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-rw-r--r--src/H5Dmodule.h11
-rw-r--r--src/H5Dpublic.h1261
-rw-r--r--src/H5Gmodule.h7
-rw-r--r--src/H5Gpublic.h337
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);