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A dataset region reference points to the dataset selection by storing the
relative file address of the dataset header and the global heap offset of
the referenced selection. The selection referenced is located by retrieving
the coordinates of the areas in the selection from the global heap. This
internal mechanism of storing and retrieving dataset selections is transparent
to the user. A reference to the dataset selection ( region ) is constant for
the life of the dataset.
Creating and Storing References to Dataset Regions
The following steps are involved in creating and storing references to
the dataset regions:
Programming Example
Description
The example below creates a dataset in the file. Then it creates a
dataset to store references to the dataset regions (selections).
The first selection is a 6 x 6 hyperslab. The second selection is a point
selection in the same dataset.
References to both selections are created and stored in the buffer, and then
written to the dataset in the file.
[Download h5_ref2regw.c]
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#include <stdlib.h>
#include <hdf5.h>
#define FILE2 "trefer2.h5"
#define SPACE1_NAME "Space1"
#define SPACE1_RANK 1
#define SPACE1_DIM1 4
/* Dataset with fixed dimensions */
#define SPACE2_NAME "Space2"
#define SPACE2_RANK 2
#define SPACE2_DIM1 10
#define SPACE2_DIM2 10
/* Element selection information */
#define POINT1_NPOINTS 10
int
main(void)
{
hid_t fid1; /* HDF5 File IDs */
hid_t dset1, /* Dataset ID */
dset2; /* Dereferenced dataset ID */
hid_t sid1, /* Dataspace ID #1 */
sid2; /* Dataspace ID #2 */
hsize_t dims1[] = {SPACE1_DIM1},
dims2[] = {SPACE2_DIM1, SPACE2_DIM2};
hssize_t start[SPACE2_RANK]; /* Starting location of hyperslab */
hsize_t stride[SPACE2_RANK]; /* Stride of hyperslab */
hsize_t count[SPACE2_RANK]; /* Element count of hyperslab */
hsize_t block[SPACE2_RANK]; /* Block size of hyperslab */
hssize_t coord1[POINT1_NPOINTS][SPACE2_RANK];
/* Coordinates for point selection */
hdset_reg_ref_t *wbuf; /* buffer to write to disk */
int *dwbuf; /* Buffer for writing numeric data to disk */
int i; /* counting variables */
herr_t ret; /* Generic return value */
/* Allocate write & read buffers */
wbuf=calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1);
dwbuf=malloc(sizeof(int)*SPACE2_DIM1*SPACE2_DIM2);
/* Create file */
fid1 = H5Fcreate(FILE2, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create dataspace for datasets */
sid2 = H5Screate_simple(SPACE2_RANK, dims2, NULL);
/* Create a dataset */
dset2=H5Dcreate(fid1,"Dataset2",H5T_STD_U8LE,sid2,H5P_DEFAULT);
for(i=0; i < SPACE2_DIM1*SPACE2_DIM2; i++)
dwbuf[i]=i*3;
/* Write selection to disk */
ret=H5Dwrite(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,dwbuf);
/* Close Dataset */
ret = H5Dclose(dset2);
/* Create dataspace for the reference dataset */
sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
/* Create a dataset */
dset1=H5Dcreate(fid1,"Dataset1",H5T_STD_REF_DSETREG,sid1,H5P_DEFAULT);
/* Create references */
/* Select 6x6 hyperslab for first reference */
start[0]=2; start[1]=2;
stride[0]=1; stride[1]=1;
count[0]=6; count[1]=6;
block[0]=1; block[1]=1;
ret = H5Sselect_hyperslab(sid2,H5S_SELECT_SET,start,stride,count,block);
/* Store first dataset region */
ret = H5Rcreate(&wbuf[0],fid1,"/Dataset2",H5R_DATASET_REGION,sid2);
/* Select sequence of ten points for second reference */
coord1[0][0]=6; coord1[0][1]=9;
coord1[1][0]=2; coord1[1][1]=2;
coord1[2][0]=8; coord1[2][1]=4;
coord1[3][0]=1; coord1[3][1]=6;
coord1[4][0]=2; coord1[4][1]=8;
coord1[5][0]=3; coord1[5][1]=2;
coord1[6][0]=0; coord1[6][1]=4;
coord1[7][0]=9; coord1[7][1]=0;
coord1[8][0]=7; coord1[8][1]=1;
coord1[9][0]=3; coord1[9][1]=3;
ret = H5Sselect_elements(sid2,H5S_SELECT_SET,POINT1_NPOINTS,(const hssize_t **)coord1);
/* Store second dataset region */
ret = H5Rcreate(&wbuf[1],fid1,"/Dataset2",H5R_DATASET_REGION,sid2);
/* Write selection to disk */
ret=H5Dwrite(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,wbuf);
/* Close all objects */
ret = H5Sclose(sid1);
ret = H5Dclose(dset1);
ret = H5Sclose(sid2);
/* Close file */
ret = H5Fclose(fid1);
free(wbuf);
free(dwbuf);
return 0;
}
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
dset1=H5Dcreate(fid1,"Dataset1",H5T_STD_REF_DSETREG,sid1,H5P_DEFAULT);
creates a dataset to store references to the dataset(s) regions(selections).
Notice that the H5T_STD_REF_DSETREG data type is used.
herr_t H5Rcreate(void *buf, hid_t loc_id, const char *name,
H5R_type_t ref_type, hid_t space_id)
HDF5 "trefer2.h5" {
GROUP "/" {
DATASET "Dataset1" {
DATATYPE { H5T_REFERENCE }
DATASPACE { SIMPLE ( 4 ) / ( 4 ) }
DATA {
DATASET 0:744 {(2,2)-(7,7)}, DATASET 0:744 {(6,9), (2,2), (8,4), (1,6),
(2,8), (3,2), (0,4), (9,0), (7,1), (3,3)}, NULL, NULL
}
}
DATASET "Dataset2" {
DATATYPE { H5T_STD_U8LE }
DATASPACE { SIMPLE ( 10, 10 ) / ( 10, 10 ) }
DATA {
0, 3, 6, 9, 12, 15, 18, 21, 24, 27,
30, 33, 36, 39, 42, 45, 48, 51, 54, 57,
60, 63, 66, 69, 72, 75, 78, 81, 84, 87,
90, 93, 96, 99, 102, 105, 108, 111, 114, 117,
120, 123, 126, 129, 132, 135, 138, 141, 144, 147,
150, 153, 156, 159, 162, 165, 168, 171, 174, 177,
180, 183, 186, 189, 192, 195, 198, 201, 204, 207,
210, 213, 216, 219, 222, 225, 228, 231, 234, 237,
240, 243, 246, 249, 252, 255, 255, 255, 255, 255,
255, 255, 255, 255, 255, 255, 255, 255, 255, 255
}
}
}
}
Notice how raw data of the dataset with the dataset regions is displayed.
Each element of the raw data consists of a reference to the dataset
(DATASET number1:number2) and its selected region.
If the selection is a hyperslab, the corner coordinates of the hyperslab
are displayed.
For the point selection, the coordinates of each point are displayed.
Since only two selections were stored, the third and fourth elements of the
dataset "Dataset1" are set to NULL. This was done by the buffer
inizialization in the program.
OR
Use H5Rget_region to obtain the dataspace identifier for the dataset
containing the selection from the read dataset region reference.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#include <stdlib.h>
#include <hdf5.h>
#define FILE2 "trefer2.h5"
#define NPOINTS 10
/* 1-D dataset with fixed dimensions */
#define SPACE1_NAME "Space1"
#define SPACE1_RANK 1
#define SPACE1_DIM1 4
/* 2-D dataset with fixed dimensions */
#define SPACE2_NAME "Space2"
#define SPACE2_RANK 2
#define SPACE2_DIM1 10
#define SPACE2_DIM2 10
int
main(void)
{
hid_t fid1; /* HDF5 File IDs */
hid_t dset1, /* Dataset ID */
dset2; /* Dereferenced dataset ID */
hid_t sid1, /* Dataspace ID #1 */
sid2; /* Dataspace ID #2 */
hsize_t * coords; /* Coordinate buffer */
hsize_t low[SPACE2_RANK]; /* Selection bounds */
hsize_t high[SPACE2_RANK]; /* Selection bounds */
hdset_reg_ref_t *rbuf; /* buffer to to read disk */
int *drbuf; /* Buffer for reading numeric data from disk */
int i, j; /* counting variables */
herr_t ret; /* Generic return value */
/* Output message about test being performed */
/* Allocate write & read buffers */
rbuf=malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1);
drbuf=calloc(sizeof(int),SPACE2_DIM1*SPACE2_DIM2);
/* Open the file */
fid1 = H5Fopen(FILE2, H5F_ACC_RDWR, H5P_DEFAULT);
/* Open the dataset */
dset1=H5Dopen(fid1,"/Dataset1");
/* Read selection from disk */
ret=H5Dread(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,rbuf);
/* Try to open objects */
dset2 = H5Rdereference(dset1,H5R_DATASET_REGION,&rbuf[0]);
/* Check information in referenced dataset */
sid1 = H5Dget_space(dset2);
ret=H5Sget_simple_extent_npoints(sid1);
printf(" Number of elements in the dataset is : %d\n",ret);
/* Read from disk */
ret=H5Dread(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,drbuf);
for(i=0; i < SPACE2_DIM1; i++) {
for (j=0; j < SPACE2_DIM2; j++) printf (" %d ", drbuf[i*SPACE2_DIM2+j]);
printf("\n"); }
/* Get the hyperslab selection */
sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[0]);
/* Verify correct hyperslab selected */
ret = H5Sget_select_npoints(sid2);
printf(" Number of elements in the hyperslab is : %d \n", ret);
ret = H5Sget_select_hyper_nblocks(sid2);
coords=malloc(ret*SPACE2_RANK*sizeof(hsize_t)*2); /* allocate space for the hyperslab blocks */
ret = H5Sget_select_hyper_blocklist(sid2,0,ret,coords);
printf(" Hyperslab coordinates are : \n");
printf (" ( %lu , %lu ) ( %lu , %lu ) \n", \
(unsigned long)coords[0],(unsigned long)coords[1],(unsigned long)coords[2],(unsigned long)coords[3]);
free(coords);
ret = H5Sget_select_bounds(sid2,low,high);
/* Close region space */
ret = H5Sclose(sid2);
/* Get the element selection */
sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[1]);
/* Verify correct elements selected */
ret = H5Sget_select_elem_npoints(sid2);
printf(" Number of selected elements is : %d\n", ret);
/* Allocate space for the element points */
coords= malloc(ret*SPACE2_RANK*sizeof(hsize_t));
ret = H5Sget_select_elem_pointlist(sid2,0,ret,coords);
printf(" Coordinates of selected elements are : \n");
for (i=0; i < 2*NPOINTS; i=i+2)
printf(" ( %lu , %lu ) \n", (unsigned long)coords[i],(unsigned long)coords[i+1]);
free(coords);
ret = H5Sget_select_bounds(sid2,low,high);
/* Close region space */
ret = H5Sclose(sid2);
/* Close first space */
ret = H5Sclose(sid1);
/* Close dereferenced Dataset */
ret = H5Dclose(dset2);
/* Close Dataset */
ret = H5Dclose(dset1);
/* Close file */
ret = H5Fclose(fid1);
/* Free memory buffers */
free(rbuf);
free(drbuf);
return 0;
}
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Output of this program is :
Number of elements in the dataset is : 100 0 3 6 9 12 15 18 21 24 27 30 33 36 39 42 45 48 51 54 57 60 63 66 69 72 75 78 81 84 87 90 93 96 99 102 105 108 111 114 117 120 123 126 129 132 135 138 141 144 147 150 153 156 159 162 165 168 171 174 177 180 183 186 189 192 195 198 201 204 207 210 213 216 219 222 225 228 231 234 237 240 243 246 249 252 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 Number of elements in the hyperslab is : 36 Hyperslab coordinates are : ( 2 , 2 ) ( 7 , 7 ) Number of selected elements is : 10 Coordinates of selected elements are : ( 6 , 9 ) ( 2 , 2 ) ( 8 , 4 ) ( 1 , 6 ) ( 2 , 8 ) ( 3 , 2 ) ( 0 , 4 ) ( 9 , 0 ) ( 7 , 1 ) ( 3 , 3 ) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
dset2 = H5Rdereference (dset1,H5R_DATASET_REGION,&rbuf[0]);
or to obtain spacial information ( dataspace and selection ) with the call
to H5Rget_region:
sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[0]);
The reference to the dataset region has information for both the dataset
itself and its selection. In both functions: