An object reference points to an entire object in the current HDF5 file by storing the relative file address (OID) of the object header for the object pointed to. The relative file address of an object header is constant for the life of the object. An object reference is of a fixed size in the file.
A dataset region reference points to a region of a dataset in the current HDF5 file by storing the OID of the dataset and the global heap offset of the region referenced. The region referenced is located by retrieving the coordinates of the areas in the region from the global heap. A dataset region reference is of a variable size in the file.
| Reference Type | Value | Description |
|---|---|---|
H5R_OBJECT |
0 |
Object reference |
H5R_DATASET_REGION |
1 |
Dataset region reference |
H5Rcreate(void *reference,
hid_t loc_id,
const char *name,
H5R_type_t type,
hid_t space_id)
H5Rcreate creates an object which is a
particular type of reference (specified with the
type parameter) to some file object and/or
location specified with the space_id parameter.
For dataset region references, the selection specified
in the dataspace is the portion of the dataset which
will be referred to.
H5Rdereference(hid_t dset,
H5R_type_t rtype,
void *reference)
H5Rdereference opens the object referenced
and returns an identifier for that object.
The parameter reference specifies a reference of
type rtype that is stored in the dataset
dset.
H5Rget_object_type(hid_t obj_id,
void *reference)
H5Rget_object_type retrieves the type of object
that an object reference points to.
The parameter obj_id specifies the dataset
containing the reference object or the location identifier
of the object that the dataset is located within.
The parameter reference specifies the
reference being queried.
H5Rget_region(H5D_t dataset,
H5R_type_t type,
void *reference)
H5Rget_region creates a copy of dataspace of
the dataset that is pointed to and defines a selection in
the copy which is the location (or region) pointed to.
The parameter ref specifies a reference of
type rtype that is stored in the dataset
dset.
H5Iget_type(hid_t id)
id. Valid return values appear
in the following list:
H5I_FILE |
File objects |
H5I_GROUP |
Group objects |
H5I_DATATYPE |
Datatype objects |
H5I_DATASPACE |
Dataspace objects |
H5I_DATASET |
Dataset objects |
H5I_ATTR |
Attribute objects |
This function was inspired by the need of users to figure
out which type of object closing function
(H5Dclose, H5Gclose, etc.)
to call after a call to H5Rdereference,
but it is also of general use.
{
hid_t file1;
hid_t dataset1;
hid_t datatype, dataspace;
char buf[128];
hobj_ref_t link;
hobj_ref_t data[10][10];
int rank;
size_t dimsf[2];
int i, j;
/* Open the file */
file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
/* Describe the size of the array and create the data space */
rank=2;
dimsf[0] = 10;
dimsf[1] = 10;
dataspace = H5Screate_simple(rank, dimsf, NULL);
/* Define datatype */
datatype = H5Tcopy(H5T_STD_REF_OBJ);
/* Create a dataset */
dataset1=H5Dcreate(file1,"Dataset One",datatype,dataspace,H5P_DEFAULT);
/* Construct array of OIDs for other datasets in the file */
/* somewhat hokey and artificial, but demonstrates the point */
for(i=0; i<10; i++)
for(j=0; j<10; j++)
{
sprintf(buf,"/Group/Linked Set %d-%d",i,j);
if(H5Rcreate(&link,file1,buf,H5R_OBJECT,-1)>0)
data[i][j]=link;
} /* end for */
/* Write the data to the dataset using default transfer properties. */
H5Dwrite(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
/* Close everything */
H5Sclose(dataspace);
H5Tclose(datatype);
H5Dclose(dataset1);
H5Fclose(file1);
}
Object Reference Reading Example
{
hid_t file1;
hid_t dataset1, tmp_dset;
href_t data[10][10];
int i, j;
/* Open the file */
file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
/* Open the dataset */
dataset1=H5Dopen(file1,"Dataset One",H5P_DEFAULT);
/*
* Read the data to the dataset using default transfer properties.
* (we are assuming the dataset is the same and not querying the
* dimensions, etc.)
*/
H5Dread(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
/* Analyze array of OIDs of linked datasets in the file */
/* somewhat hokey and artificial, but demonstrates the point */
for(i=0; i<10; i++)
for(j=0; j<10; i++)
{
if((tmp_dset=H5Rdereference(dataset, H5T_STD_REF_OBJ, data[i][j]))>0)
{
} /* end if */
H5Dclose(tmp_dset);
} /* end for */
/* Close everything */
H5Dclose(dataset1);
H5Fclose(file1);
}
Dataset Region Reference Writing Example
{
hid_t file1;
hid_t dataset1, dataset2;
hid_t datatype, dataspace1, dataspace2;
char buf[128];
href_t link;
href_t data[10][10]; /* HDF5 reference type */
int rank;
size_t dimsf[2];
hsize_t start[3],count[3];
int i, j;
/* Open the file */
file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
/* Describe the size of the array and create the data space */
rank=2;
dimsf[0] = 10;
dimsf[1] = 10;
dataspace1 = H5Screate_simple(rank, dimsf, NULL);
/* Define Dataset Region Reference datatype */
datatype = H5Tcopy(H5T_STD_REF_DATAREG);
/* Create a dataset */
dataset1=H5Dcreate(file1,"Dataset One",datatype,dataspace1,H5P_DEFAULT);
/* Construct array of OIDs for other datasets in the file */
/* (somewhat artificial, but demonstrates the point) */
for(i=0; i<10; i++)
for(j=0; j<10; i++)
{
sprintf(buf,"/Group/Linked Set %d-%d",i,j);
/* Get the dataspace for the object to point to */
dataset2=H5Dopen(file1,buf,H5P_DEFAULT);
dataspace2=H5Dget_space(dataspace2);
/* Select the region to point to */
/* (could be different region for each pointer) */
start[0]=5; start[1]=4; start[2]=3;
count[0]=2; count[1]=4; count[2]=1;
H5Sselect_hyperslab(dataspace2,H5S_SELECT_SET,start,NULL,count,NULL);
if(H5Rcreate(&link,file1,buf,H5R_REF_DATAREG,dataspace2)>0)
/* Store the reference */
data[i][j]=link;
H5Sclose(dataspace2);
H5Dclose(dataspace2);
} /* end for */
/* Write the data to the dataset using default transfer properties. */
H5Dwrite(dataset, H5T_STD_REF_DATAREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
/* Close everything */
H5Sclose(dataspace);
H5Tclose(datatype);
H5Dclose(dataset1);
H5Fclose(file1);
}
Dataset Region Reference Reading Example
{
hid_t file1;
hid_t dataset1, tmp_dset;
hid_t dataspace;
href_t data[10][10]; /* HDF5 reference type */
int i, j;
/* Open the file */
file1=H5Fopen("example.h5", H5F_ACC_RDWR, H5P_DEFAULT);
/* Open the dataset */
dataset1=H5Dopen(file1,"Dataset One",H5P_DEFAULT);
/*
* Read the data to the dataset using default transfer properties.
* (we are assuming the dataset is the same and not querying the
* dimensions, etc.)
*/
H5Dread(dataset, H5T_STD_REF_DATAREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
/* Analyze array of OIDs of linked datasets in the file */
/* (somewhat artificial, but demonstrates the point) */
for(i=0; i<10; i++)
for(j=0; j<10; i++)
{
if((tmp_dset=H5Rdereference(dataset, H5D_STD_REF_DATAREG,data[i][j]))>0)
{
/* Get the dataspace with the pointed to region selected */
dataspace=H5Rget_space(data[i][j]);
H5Sclose(dataspace);
} /* end if */
H5Dclose(tmp_dset);
} /* end for */
/* Close everything */
H5Dclose(dataset1);
H5Fclose(file1);
}
