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/** \defgroup H5LR Extensions
*
* <em>Working with region references, hyperslab selections,
* and bit-fields (H5LR, H5LT)</em>
*
* The following reference manual entries describe high-level HDF5 C and Fortran APIs
* for working with region references, hyperslab selections, and bit-fields.
* These functions were created as part of a project supporting
* NPP/NPOESS Data Production and Exploitation (
* <a href="https://support.hdfgroup.org/projects/jpss/documentation">
* project</a>, <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source">
* software </a>).
* While they were written to facilitate access to NPP, NPOESS, and JPSS
* data in the HDF5 format, these functions may be useful to anyone working
* with region references, hyperslab selections, or bit-fields.
*
* Note that these functions are not part of the standard HDF5 distribution;
* the <a href="https://gamma.hdfgroup.org/ftp/pub/outgoing/NPOESS/source">
* software </a>
* must be separately downloaded and installed.
*
* A comprehensive guide to this library,
* <a href="https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf">
* <em>User Guide to the HDF5 High-level Library for Handling Region References and Hyperslab Selections</em></a>
* is available at
* https://support.hdfgroup.org/projects/jpss/documentation/HL/UG/NPOESS_HL-UG.pdf.
*
* - \ref H5LRcopy_reference
* \n Copies data from the specified dataset to a new location and creates a reference to it.
* - \ref H5LRcopy_region
* \n Copies data from a referenced region to a region in a destination dataset.
* - \ref H5LRcreate_ref_to_all
* \n Creates a dataset with the region references to the data in all datasets located under a
* specified group in a file or creates a dataset with object references to all objects (groups or datasets)
* located under a specified group in a file.
* - \ref H5LRcreate_region_references
* \n Creates an array of region references using an array of paths to
* datasets and an array of corresponding hyperslab descriptions.
* - \ref H5LRget_region_info
* \n Retrieves information about the data a region reference points to.
* - \ref H5LRmake_dataset
* \n Creates and writes a dataset containing a list of region references.
* - \ref H5LRread_region
* \n Retrieves raw data pointed to by a region reference to an application buffer.
* - \ref H5LTcopy_region
* \n Copies data from a specified region in a source dataset to a specified region in a destination dataset.
* - \ref H5LTread_bitfield_value
* \n Retrieves the values of quality flags for each element to the application provided buffer.
* - \ref H5LTread_region
* \n Reads selected data to an application buffer.
*
*/
/*-------------------------------------------------------------------------
*
* Make dataset functions
*
*-------------------------------------------------------------------------
*/
/**
* --------------------------------------------------------------------------
* \ingroup H5LR
*
* \brief Creates and writes a dataset containing a list of region references.
*
* \fgdta_loc_id
* \param[in] path Path to the dataset being created
* \param[in] type_id Datatype of the dataset
* \param[in] buf_size Size of the \p loc_id_ref and \p buf arrays
* \param[in] loc_id_ref Array of object identifiers; each identifier
* describes to which HDF5 file the corresponding
* region reference belongs to
* \param[in] buf Array of region references
*
* \return \herr_t
*
* \details Given an array of size \p buf_size of region references \p buf,
* the function will create a dataset with path \p path, at location
* specified by \p loc_id and of a datatype specified by \p type_id,
* and will write data associated with each region reference in the order
* corresponding to the order of the region references in the buffer.
* It is assumed that all referenced hyperslabs have the same dimensionality,
* and only the size of the slowest changing dimension may differ.
* Each reference in the \p buf array belongs to the file identified
* by the corresponding object identifiers in the array \p loc_id_ref.
*
* If \p path does not exist in \p loc_id then the function will
* create the path specified by \p path automatically.
*
* \version 1.1 Fortran wrapper introduced in this release.
*
* \since 1.0
*
*/
H5_HLRDLL herr_t H5LRmake_dataset(hid_t loc_id,
const char *path,
hid_t type_id, const size_t buf_size,
const hid_t *loc_id_ref,
const hdset_reg_ref_t *buf);
/*-------------------------------------------------------------------------
*
* Make and manipulate dataset region references functions
*
*-------------------------------------------------------------------------
*/
/**
* --------------------------------------------------------------------------
* \ingroup H5LR
*
* \brief Creates an array of region references using an array of paths to
* datasets and an array of corresponding hyperslab descriptions.
*
* \param[in] obj_id File identifier for the HDF5 file containing
* the referenced regions or an object identifier
* for any object in that file
* \param[in] num_elem Number of elements in the \p path and \p buf arrays
* \param[in] path Array of pointers to strings, which contain
* the paths to the target datasets for the region references
* \param[in] block_coord Array of hyperslab coordinate
* \param[out] buf Buffer for returning an array of region references
*
* \return \herr_t
*
* \note **Motivation:**
* \note H5LRcreate_region_references() is useful when creating
* large numbers of similar region references.
*
* \details H5LRcreate_region_references() creates a list of region references
* given an array of paths to datasets and another array listing the
* corner coordinates of the corresponding hyperslabs.
*
* \p path parameter is an array of pointers to strings.
*
* \p num_elem specifies the number of region references to be created,
* thus specifying the size of the \p path and \p _buf arrays.
*
* Buffer \p block_coord has size 2*rank and is the coordinates of the
* starting point following by the coordinates of the ending point of
* the hyperslab, repeated \p num_elem times for each hyperslab.
* For example, creating two region references to two hyperslabs,
* one with a rectangular hyperslab region starting at element (2,2)
* to element (5,4) and the second rectangular region starting at
* element (7,7) to element (9,10), results in \p block_coord
* being {2,2,5,4, 7,7,9,10}.
*
* The rank of the hyperslab will be the same as the rank of the
* target dataset. H5LRcreate_region_references() will retrieve
* the rank for each dataset and will use those values to interpret
* the values in the buffer. Please note that rank may vary from one
* dataset to another.
*
* \version 1.1 Fortran wrapper introduced in this release.
*
* \since 1.0
*
*/
H5_HLRDLL herr_t H5LRcreate_region_references(hid_t obj_id,
size_t num_elem,
const char **path,
const hsize_t *block_coord,
hdset_reg_ref_t *buf);
/**
* --------------------------------------------------------------------------
* \ingroup H5LR
*
* \brief Copies data from the specified dataset to a new location and creates a reference to it.
*
* \param[in] obj_id Identifier of any object in a file an HDF5 reference belongs to
* \param[in] ref Reference to the datasets region
* \param[in] file Name of the destination file
* \param[in] path Full path to the destination dataset
* \param[in] block_coord Hyperslab coordinates in the destination dataset
* \param[out] ref_new Region reference to the new location of data
*
* \return \herr_t
*
* \details Given a data set pointed to by a region reference, the function
* H5LRcopy_reference() will copy the hyperslab data referenced by
* a datasets region reference into existing dataset specified by
* its path \p path in the file with the name \p file, and to location
* specified by the hyperslab coordinates \p block_coord. It will
* create the region reference \p ref_new to point to the new location.
* The number of elements in the old and newly specified regions has
* to be the same.
*
* Buffer \p block_coord has size 2*rank and is the coordinates of
* the starting point following by the coordinates of the ending
* point of the hyperslab. For example, to extract a rectangular
* hyperslab region starting at element (2,2) to element (5,4)
* then \p block_coord would be {2, 2, 5, 4}.
*
* \version 1.1 Fortran wrapper introduced in this release.
*
* \since 1.0
*
*/
H5_HLRDLL herr_t H5LRcopy_reference(hid_t obj_id, hdset_reg_ref_t *ref, const char *file,
const char *path, const hsize_t *block_coord,
hdset_reg_ref_t *ref_new);
/**
* --------------------------------------------------------------------------
* \ingroup H5LR
*
* \brief Copies data from a referenced region to a region in a destination dataset.
*
* \param[in] obj_id Identifier of any object in a file
* dataset region reference belongs to
* \param[in] ref Dataset region reference
* \param[in] file Name of the destination file
* \param[in] path Full path to the destination dataset
* \param[in] block_coord Hyperslab coordinates in the destination dataset
*
* \return \herr_t
*
* \details Given a dataset region reference \p ref in a source file
* specified by an identifier of any object in that file
* \p obj_id, the function will write data to the existing
* dataset \p path in file \p file to the simple hyperslab
* specified by \p block_coord.
*
* Buffer \p block_coord has size 2*rank and is the coordinates
* of the starting point following by the coordinates of the
* ending point of the hyperslab. For example, to specify a
* rectangular hyperslab destination region starting at element
* (2,2) to element (5,4) then \p block_coord would be {2, 2, 5, 4}.
*
* If \p path does not exist in the destination file (as may be
* the case when writing to a new file) then the dataset will be
* copied directly to the \p path and \p block_coord will be
* disregarded.
*
* \version 1.1 Fortran wrapper introduced in this release.
*
* \since 1.0
*
*/
H5_HLRDLL herr_t H5LRcopy_region(hid_t obj_id,
hdset_reg_ref_t *ref,
const char *file,
const char *path,
const hsize_t *block_coord);
/**
* --------------------------------------------------------------------------
* \ingroup H5LR
*
* \brief Creates a dataset with the region references to the data
* in all datasets located under a specified group in a file
* or creates a dataset with object references to all objects
* (groups or datasets) located under a specified group in a file.
*
* \fg_loc_id
* \param[in] group_path Absolute or relative path to the group at which traversal starts
* \param[in] ds_path Absolute or relative path to the dataset with region references to be created
* \param[in] index_type Index_type; see valid values below in description
* \param[in] order Order in which index is traversed; see valid values below in description
* \param[in] ref_type Reference type; see valid values below in description
*
* \return \herr_t
*
* \details H5LRcreate_ref_to_all() creates a dataset with the
* region references to the data in all datasets located
* under a specified group in a file or creates a dataset with
* object references to all objects (groups or datasets) located
* under a specified group in a file.
*
* Given a dataset path \p ds_path in a file specified by the
* \p loc_id identifier, the function H5LRcreate_ref_to_all()
* will create a contiguous one-dimensional dataset with the
* region references or object references depending on the value
* of the \p ref_type parameter. When \p ref_type is
* #H5R_DATASET_REGION, each region reference points to all data
* in a dataset encountered by an internally called H5Lvisit()
* routine, which starts at the group specified by the \p loc_id
* and \p group_path parameters. In a like manner, when
* \p ref_type is #H5R_OBJECT, each object reference points to
* an object (a group or a dataset) encountered by H5Lvisit().
*
* If \p ds_path does not exist in \p loc_id then the function
* will create the path specified by \p ds_path automatically.
*
* \p index_type specifies the index to be used.
* Valid values include the following:
* - #H5_INDEX_NAME Alphanumeric index on name
* - #H5_INDEX_CRT_ORDER Index on creation order
*
* \p order specifies the order in which objects are to be
* inspected along the index specified in \p index_type.
* Valid values include the following:
* - #H5_ITER_INC Increasing order
* - #H5_ITER_DEC Decreasing order
* - #H5_ITER_NATIVE Fastest available order
*
* For more detailed information on these two parameters,
* @see H5Lvisit().
*
* \p ref_type specifies the type of the reference to be used.
* Valid values include the following:
* - #H5R_DATASET_REGION Dataset region reference
* - #H5R_OBJECT Object reference
*
* \version 1.1 Fortran wrapper introduced in this release.
*
* \since 1.0
*
*/
H5_HLRDLL herr_t H5LRcreate_ref_to_all(hid_t loc_id, const char *group_path,
const char *ds_path, H5_index_t index_type, H5_iter_order_t order, H5R_type_t ref_type);
/*-------------------------------------------------------------------------
*
* Read dataset functions
*
*-------------------------------------------------------------------------
*/
/**
* --------------------------------------------------------------------------
* \ingroup H5LR
*
* \brief Retrieves raw data pointed to by a region reference
* to an application buffer.
*
* \param[in] obj_id File identifier for the HDF5 file containing
* the dataset with the referenced region or an
* object identifier for any object in that file
* \param[in] ref Region reference specifying data to be read in
* \param[in] mem_type Memory datatype of data read from referenced
* region into the application buffer
* \param[in,out] numelem Number of elements to be read into buffer \p buf
* \param[out] buf Buffer in which data is returned to the application
*
* \return \herr_t
*
* \details H5LRread_region() reads data pointed to by the region
* reference \p ref into the buffer \p buf.
*
* \p numelem specifies the number of elements to be read
* into \p buf. When the size of the reference region is unknown,
* H5LRread_region() can be called with \p buf set to NULL;
* the number of elements in the referenced region will be returned
* in \p numelem.
*
* The buffer buf must be big enough to hold \p numelem elements
* of type \p mem_type. For example, if data is read from the referenced
* region into an integer buffer, \p mem_type should be #H5T_NATIVE_INT
* and the buffer must be at least \c sizeof(int) * \p numelem bytes
* in size. This buffer must be allocated by the application.
*
* \version 1.1 Fortran wrapper introduced in this release.
*
* \since 1.0
*
*/
H5_HLRDLL herr_t H5LRread_region(hid_t obj_id,
const hdset_reg_ref_t *ref,
hid_t mem_type,
size_t *numelem,
void *buf );
/*-------------------------------------------------------------------------
*
* Query dataset functions
*
*-------------------------------------------------------------------------
*/
/**
* --------------------------------------------------------------------------
* \ingroup H5LR
*
* \brief Retrieves information about the data a region reference points to.
*
* \param[in] obj_id Identifier of any object in an HDF5 file the region reference belongs to.
* \param[in] ref Region reference to query
* \param[in,out] len Size of the buffer to store \p path in.
* NOTE: if \p *path is not NULL then \p *len must be the appropriate length
* \param[out] path Full path that a region reference points to
* \param[out] rank The number of dimensions of the dataset
* dimensions of the dataset pointed by region reference.
* \param[out] dtype Datatype of the dataset pointed by the region reference.
* \param[out] sel_type Type of the selection (point or hyperslab)
* \param[in,out] numelem Number of coordinate blocks or selected elements.
* \param[out] buf Buffer containing description of the region pointed by region reference
*
* \return \herr_t
*
* \details H5LRget_region_info() queries information about the data
* pointed by a region reference \p ref. It returns one of the
* absolute paths to a dataset, length of the path, dataset’s rank
* and datatype, description of the referenced region and type of
* the referenced region. Any output argument can be NULL if that
* argument does not need to be returned.
*
* The parameter \p obj_id is an identifier for any object in the
* HDF5 file containing the referenced object. For example, it can
* be an identifier of a dataset the region reference belongs to
* or an identifier of an HDF5 file the dataset with region references
* is stored in.
*
* The parameter \p ref is a region reference to query.
*
* The parameter \p path is a pointer to application allocated
* buffer of size \p len+1 to return an absolute path to a dataset
* the region reference points to.
*
* The parameter \p len is a length of absolute path string plus
* the \0 string terminator. If path parameter is NULL, actual
* length of the path (+1 for \0 string terminator) is returned to
* application and can be used to allocate buffer path of an
* appropriate length \p len.
*
* The parameter \p sel_type describes the type of the selected
* region. Possible values can be #H5S_SEL_POINTS for point
* selection and #H5S_SEL_HYPERSLABS for hyperslab selection.
*
* The parameter \p numelem describes how many elements will be
* placed in the buffer \p buf. The number should be interpreted
* using the value of \p sel_type.
*
* If value of \p sel_type is #H5S_SEL_HYPERSLABS, the parameter
* \p buf contains \p numelem blocks of the coordinates for each
* simple hyperslab of the referenced region. Each block has
* length \c 2*\p rank and is organized as follows: <"start" coordinate>,
* immediately followed by <"opposite" corner coordinate>.
* The total size of the buffer to hold the description of the
* region will be \c 2*\p rank*\p numelem. If region reference
* points to a contiguous sub-array, then the value of \p numelem
* is 1 and the block contains coordinates of the upper left and
* lower right corners of the sub-array (or simple hyperslab).
*
* If value of \p sel_type is #H5S_SEL_POINTS, the parameter \p buf
* contains \p numelem blocks of the coordinates for each selected
* point of the referenced region. Each block has length \p rank
* and contains coordinates of the element. The total size of the
* buffer to hold the description of the region will be
* \p rank* \p numelem.
*
*
* \version 1.1 Fortran wrapper introduced in this release.
*
* \since 1.0
*
*/
H5_HLRDLL herr_t H5LRget_region_info(hid_t obj_id,
const hdset_reg_ref_t *ref,
size_t *len,
char *path,
int *rank,
hid_t *dtype,
H5S_sel_type *sel_type,
size_t *numelem,
hsize_t *buf );
/*-------------------------------------------------------------------------
*
* Make dataset functions
*
*-------------------------------------------------------------------------
*/
/**
* --------------------------------------------------------------------------
* \ingroup H5LR
*
* \brief Copies data from a specified region in a source dataset
* to a specified region in a destination dataset
*
* \param[in] file_src Name of the source file
* \param[in] path_src Full path to the source dataset
* \param[in] block_coord_src Hyperslab coordinates in the source dataset
* \param[in] file_dest Name of the destination file
* \param[in] path_dest Full path to the destination dataset
* \param[in] block_coord_dset Hyperslab coordinates in the destination dataset
*
* \return \herr_t
*
* \details Given a path to a dataset \p path_src in a file with the
* name \p file_src, and description of a simple hyperslab of
* the source \p block_coord_src, the function will write data
* to the dataset \p path_dest in file \p file_dest to the
* simple hyperslab specified by \p block_coord_dset.
* The arrays \p block_coord_src and \p block_coord_dset have
* a length of 2*rank and are the coordinates of the starting
* point following by the coordinates of the ending point of the
* hyperslab. For example, to specify a rectangular hyperslab
* destination region starting at element (2,2) to element (5,4)
* then \p block_coord_dset would be {2, 2, 5, 4}.
*
* If \p path_dest does not exist in the destination file
* (as may be the case when writing to a new file) then the
* dataset will be copied directly to the \p path_dest and
* \p block_coord_dset will be disregarded.
*
* \version 1.1 Fortran wrapper introduced in this release.
*
* \since 1.0
*
*/
H5_HLRDLL herr_t H5LTcopy_region(const char *file_src,
const char *path_src,
const hsize_t *block_coord_src,
const char *file_dest,
const char *path_dest,
const hsize_t *block_coord_dset);
/*-------------------------------------------------------------------------
*
* Read dataset functions
*
*-------------------------------------------------------------------------
*/
/**
* --------------------------------------------------------------------------
* \ingroup H5LR
*
* \brief Reads selected data to an application buffer.
*
* \param[in] file Name of file
* \param[in] path Full path to a dataset
* \param[in] block_coord Hyperslab coordinates
* \param[in] mem_type Memory datatype, describing the buffer the referenced data will be read into
* \param[out] buf Buffer containing data from the referenced region
*
* \return \herr_t
*
* \details H5LTread_region() reads data from a region described by
* the hyperslab coordinates in \p block_coord, located in
* the dataset specified by its absolute path \p path in a
* file specified by its name \p file. Data is read into a
* buffer \p buf of the datatype that corresponds to the
* HDF5 datatype specified by \p mem_type.
*
* Buffer \p block_coord has size 2*rank and is the coordinates
* of the starting point following by the coordinates of the
* ending point of the hyperslab. For example, to extract a
* rectangular hyperslab region starting at element (2,2) to
* element (5,4) then \p block_coord would be {2, 2, 5, 4}.
*
* Buffer \p buf should be big enough to hold selected elements
* of the type that corresponds to the \p mem_type
*
* \version 1.1 Fortran wrapper introduced in this release.
*
* \since 1.0
*
*/
H5_HLRDLL herr_t H5LTread_region(const char *file,
const char *path,
const hsize_t *block_coord,
hid_t mem_type,
void *buf );
/**
* --------------------------------------------------------------------------
* \ingroup H5LR
*
* \brief Retrieves the values of quality flags for each element
* to the application provided buffer.
*
* \param[in] dset_id Identifier of the dataset with bit-field values
* \param[in] num_values Number of the values to be extracted
* \param[in] offset Array of staring bits to be extracted from
* the element; valid values: 0 (zero) through 7
* \param[in] lengths Array of the number of bits to be extracted for each value
* \param[in] space Dataspace identifier, describing the elements
* to be read from the dataset with bit-field values
* \param[out] buf Buffer to read the values in
*
* \return \herr_t
*
* \details H5LTread_bitfield_value() reads selected elements from a
* dataset specified by its identifier \p dset_id, and unpacks
* the bit-field values to a buffer \p buf.
*
* The parameter \p space is a space identifier that indicates
* which elements of the dataset should be read.
*
* The parameter \p offset is an array of length \p num_values;
* the i<sup>th</sup> element of the array holds the value of the
* starting bit of the i<sup>th</sup> bit-field value.
* Valid values are: 0 (zero) through 7.
*
* The parameter \p lengths is an array of length \p num_values;
* the i<sup>th</sup> element of the array holds the number of
* bits to be extracted for the i<sup>th</sup> bit-field value.
* Extracted bits will be interpreted as a base-2 integer value.
* Each value will be converted to the base-10 integer value and
* stored in the application buffer.
*
* Buffer \p buf is allocated by the application and should be big
* enough to hold \c num_sel_elem * \p num_values elements of the
* specified type, where \c num_sel_elem is a number of the elements
* to be read from the dataset. Data in the buffer is organized
* as \p num_values values for the first element, followed by the
* \p num_values values for the second element, ... , followed by
* the \p num_values values for the
* \c num_selected_elem<sup>th</sup> element.
*
* \version 1.1 Fortran wrapper introduced in this release.
*
* \since 1.0
*
*/
H5_HLRDLL herr_t H5LTread_bitfield_value(hid_t dset_id, int num_values, const unsigned *offset,
const unsigned *lengths, hid_t space, int *buf);
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