the dataset from all processes. + * + * \see H5Pset_fill_time(), H5Pset_alloc_time() + * + */ H5_DLL herr_t H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, - hid_t plist_id, const void *buf); + hid_t dxpl_id, const void *buf); + H5_DLL herr_t H5Dwrite_async(const char *app_file, const char *app_func, unsigned app_line, hid_t dset_id, - hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, + hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id, const void *buf, hid_t es_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Writes a raw data chunk from a buffer directly to a dataset in a file + * + * \dset_id + * \dxpl_id + * \param[in] filters Mask for identifying the filters in use + * \param[in] offset Logical position of the chunk’s first element in the + * dataspace + * \param[in] data_size Size of the actual data to be written in bytes + * \param[in] buf Buffer containing data to be written to the chunk + * + * \return \herr_t + * + * \details H5Dwrite_chunk() writes a raw data chunk as specified + * by its logical offset \p offset in a chunked dataset \p dset_id + * from the application memory buffer \p buf to the dataset in + * the file. Typically, the data in \p buf is preprocessed in + * memory by a custom transformation, such as compression. The + * chunk will bypass the library’s internal data transfer + * pipeline, including filters, and will be written directly to + * the file. Only one chunk can be written with this function. + * + * H5Dwrite_chunk() replaces the now deprecated H5DOwrite_chunk() + * function, which was located in the high level optimization + * library. The parameters and behavior are identical to the + * original. + * + * \p filters is a mask providing a record of which filters are + * used with the the chunk. The default value of the mask is + * zero (0), indicating that all enabled filters are applied. A + * filter is skipped if the bit corresponding to the filter’s + * position in the pipeline (0 ≤ position < 32) is turned on. + * This mask is saved with the chunk in the file. + * + * \p offset is an array specifying the logical position of the + * first element of the chunk in the dataset’s dataspace. The + * length of the offset array must equal the number of dimensions, + * or rank, of the dataspace. The values in offset must not exceed + * the dimension limits and must specify a point that falls on + * a dataset chunk boundary. + * + * \p data_size is the size in bytes of the chunk, representing + * the number of bytes to be read from the buffer \p buf. If the + * data chunk has been precompressed, \p data_size should be the + * size of the compressed data. + * + * \p buf is the memory buffer containing data to be written to + * the chunk in the file. + * + * \attention Exercise caution when using H5Dread_chunk() and + * H5Dwrite_chunk(), as they read and write data chunks directly + * in a file. H5Dwrite_chunk() bypasses hyperslab selection, the + * conversion of data from one datatype to another, and the filter + * pipeline to write the chunk. Developers should have experience + * with these processes before using this function. Please see + * Using the Direct Chunk Write Function for more information. + * + * \note H5Dread_chunk() and H5Dwrite_chunk() are not supported under + * parallel and do not support variable length types. + * + * \since 1.10.2 + * + */ H5_DLL herr_t H5Dwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, size_t data_size, const void *buf); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Reads a raw data chunk directly from a dataset in a file into + * a buffer + * + * \dset_id + * \dxpl_id + * \param[in] offset Logical position of the chunk’s first element in the + * dataspace + * \param[in,out] filters Mask for identifying the filters in use + * \param[out] buf Buffer containing data to be written to the chunk + * + * \return \herr_t + * + * \details H5Dread_chunk() reads a raw data chunk as specified by + * its logical offset \p offset in a chunked dataset \p dset_id + * from the dataset in the file into the application memory + * buffer \p buf. The data in \p buf is read directly from the + * file bypassing the library’s internal data transfer pipeline, + * including filters. + * + * \p offset is an array specifying the logical position of the + * first element of the chunk in the dataset’s dataspace. The + * length of the \p offset array must equal the number of dimensions, + * or rank, of the dataspace. The values in \p offset must not exceed + * the dimension limits and must specify a point that falls on + * a dataset chunk boundary. + * + * The mask \p filters indicates which filters are used with the + * chunk when written. A zero value indicates that all enabled + * filters are applied on the chunk. A filter is skipped if the + * bit corresponding to the filter’s position in the pipeline + * (0 ≤ position < 32) is turned on. + * + * \p buf is the memory buffer containing the chunk read from + * the dataset in the file. + * + * \attention Exercise caution when using H5Dread_chunk() and + * H5Dwrite_chunk(), as they read and write data chunks directly + * in a file. H5Dwrite_chunk() bypasses hyperslab selection, the + * conversion of data from one datatype to another, and the filter + * pipeline to write the chunk. Developers should have experience + * with these processes before using this function. Please see + * Using the Direct Chunk Write Function for more information. + * + * \note H5Dread_chunk() and H5Dwrite_chunk() are not supported under + * parallel and do not support variable length types. + * + * \since 1.10.2 + * + */ H5_DLL herr_t H5Dread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters, void *buf); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Iterates over all selected elements in a dataspace + * + * \param[in,out] buf Buffer containing the elements to iterate over + * \type_id + * \space_id + * \param[in] op Function pointer + * \param[in,out] operator_data User-defined 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 H5Diterate() iterates over all the data elements + * in the memory buffer \p buf, executing the callback function + * \p op once for each such data element. + * + * The prototype of the callback function \p op is as follows + * (as defined in the source code file H5Lpublic.h): + * \snippet this H5D_operator_t_snip + * The parameters of this callback function are: + * + * <table> + * <tr><td>\c elem</td> + * <td><tt>[in,out]</tt></td> + * <td>Pointer to the memory buffer containing the current + * data element</td></tr> + * <tr><td>\c type_id</td> + * <td><tt>[in]</tt></td> + * <td>Datatype identifier of the elements stored in elem</td></tr> + * <tr><td>\c ndim</td> + * <td><tt>[in]</tt></td> + * <td>Number of dimensions for the point array</td></tr> + * <tr><td>\c point</td> + * <td><tt>[in]</tt></td> + * <td>Array containing the location of the element within + * the original dataspace</td></tr> + * <tr><td>\c operator_data</td> + * <td><tt>[in,out]</tt></td> + * <td>Pointer to any user-defined data associated with the + * operation</td></tr> + * </table> + * + * The possible return values from the callback function, and + * the effect ofeach,are as follows: + * + * \li Zero causes the iterator to continue, returning zero + * when all data elements have been processed. + * \li A positive value causes the iterator to immediately + * return that positive value, indicating short-circuit success. + * \li A negative value causes the iterator to immediately return + * that value, indicating failure. + * + * The \p operator_data parameter is a user-defined pointer to + * the data required to process dataset elements in the course + * of the iteration. If operator needs to pass data back to the + * application, such data can be returned in this same buffer. This + * pointer is passed back to each step of the iteration in the + * operator callback function’s operator_data parameter. + * + * Unlike other HDF5 iterators, this iteration operation cannot + * be restarted at the point of exit; a second H5Diterate() + * call will always restart at the beginning. + * + * + * \since 1.10.2 + * + */ H5_DLL herr_t H5Diterate(void *buf, hid_t type_id, hid_t space_id, H5D_operator_t op, void *operator_data); -H5_DLL herr_t H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id, hsize_t *size); -H5_DLL herr_t H5Dfill(const void *fill, hid_t fill_type, void *buf, hid_t buf_type, hid_t space); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Determines the number of bytes required to store variable-length + * (VL) data + * + * \dset_id + * \type_id + * \space_id + * \param[out] size Size in bytes of the memory buffer required to store + * the VL data + * + * \return \herr_t + * + * \details H5Dvlen_get_buf_size() determines the number of bytes + * required to store the VL data from the dataset, using \p + * space_id for the selection in the dataset on disk and the \p + * type_id for the memory representation of the VL data in memory. + * \p size is returned with the number of bytes required to store + * the VL data in memory. + * + * \since 1.10.2 + * + */ +H5_DLL herr_t H5Dvlen_get_buf_size(hid_t dset_id, hid_t type_id, hid_t space_id, hsize_t *size); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Fills dataspace elements with a fill value in a memory buffer + * + * \param[in] fill Pointer to the fill value to be used + * \param[in] fill_type_id Fill value datatype identifier + * \param[in,out] buf Pointer to the memory buffer containing the + * selection to be filled + * \param[in] buf_type_id Datatype of dataspace elements to be filled + * \space_id + * + * \return \herr_t + * + * \details H5Dfill() fills the dataspace selection in memory, \p space_id, + * with the fill value specified in \p fill. If \p fill is NULL, + * a fill value of 0 (zero) is used. + * + * \p fill_type_id specifies the datatype of the fill value. + * \p buf specifies the buffer in which the dataspace elements + * will be written. + * \p buf_type_id specifies the datatype of those data elements. + * + * \note Note that if the fill value datatype differs from the memory + * buffer datatype, the fill value will be converted to the memory + * buffer datatype before filling the selection. + * + * \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. See the following + * function for more information: + * - H5Pset_fill_value() + * - H5Pget_fill_value() + * - H5Pfill_value_defined() + * - H5Pset_fill_time() + * - H5Pget_fill_time() + * - H5Pcreate() + * - H5Pcreate_anon() + * + */ +H5_DLL herr_t H5Dfill(const void *fill, hid_t fill_type_id, void *buf, hid_t buf_type_id, hid_t space_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Changes the sizes of a dataset’s dimensions + * + * \dset_id + * \param[in] size[] Array containing the new magnitude of each dimension + * of the dataset + * + * \return \herr_t + * + * \details H5Dset_extent() sets the current dimensions of the + * chunked dataset \p dset_id to the sizes specified in size. + * + * \p size is a 1-dimensional array with n elements, where \p n is + * the rank of the dataset’s current dataspace. + * + * This function can be applied to the following datasets: + * - A chunked dataset with unlimited dimensions + * - A chunked dataset with fixed dimensions if the new dimension + * sizes are less than the maximum sizes set with maxdims (see + * H5Screate_simple()) + * - An external dataset with unlimited dimensions + * - An external dataset with fixed dimensions if the new dimension + * sizes are less than the maximum sizes set with \p maxdims + * + * Note that external datasets are always contiguous and can be + * extended only along the first dimension. + * + * Space on disk is immediately allocated for the new dataset extent if + * the dataset’s space allocation time is set to #H5D_ALLOC_TIME_EARLY. + * + * Fill values will be written to the dataset in either of the + * following situations, but not otherwise: + * + * - If the dataset’s fill time is set to #H5D_FILL_TIME_IFSET and a + * fill value is defined (see H5Pset_fill_time() and + * H5Pset_fill_value()) + * - If the dataset’s fill time is set to #H5D_FILL_TIME_ALLOC + * (see H5Pset_alloc_time()) + * + * \note + * \li If the sizes specified in \p size array are smaller than + * the dataset’s current dimension sizes, H5Dset_extent() will reduce + * the dataset’s dimension sizes to the specified values. It is the + * user application’s responsibility to ensure that valuable data is + * not lost as H5Dset_extent() does not check. + * + * \li Except for external datasets, H5Dset_extent() is for use with + * chunked datasets only, not contiguous datasets. + * + * \li A call to H5Dset_extent() affects the dataspace of a dataset. + * If a dataspace handle was opened for a dataset prior to a call to + * H5Dset_extent() then that dataspace handle will no longer reflect + * the correct dataspace extent of the dataset. H5Dget_space() must + * be called (after closing the previous handle) to obtain the current + * dataspace extent. + * + * \since 1.8.0 + * + */ H5_DLL herr_t H5Dset_extent(hid_t dset_id, const hsize_t size[]); H5_DLL herr_t H5Dset_extent_async(const char *app_file, const char *app_func, unsigned app_line, hid_t dset_id, const hsize_t size[], hid_t es_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Flushes all buffers associated with a dataset to disk + * + * \dset_id + * + * \return \herr_t + * + * \details H5Dflush() causes all buffers associated with a + * dataset to be immediately flushed to disk without removing + * the data from the cache. + * + * \note HDF5 does not possess full control over buffering. + * H5Dflush() 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. + * + */ H5_DLL herr_t H5Dflush(hid_t dset_id); + H5_DLL herr_t H5Dwait(hid_t dset_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Refreshes all buffers associated with a dataset + * + * \dset_id + * + * \return \herr_t + * + * \details H5Drefresh() causes all buffers associated with a + * dataset to be cleared and immediately re-loaded with updated + * contents from disk. + * + * This function essentially closes the dataset, evicts all + * metadata associated with it from the cache, and then re-opens + * the dataset. The reopened dataset is automatically re-registered + * with the same identifier. + * + * \since 1.10.2 + * + */ H5_DLL herr_t H5Drefresh(hid_t dset_id); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Scatters data into a selection within a memory buffer + * + * \param[in] op Callback function which provides data to be scattered + * \param[in] op_data User-defined pointer to data required by op + * \param[in] type_id Identifier for the datatype describing the data in + * both the source and destination buffers + * \param[in] dst_space_id Identifier for the dataspace for destination + * \param[out] dst_buf Destination buffer which the data will be scattered to + * + * \return \herr_t + * + * \details H5Dscatter() retrieves data from the supplied callback + * \p op and scatters it to the supplied buffer \p dst_buf in a + * manner similar to data being written to a dataset. + * + * \p dst_space_id is a dataspace which defines the extent of \p + * dst_buf and the selection within it to scatter the data to. + * + * \p type_id is the datatype of the data to be scattered in both + * the source and destination buffers. + * + * \p dst_buf must be at least as large as the number of elements + * in the extent of \p dst_space_id times the size in bytes of + * \p type_id. + * + * To retrieve the data to be scattered, H5Dscatter() repeatedly + * calls \p op, which should return a valid source buffer, until + * enough data to fill the selection has been retrieved. The + * prototype of the callback function \p op is as follows (as + * defined in the source code file H5Dpublic.h): + * \snippet this H5D_scatter_func_t_snip + * The parameters of this callback function are described below: + * + * <table> + * <tr><td>\c src_buf</td> + * <td><tt>[out]</tt></td> + * <td>Pointer to the buffer holding the next set of elements to + * scatter. On entry, the value of where \c src_buf points to + * is undefined. The callback function should set \c src_buf + * to point to the next set of elements.</td></tr> + * <tr><td>\c src_buf_bytes_used</td> + * <td><tt>[out]</tt></td> + * <td>Pointer to the number of valid bytes in \c src_buf. On + * entry, the value where \c src_buf_bytes_used points to is + * undefined. The callback function should set + * \c src_buf_bytes_used to the of valid bytes in \c src_buf. + * This number must be a multiple of the datatype size. + * </td></tr> + * <tr><td>\c op_data</td> + * <td><tt>[in,out]</tt></td> + * <td>User-defined pointer to data required by the callback + * function. A pass-through of the \c op_data pointer provided + * with the H5Dscatter() function call.</td></tr> + * </table> + * + * The callback function should always return at least one + * element in \p src_buf, and must not return more elements + * than are remaining to be scattered. This function will be + * repeatedly called until all elements to be scattered have + * been returned. The callback function should return zero (0) + * to indicate success, and a negative value to indicate failure. + * + * \since 1.10.2 + * + */ H5_DLL herr_t H5Dscatter(H5D_scatter_func_t op, void *op_data, hid_t type_id, hid_t dst_space_id, void *dst_buf); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Gathers data from a selection within a memory buffer + * raw data chunk in a dataset + * + * \param[in] src_space_id Dataspace identifier for the source buffer + * \param[in] src_buf Source buffer which the data will be gathered from + * \param[in] type_id Datatype identifier for the source + * \param[in] dst_buf_size Size in bytes of \p dst_buf + * \param[out] dst_buf Destination buffer for the gathered data + * \param[in] op Callback function which handles the gathered data + * \param[in] op_data User-defined pointer to data required by \p op + * + * \return \herr_t + * + * \details H5Dgather() retrieves data from a selection within the supplied + * buffer src_buf and passes it to the supplied callback function + * \p op in a contiguous form. + * + * The dataspace \p src_space_id describes both the dimensions of + * the source buffer and the selection within the source buffer + * to gather data from. + * + * \p src_buf must be at least the size of the gathered data, that + * is, the number of elements in the extent of \p src_space_id + * times the size in bytes of \p type_id. + * + * The datatype \p type_id describes the data in both the source + * and destination buffers. This information is used to calculate + * the element size. + * + * The data is gathered into \p dst_buf, which needs to be large + * enough to hold all the data if the callback function \p op is + * not provided. + * + * \p op is a callback function which handles the gathered data. + * It is optional if \p dst_buf is large enough to hold all of the + * gathered data; required otherwise. + * + * If no callback function is provided, H5Dgather() simply gathers + * the data into \p dst_buf and returns. If a callback function is + * provided, H5Dgather() repeatedly gathers up to \p dst_buf_size + * bytes to process the serialized data. The prototype of the + * callback function \p op is as follows (as defined in the source + * code file H5Dpublic.h): + * \snippet this H5D_gather_func_t_snip + * The parameters of this callback function are described in the + * table below. + * <table> + * <tr><td>\c dst_buf</td> + * <td>Pointer to the destination buffer which has been filled + * with the next set of elements gathered. This will always be + * identical to the \p dst_buf passed to H5Dgather().</td></tr> + * <tr><td>\c dst_buf_bytes_used</td> + * <td>Pointer to the number of valid bytes in \p dst_buf. + * This number must be a multiple of the datatype + * size.</td></tr> + * <tr><td>\c op_data</td> + * <td>User-defined pointer to data required by the callback + * function; a pass-through of the \p op_data pointer + * provided with the H5Dgather() function call.</td></tr> + * </table> + * The callback function should process, store, or otherwise, + * make use of the data returned in \p dst_buf before it returns, + * because the buffer will be overwritten unless it is the last + * call to the callback. This function will be repeatedly called + * until all gathered elements have been passed to the callback + * in \p dst_buf. The callback function should return zero (0) + * to indicate success, and a negative value to indicate failure. + * + * \since 1.10.2 + * + */ H5_DLL herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id, size_t dst_buf_size, void *dst_buf, H5D_gather_func_t op, void *op_data); + +/** + * -------------------------------------------------------------------------- + * \ingroup H5D + * + * \brief Closes the specified dataset + * + * \dset_id + * + * \return \herr_t + * + * \details H5Dclose() ends access to a dataset specified by \p dset_id + * and releases resources used by it. + * + * \attention Further use of a released dataset identifier is illegal; a + * function using such an identifier will generate an error. + * + * \since 1.8.0 + * + * \see H5Dcreate2(), H5Dopen2() + * + */ H5_DLL herr_t H5Dclose(hid_t dset_id); H5_DLL herr_t H5Dclose_async(const char *app_file, const char *app_func, unsigned app_line, hid_t dset_id, hid_t es_id); @@ -236,10 +1465,10 @@ H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type); /* Typedefs */ /* Function prototypes */ -H5_DLL hid_t H5Dcreate1(hid_t file_id, const char *name, hid_t type_id, hid_t space_id, hid_t dcpl_id); -H5_DLL hid_t H5Dopen1(hid_t file_id, const char *name); +H5_DLL hid_t H5Dcreate1(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id, hid_t dcpl_id); +H5_DLL hid_t H5Dopen1(hid_t loc_id, const char *name); H5_DLL herr_t H5Dextend(hid_t dset_id, const hsize_t size[]); -H5_DLL herr_t H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf); +H5_DLL herr_t H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t dxpl_id, void *buf); #endif /* H5_NO_DEPRECATED_SYMBOLS */ diff --git a/src/H5Gmodule.h b/src/H5Gmodule.h index 5f06405..ed617ec 100644 --- a/src/H5Gmodule.h +++ b/src/H5Gmodule.h @@ -29,4 +29,11 @@ #define H5_MY_PKG_ERR H5E_SYM #define H5_MY_PKG_INIT YES +/** + * \defgroup H5G H5G + * \brief Group Interface + * \details The HDF5 Group Interface, H5G, provides a mechanism for managing + * HDF5 groups and their members, which are other HDF5 objects. + */ + #endif /* _H5Gmodule_H */ diff --git a/src/H5Gpublic.h b/src/H5Gpublic.h index f209c3d..e46bef6 100644 --- a/src/H5Gpublic.h +++ b/src/H5Gpublic.h @@ -51,12 +51,15 @@ typedef enum H5G_storage_type_t { } H5G_storage_type_t; /* Information struct for group (for H5Gget_info/H5Gget_info_by_name/H5Gget_info_by_idx) */ +//! [H5G_info_t_snip] typedef struct H5G_info_t { H5G_storage_type_t storage_type; /* Type of storage for links in group */ hsize_t nlinks; /* Number of links in group */ int64_t max_corder; /* Current max. creation order value for group */ hbool_t mounted; /* Whether group has a file mounted on it */ } H5G_info_t; +//! [H5G_info_t_snip] + /********************/ /* Public Variables */ @@ -69,29 +72,355 @@ typedef struct H5G_info_t { extern "C" { #endif +/** + *------------------------------------------------------------------------- + * \ingroup H5G + * + * \brief Creates a new group and links it into the file + * + * \fgdta_loc_id + * \param[in] name Name of the group to create + * \lcpl_id + * \gcpl_id + * \gapl_id + * + * \return \hid_t{group} + * + * \details H5Gcreate2() creates a new group in a file. After a + * group has been created, links to datasets and to other groups + * can be added. + * + * The \p loc_id and \p name parameters specify where the group + * is located. \p loc_id may be a file, group, dataset, named + * datatype or attribute in the file. If an attribute, dataset, + * or named datatype is specified for \p loc_id then the group + * will be created at the location where the attribute, dataset, + * or named datatype is attached. \p name is the link to the group; + * \p name may be either an absolute path in the file (the links + * from the root group to the new group) or a relative path from + * \p loc_id (the link(s) from the group specified by \p loc_id + * to the new group). + * + * \p lcpl_id, \p gcpl_id, and \p gapl_id are property list + * identifiers. These property lists govern how the link to the + * group is created, how the group is created, and how the group + * can be accessed in the future, respectively. #H5P_DEFAULT can + * be passed in if the default properties are appropriate for + * these property lists. Currently, there are no APIs for the + * group access property list; use #H5P_DEFAULT. + * + * The group identifier should be closed by H5Gclose() when access + * is no longer required to prevent resource leaks. + * + * \since 1.8.0 + * + * \see H5Gopen2(), H5Gclose() + * + */ H5_DLL hid_t H5Gcreate2(hid_t loc_id, const char *name, hid_t lcpl_id, hid_t gcpl_id, hid_t gapl_id); H5_DLL hid_t H5Gcreate_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id, const char *name, hid_t lcpl_id, hid_t gcpl_id, hid_t gapl_id, hid_t es_id); + +/** + *------------------------------------------------------------------------- + * \ingroup H5G + * + * \brief Creates a new empty group without linking it into the file structure + * + * \fgdta_loc_id + * \gcpl_id + * \gapl_id + * + * \return \hid_t{group} + * + * \details H5Gcreate_anon() creates a new empty group in the file + * specified by \p loc_id. With default settings, H5Gcreate_anon() + * provides similar functionality to that provided by + * H5Gcreate1(), with the differences described in the list below. + * + * The new group’s creation and access properties are specified + * in \p gcpl_id and \p gapl_id, respectively. + * + * H5Gcreate_anon() returns a new group identifier. This identifier + * 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 H5Gcreate1() are + * as follows: + * + * \li H5Gcreate1() does not provide for the use of custom property + * lists; H5Gcreate1() always uses default properties. + * \li H5Gcreate_anon() neither provides the new group’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. + * \li H5Gcreate_anon() does not directly provide a hint mechanism + * for the group’s heap size. Comparable information can be + * included in the group creation property list \p gcpl_id through + * a H5Pset_local_heap_size_hint() call. + * + * A group created with this function should be closed with + * H5Gclose() when the group is no longer needed so that resource + * leaks will not develop. + * + * \see H5Olink(), H5Dcreate(), Using Identifiers + * + * \since 1.8.0 + * + */ H5_DLL hid_t H5Gcreate_anon(hid_t loc_id, hid_t gcpl_id, hid_t gapl_id); + +/** + *------------------------------------------------------------------------- + * \ingroup H5G + * + * \brief Opens an existing group in a file + * + * \fgdta_loc_id + * \param[in] name Name of the group to open + * \gapl_id + * + * \return \hid_t{group} + * + * \details H5Gopen2() opens an existing group, \p name, at the location + * specified by \p loc_id. + * + * With default settings, H5Gopen2() provides similar functionality + * to that provided by H5Gopen(). The only difference is that + * H5Gopen2() can provide a group access property list, \p gapl_id. + * + * H5Gopen2() returns a group identifier for the group that was + * opened. This group identifier should be released by H5Gclose() + * when it is no longer needed to prevent resource leaks. + * + * \since 1.8.0 + * + * \see H5Gcreate2(), H5Gclose() + * + */ H5_DLL hid_t H5Gopen2(hid_t loc_id, const char *name, hid_t gapl_id); H5_DLL hid_t H5Gopen_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id, const char *name, hid_t gapl_id, hid_t es_id); + +/** + *------------------------------------------------------------------------- + * \ingroup H5G + * + * \brief Gets a group creation property list identifier + * + * \group_id + * + * \return \hid_t{creation property list} + * + * \details H5Gget_create_plist() returns an identifier for the group creation + * property list associated with the group specified by \p group_id. + * + * The creation property list identifier should be released with + * H5Gclose() to prevent resource leaks. + * + * \since 1.8.0 + * + * \see H5Gcreate2(), H5Gclose() + * + */ H5_DLL hid_t H5Gget_create_plist(hid_t group_id); + +/** + *------------------------------------------------------------------------- + * \ingroup H5G + * + * \brief Retrieves information about a group + * + * \fgdta_loc_id + * \param[out] ginfo Struct in which group information is returned + * + * \return \hid_t{group} + * + * \details H5Gget_info() retrieves information about the group at location + * specified by \p loc_id. The information is returned in the \p ginfo. + * + * \p ginfo is an H5G_info_t struct and is defined (in H5Gpublic.h) + * as follows: + * + * \snippet this H5G_info_t_snip + * Possible values of \p storage_type are: + * \storage_type + * + * \since 1.8.0 + * + * \see H5Gcreate2(), H5Gclose() + * + */ H5_DLL herr_t H5Gget_info(hid_t loc_id, H5G_info_t *ginfo); + H5_DLL herr_t H5Gget_info_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id, H5G_info_t *group_info /*out*/, hid_t es_id); + +/** + *------------------------------------------------------------------------- + * \ingroup H5G + * + * \brief Retrieves information about a group by its name + * + * \fgdta_loc_id + * \param[in] name Name of the group to query + * \param[out] ginfo Struct in which group information is returned + * \lapl_id + * + * \return \herr_t + * + * \details H5Gget_info_by_name() retrieves information about the group \p name + * at location specified by \p loc_id. The information is returned in + * the \p ginfo struct. + * + * If \p loc_id specifies the group for which information is queried, + * then the group's \p name can be a dot (.). + * + * \p ginfo is an H5G_info_t struct and is defined (in H5Gpublic.h) + * as follows: + * + * \snippet this H5G_info_t_snip + * Possible values of \p storage_type are: + * \storage_type + * + * \since 1.8.0 + * + * \see H5Gcreate2(), H5Gclose() + * + */ H5_DLL herr_t H5Gget_info_by_name(hid_t loc_id, const char *name, H5G_info_t *ginfo, hid_t lapl_id); H5_DLL herr_t H5Gget_info_by_name_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id, const char *name, H5G_info_t *group_info /*out*/, hid_t lapl_id, hid_t es_id); + +/** + *------------------------------------------------------------------------- + * \ingroup H5G + * + * \brief Retrieves information about a group, according to the group’s + * position within an index + * + * \fgdta_loc_id + * \param[in] group_name Name of the group to query + * \param[in] idx_type Transient index identifying object + * \param[in] order Transient index identifying object + * \param[in] n Position in the index of the group to query + * \param[out] ginfo Struct in which group information is returned + * \lapl_id + * + * \return Returns + * \li The size of the object name if successful, or + * \li 0 if no name is associated with the group identifier, or + * \li negative value, if failure occurred + * + * \details H5Gget_info_by_idx() retrieves the same information + * about a group as retrieved by the function H5Gget_info(), + * but the means of identifying the group differs; the group is + * identified by position in an index rather than by name. + * + * \p loc_id and \p group_name specify the group containing + * the group for which information is sought. The groups in \p + * group_name are indexed by \p idx_type; the group for which + * information is retrieved is identified in that index by index + * order, \p order, and index position, \p n. + * + * If \p loc_id specifies the group containing the group for + * which information is queried, \p group_name can be a dot (.). + * + * Valid values for \p index_type are as follows: + * \indexes + * The order in which the index is to be examined, as specified + * by \p order, can be one of the following: + * \orders + * + * \since 1.8.0 + * + * \see H5Gcreate2(), H5Gclose() + * + */ H5_DLL herr_t H5Gget_info_by_idx(hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, H5G_info_t *ginfo, hid_t lapl_id); H5_DLL herr_t H5Gget_info_by_idx_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id, const char *group_name, H5_index_t idx_type, H5_iter_order_t order, hsize_t n, H5G_info_t *group_info /*out*/, hid_t lapl_id, hid_t es_id); + +/** + *------------------------------------------------------------------------- + * \ingroup H5G + * + * \brief Flushes all buffers associated with a group to disk + * + * \group_id + * + * \return \herr_t + * + * \details H5Gflush() causes all buffers associated with a group to be + * immediately flushed to disk without removing the data from + * the cache. + * + * \attention + * HDF5 does not possess full control over buffering. H5G_FLUSH + * 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. + * + * \since 1.8.0 + * + * \see H5Gcreate2(), H5Gclose() + * + */ H5_DLL herr_t H5Gflush(hid_t group_id); + +/** + *------------------------------------------------------------------------- + * \ingroup H5G + * + * \brief Refreshes all buffers associated with a group + * + * \group_id + * + * \return \herr_t + * + * \details H5Grefresh() causes all buffers associated with a group to be + * cleared and immediately re-loaded with updated contents from disk. + * + * This function essentially closes the group, evicts all + * metadata associated with it from the cache, and then re-opens + * the group. The reopened group is automatically re-registered + * with the same identifier. + * + * \since 1.8.0 + * + * \see H5Gcreate2(), H5Gclose() + * + */ H5_DLL herr_t H5Grefresh(hid_t group_id); + +/** + *------------------------------------------------------------------------- + * \ingroup H5G + * + * \brief Closes the specified group + * + * \group_id + * + * \return \herr_t + * + * \details H5Gclose() releases resources used by a group which was + * opened by H5Gcreate() or H5Gopen(). After closing a group, + * \p group_id cannot be used again until another H5Gcreate() + * or H5Gopen() is called on it. + * + * Failure to release a group with this call will result in + * resource leaks. + * + * \since 1.0.0 + * + * \version 1.4.0 Fortran function introduced in this release + * + */ H5_DLL herr_t H5Gclose(hid_t group_id); H5_DLL herr_t H5Gclose_async(const char *app_file, const char *app_func, unsigned app_line, hid_t group_id, hid_t es_id); @@ -160,10 +489,13 @@ typedef enum H5G_obj_t { H5G_RESERVED_7 /* Reserved for future use */ } H5G_obj_t; -/* Prototype for H5Giterate() operator */ +/** Define the operator function pointer for for H5Giterate() */ +//! [H5G_iterate_t_snip] typedef herr_t (*H5G_iterate_t)(hid_t group, const char *name, void *op_data); +//! [H5G_iterate_t_snip] -/* Information about an object */ +/** Information about an object */ +//! [H5G_stat_t_snip] typedef struct H5G_stat_t { unsigned long fileno[2]; /*file number */ unsigned long objno[2]; /*object number */ @@ -173,6 +505,7 @@ typedef struct H5G_stat_t { size_t linklen; /*symbolic link value length */ H5O_stat_t ohdr; /* Object header information */ } H5G_stat_t; +//! [H5G_stat_t_snip] /* Function prototypes */ H5_DLL hid_t H5Gcreate1(hid_t loc_id, const char *name, size_t size_hint); |