H5R

Detailed Description

Use the functions in this module to manage HDF5 references. Referents can be HDF5 objects, attributes, and selections on datasets a.k.a. dataset regions.

Create	Read
{ __label__ fail_file, fail_fspace, fail_dset, fail_sel, fail_aspace, fail_attr, fail_awrite; hid_t file, fspace, dset, aspace, attr; H5R_ref_t ref; if ((file = H5Fcreate("reference.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) == H5I_INVALID_HID) { ret_val = EXIT_FAILURE; goto fail_file; } // create a region reference which selects all elements of the dataset at "/data" if ((fspace = H5Screate_simple(2, (hsize_t[]){10, 20}, NULL)) == H5I_INVALID_HID) { ret_val = EXIT_FAILURE; goto fail_fspace; } if ((dset = H5Dcreate(file, "data", H5T_STD_I32LE, fspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) == H5I_INVALID_HID) { ret_val = EXIT_FAILURE; goto fail_dset; } if (H5Sselect_all(fspace) < 0 || H5Rcreate_region(file, "data", fspace, H5P_DEFAULT, &ref) < 0) { ret_val = EXIT_FAILURE; goto fail_sel; } // store the region reference in a scalar attribute of the root group called "region" if ((aspace = H5Screate(H5S_SCALAR)) == H5I_INVALID_HID) { ret_val = EXIT_FAILURE; goto fail_aspace; } if ((attr = H5Acreate(file, "region", H5T_STD_REF, aspace, H5P_DEFAULT, H5P_DEFAULT)) == H5I_INVALID_HID) { ret_val = EXIT_FAILURE; goto fail_attr; } if (H5Awrite(attr, H5T_STD_REF, &ref) < 0) { ret_val = EXIT_FAILURE; goto fail_awrite; } fail_awrite: H5Aclose(attr); fail_attr: H5Sclose(aspace); fail_aspace: H5Rdestroy(&ref); fail_sel: H5Dclose(dset); fail_dset: H5Sclose(fspace); fail_fspace: H5Fclose(file); fail_file:; }	{ __label__ fail_file, fail_attr, fail_aread; hid_t file, attr; H5R_ref_t ref; if ((file = H5Fopen("reference.h5", H5F_ACC_RDONLY, H5P_DEFAULT)) == H5I_INVALID_HID) { ret_val = EXIT_FAILURE; goto fail_file; } // read the dataset region reference from the attribute if ((attr = H5Aopen(file, "region", H5P_DEFAULT)) == H5I_INVALID_HID) { ret_val = EXIT_FAILURE; goto fail_attr; } if (H5Aread(attr, H5T_STD_REF, &ref) < 0) { ret_val = EXIT_FAILURE; goto fail_aread; } assert(H5Rget_type(&ref) == H5R_DATASET_REGION2); // get an HDF5 path name for the dataset of the region reference { char buf[255]; if (H5Rget_obj_name(&ref, H5P_DEFAULT, buf, 255) < 0) { ret_val = EXIT_FAILURE; } printf("Object name: \"%s\"\n", buf); } H5Rdestroy(&ref); fail_aread: H5Aclose(attr); fail_attr: H5Fclose(file); fail_file:; }
Update	Delete
{ __label__ fail_file, fail_attr, fail_ref; hid_t file, attr; H5R_ref_t ref; if ((file = H5Fopen("reference.h5", H5F_ACC_RDWR, H5P_DEFAULT)) == H5I_INVALID_HID) { ret_val = EXIT_FAILURE; goto fail_file; } // H5T_STD_REF is a generic reference type // we can "update" the attribute value to refer to the attribute itself if ((attr = H5Aopen(file, "region", H5P_DEFAULT)) == H5I_INVALID_HID) { ret_val = EXIT_FAILURE; goto fail_attr; } if (H5Rcreate_attr(file, "data", "region", H5P_DEFAULT, &ref) < 0) { ret_val = EXIT_FAILURE; goto fail_ref; } assert(H5Rget_type(&ref) == H5R_ATTR); if (H5Awrite(attr, H5T_STD_REF, &ref) < 0) { ret_val = EXIT_FAILURE; } H5Rdestroy(&ref); fail_ref: H5Aclose(attr); fail_attr: H5Fclose(file); fail_file:; }	{ __label__ fail_file, fail_ref; hid_t file; H5R_ref_t ref; // create an HDF5 object reference to the root group if ((file = H5Fopen("reference.h5", H5F_ACC_RDONLY, H5P_DEFAULT)) == H5I_INVALID_HID) { ret_val = EXIT_FAILURE; goto fail_file; } if (H5Rcreate_object(file, ".", H5P_DEFAULT, &ref) < 0) { ret_val = EXIT_FAILURE; goto fail_ref; } // H5Rdestroy() releases all resources associated with an HDF5 reference H5Rdestroy(&ref); fail_ref: H5Fclose(file); fail_file:; }

Macros
#define	H5Rdereference   H5Rdereference2
#define	H5Rget_obj_type   H5Rget_obj_type2

Functions
herr_t	H5Rcreate (void *ref, hid_t loc_id, const char *name, H5R_type_t ref_type, hid_t space_id)
	Creates a reference. More...
hid_t	H5Rdereference2 (hid_t obj_id, hid_t oapl_id, H5R_type_t ref_type, const void *ref)
	Opens the HDF5 object referenced. More...
hid_t	H5Rget_region (hid_t dataset, H5R_type_t ref_type, const void *ref)
	Sets up a dataspace and selection as specified by a region reference. More...
herr_t	H5Rget_obj_type2 (hid_t id, H5R_type_t ref_type, const void *_ref, H5O_type_t *obj_type)
	Retrieves the type of object that an object reference points to. More...
ssize_t	H5Rget_name (hid_t loc_id, H5R_type_t ref_type, const void *ref, char *name, size_t size)
	Retrieves a name for a referenced object. More...
H5G_obj_t	H5Rget_obj_type1 (hid_t id, H5R_type_t ref_type, const void *ref)
	Retrieves the type of object that an object reference points to. More...
hid_t	H5Rdereference1 (hid_t obj_id, H5R_type_t ref_type, const void *ref)
	Opens the HDF5 object referenced. More...

Macro Definition Documentation

H5Rdereference

#define H5Rdereference   H5Rdereference2

H5Rdereference() is a macro that is mapped to either H5Rdereference1() or H5Rdereference2().

See also

API Compatibility Macros

H5Rget_obj_type

#define H5Rget_obj_type   H5Rget_obj_type2

H5Rget_obj_type() is a macro that is mapped to either H5Rget_obj_type1() or H5Rget_obj_type2() or H5R_get_obj_type3().

See also

API Compatibility Macros

Function Documentation

H5Rcreate()

herr_t H5Rcreate	(	void *	ref,
		hid_t	loc_id,
		const char *	name,
		H5R_type_t	ref_type,
		hid_t	space_id
	)

Creates a reference.

---

Parameters

[out]	ref	Reference created by the function call
[in]	loc_id	Location identifier used to locate the object being pointed to
[in]	name	Name of object at location loc_id
[in]	ref_type	Type of reference
[in]	space_id	Dataspace identifier with selection. Used only for dataset region references; pass as -1 if reference is an object reference, i.e., of type H5R_OBJECT

Returns

Returns a non-negative value if successful; otherwise returns a negative value.

H5Rcreate() creates the reference, ref, of the type specified in ref_type, pointing to the object name located at loc_id.

The HDF5 library maps the void type specified above for ref to the type specified in ref_type, which will be one of the following:

 
typedef enum {
    H5R_BADTYPE = (-1), 
    H5R_OBJECT,         
    H5R_DATASET_REGION, 
    H5R_MAXTYPE         
} H5R_type_t;

The parameters loc_id and name are used to locate the object.

The parameter space_id identifies the dataset region that a dataset region reference points to. This parameter is used only with dataset region references and should be set to -1 if the reference is an object reference, H5R_OBJECT.

Since

1.8.0

H5Rdereference1()

hid_t H5Rdereference1	(	hid_t	obj_id,
		H5R_type_t	ref_type,
		const void *	ref
	)

Opens the HDF5 object referenced.

---

Parameters

[in]	obj_id	Object identifier
[in]	ref_type	The reference type of ref
[in]	ref	Reference to open

Returns

Returns identifier of referenced object if successful; otherwise returns a negative value.

Deprecated:

This function has been renamed from H5Rdereference() and is deprecated in favor of the macro H5Rdereference() or the function H5Rdereference2().

Given a reference, ref, to an object or a region in an object, H5Rdereference1() opens that object and returns an identifier.

The parameter obj_id must be a valid identifier for an object in the HDF5 file containing the referenced object, including the file identifier.

The parameter ref_type specifies the reference type of the reference ref. ref_type may contain either of the following values:

• H5R_OBJECT
• H5R_DATASET_REGION

The object opened with this function should be closed when it is no longer needed so that resource leaks will not develop. Use the appropriate close function such as H5Oclose() or H5Dclose() for datasets.

Version

1.10.0 Function H5Rdereference() renamed to H5Rdereference1() and deprecated in this release.

Since

1.8.0

H5Rdereference2()

hid_t H5Rdereference2	(	hid_t	obj_id,
		hid_t	oapl_id,
		H5R_type_t	ref_type,
		const void *	ref
	)

Opens the HDF5 object referenced.

---

Parameters

[in]	obj_id	Object identifier
[in]	oapl_id	Object access property list identifier
[in]	ref_type	The reference type of ref
[in]	ref	Reference to open

Returns

Returns identifier of referenced object if successful; otherwise returns a negative value.

Given a reference, ref, to an object or a region in an object, H5Rdereference2() opens that object and returns an identifier.

The parameter obj_id must be a valid identifier for the HDF5 file containing the referenced object or for any object in that HDF5 file.

The parameter oapl_id is an object access property list identifier for the referenced object. The access property list must be of the same type as the object being referenced, that is a group, dataset, or datatype property list.

The parameter ref_type specifies the reference type of the reference ref. ref_type may contain either of the following values:

• H5R_OBJECT
• H5R_DATASET_REGION

The object opened with this function should be closed when it is no longer needed so that resource leaks will not develop. Use the appropriate close function such as H5Oclose() or H5Dclose() for datasets.

Since

1.10.0

H5Rget_name()

ssize_t H5Rget_name	(	hid_t	loc_id,
		H5R_type_t	ref_type,
		const void *	ref,
		char *	name,
		size_t	size
	)

Retrieves a name for a referenced object.

---

Parameters

[in]	loc_id	Identifier for the file containing the reference or for any object in that file
[in]	ref_type	Type of reference
[in]	ref	An object or dataset region reference
[out]	name	A buffer to place the name of the referenced object or dataset region. If NULL, then this call will return the size in bytes of the name.
[in]	size	The size of the name buffer. When the size is passed in, the NULL terminator needs to be included.

Returns

Returns the length of the name if successful, returning 0 (zero) if no name is associated with the identifier. Otherwise returns a negative value.

H5Rget_name() retrieves a name for the object identified by ref.
loc_id is used to identify the file containing the reference. It can be the file identifier for the file containing the reference or an identifier for any object in that file.

H5R_type_t is the reference type of ref. Valid values include the following:

 
typedef enum {
    H5R_BADTYPE = (-1), 
    H5R_OBJECT,         
    H5R_DATASET_REGION, 
    H5R_MAXTYPE         
} H5R_type_t;

ref is the reference for which the target object’s name is sought.

If ref is an object reference, name will be returned with a name for the referenced object. If ref is a dataset region reference, name will contain a name for the object containing the referenced region.

Up to size characters of the name are returned in name; additional characters, if any, are not returned to the user application.

If the length of the name, which determines the required value of size, is unknown, a preliminary H5Rget_name() call can be made. The return value of this call will be the size of the object name. That value can then be assigned to size for a second H5Rget_name() call, which will retrieve the actual name.

If there is no name associated with the object identifier or if the name is NULL, H5Rget_name() returns the size of the name buffer (the size does not include the NULL terminator).

Note that an object in an HDF5 file may have multiple paths if there are multiple links pointing to it. This function may return any one of these paths.

Since

1.8.0

H5Rget_obj_type1()

H5G_obj_t H5Rget_obj_type1	(	hid_t	id,
		H5R_type_t	ref_type,
		const void *	ref
	)

Retrieves the type of object that an object reference points to.

---

Parameters

[in]	id	The dataset containing the reference object or the group containing that dataset
[in]	ref_type	Type of reference to query
[in]	ref	Reference to query

Returns

Returns a valid object type if successful; otherwise returns a negative value (H5G_UNKNOWN).

Deprecated:

This function has been renamed from H5Rget_obj_type() and is deprecated in favor of the macro H5Rget_obj_type() or the function H5Rget_obj_type2().

Given an object reference, ref, H5Rget_obj_type1() returns the type of the referenced object.

A reference type is the type of reference, either an object reference or a dataset region reference. An object reference points to an HDF5 object while a dataset region reference points to a defined region within a dataset.

The referenced object is the object the reference points to. The referenced object type, or the type of the referenced object, is the type of the object that the reference points to.

The location identifier, id, is the identifier for either the dataset containing the object reference or the group containing that dataset.

Valid reference types, to pass in as ref_type, include the following:

 
typedef enum {
    H5R_BADTYPE = (-1), 
    H5R_OBJECT,         
    H5R_DATASET_REGION, 
    H5R_MAXTYPE         
} H5R_type_t;

If the application does not already know the object reference type, that can be determined with three preliminary calls:

• Call H5Dget_type() on the dataset containing the reference to get a datatype identifier for the dataset’s datatype.
• Using that datatype identifier, H5Tget_class() returns a datatype class.
  If the datatype class is H5T_REFERENCE, H5Tequal() can then be used to determine whether the reference’s datatype is H5T_STD_REF_OBJ or H5T_STD_REF_DSETREG:
  • If the datatype is H5T_STD_REF_OBJ, the reference object type is H5R_OBJECT.
  • If the datatype is H5T_STD_REF_DSETREG, the reference object type is H5R_DATASET_REGION.

When the function completes successfully, it returns one of the following valid object type values (defined in H5Gpublic.h):

 
typedef enum H5G_obj_t {
    H5G_UNKNOWN = -1, 
    H5G_GROUP,        
    H5G_DATASET,      
    H5G_TYPE,         
    H5G_LINK,         
    H5G_UDLINK,       
    H5G_RESERVED_5,   
    H5G_RESERVED_6,   
    H5G_RESERVED_7    
} H5G_obj_t;

Version

1.8.0 Function H5Rget_obj_type() renamed to H5Rget_obj_type1() and deprecated in this release.

Since

1.6.0

H5Rget_obj_type2()

herr_t H5Rget_obj_type2	(	hid_t	id,
		H5R_type_t	ref_type,
		const void *	_ref,
		H5O_type_t *	obj_type
	)

Retrieves the type of object that an object reference points to.

---

Parameters

[in]	id	The dataset containing the reference object or the group containing that dataset
[in]	ref_type	Type of reference to query
[in]	_ref	Reference to query
[out]	obj_type	Type of referenced object

Returns

Returns a non-negative value if successful; otherwise returns a negative value.

Given an object reference, ref, H5Rget_obj_type2() returns the type of the referenced object in obj_type.

A reference type is the type of reference, either an object reference or a dataset region reference. An object reference points to an HDF5 object while a dataset region reference points to a defined region within a dataset.

The referenced object is the object the reference points to. The referenced object type, or the type of the referenced object, is the type of the object that the reference points to.

The location identifier, id, is the identifier for either the dataset containing the object reference or the group containing that dataset.

Valid reference types, to pass in as ref_type, include the following:

 
typedef enum {
    H5R_BADTYPE = (-1), 
    H5R_OBJECT,         
    H5R_DATASET_REGION, 
    H5R_MAXTYPE         
} H5R_type_t;

If the application does not already know the object reference type, that can be determined with three preliminary calls:

• Call H5Dget_type() on the dataset containing the reference to get a datatype identifier for the dataset’s datatype.
• Using that datatype identifier, H5Tget_class() returns a datatype class.
  If the datatype class is H5T_REFERENCE, H5Tequal() can then be used to determine whether the reference’s datatype is H5T_STD_REF_OBJ or H5T_STD_REF_DSETREG:
  • If the datatype is H5T_STD_REF_OBJ, the reference object type is H5R_OBJECT.
  • If the datatype is H5T_STD_REF_DSETREG, the reference object type is H5R_DATASET_REGION.

When the function completes successfully, it returns one of the following valid object type values (defined in H5Opublic.h):

 
typedef enum H5O_type_t {
    H5O_TYPE_UNKNOWN = -1,   
    H5O_TYPE_GROUP,          
    H5O_TYPE_DATASET,        
    H5O_TYPE_NAMED_DATATYPE, 
    H5O_TYPE_NTYPES          
} H5O_type_t;

Since

1.8.0

H5Rget_region()

hid_t H5Rget_region	(	hid_t	dataset,
		H5R_type_t	ref_type,
		const void *	ref
	)

Sets up a dataspace and selection as specified by a region reference.

---

Parameters

[in]	dataset	File identifier or identifier for any object in the file containing the referenced region
[in]	ref_type	Reference type of ref, which must be H5R_DATASET_REGION
[in]	ref	Region reference to open

Returns

Returns a valid dataspace identifier if successful; otherwise returns a negative value.

H5Rget_region() creates a copy of the dataspace of the dataset pointed to by a region reference, ref, and defines a selection matching the selection pointed to by ref within the dataspace copy.

dataset is used to identify the file containing the referenced region; it can be a file identifier or an identifier for any object in the file.

The parameter ref_type specifies the reference type of ref and must contain the value H5R_DATASET_REGION.

Use H5Sclose() to release the dataspace identifier returned by this function when the identifier is no longer needed.