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<HTML><HEAD>
<TITLE>HDF5 Tutorial - References to Dataset Regions
</TITLE>
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[ <A HREF="title.html"><I>HDF5 Tutorial Top</I></A> ]
<H1><BIG><BIG><BIG><FONT COLOR="#c101cd"> References to Dataset Regions</FONT>
</BIG></BIG></BIG></H1>
<hr noshade size=1>
<BODY>
<H2>Contents:</H2>
<UL>
<LI> <A HREF="#def">References to Dataset Regions</A>
<LI> <A HREF="#def1">Creating and Storing References to Dataset Regions</A>
<LI> Programming Example
<UL>
<LI> <A HREF="#desc1">Description</A>
<LI> <A HREF="#rem1">Remarks</A>
<LI> <A HREF="#fc1">File Contents</A>
</UL>
<LI> <A HREF="#def2">Reading References to Dataset Regions</A>
<LI> Programming Example
<UL>
<LI> <A HREF="#desc2">Description</A>
<LI> <A HREF="#rem2">Remarks</A>
</UL>
</UL>
<HR>
<A NAME="def">
<H2>References to Dataset Regions</H2>
Previously you learned about creating, reading, and writing
dataset selections. Here you will learn how to store dataset
selections in a file, and how to read them back using references
to the dataset regions.
<P>
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.
<A NAME="def1">
<H2>Creating and Storing References to Dataset Regions</H2>
The following steps are involved in creating and storing references to
the dataset regions:
<OL>
<LI> Create a dataset to store the dataset regions (selections).
<P>
<LI> Create selections in the dataset(s). Dataset(s) should already exist in the
file.
<P>
<LI> Create references to the selections and store them in a buffer.
<P>
<LI> Write references to the dataset regions in the file.
<P>
<LI> Close all objects.
</OL>
<H2> Programming Example</H2>
<A NAME="desc1">
<H3><U>Description</U></H3>
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.
[<A HREF="examples/h5_ref2regw.c">Download h5_ref2regw.c</A>]
<PRE>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#include &lt;stdlib.h&gt;
#include &lt;hdf5.h&gt;
#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 &lt; 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;
}
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
</PRE>
<A NAME="rem1">
<H3><U>Remarks</U></H3>
<UL>
<LI> The code,
<PRE>
dset1=H5Dcreate(fid1,"Dataset1",H5T_STD_REF_DSETREG,sid1,H5P_DEFAULT);
</PRE>
creates a dataset to store references to the dataset(s) regions(selections).
Notice that the H5T_STD_REF_DSETREG data type is used.
<P>
<LI> This program uses hyperslab and point selections. We used the dataspace
handle <I>sid2</I> for the calls to H5Sselect_hyperslab and
H5Sselect_elements. The handle was created when dataset "Dataset2" was
created and it describes the dataset's dataspace. We did not close it when
the dataset was closed to decrease the number of function calls used
in the example.
In a real application program, one should open the dataset and determine
its dataspace using the H5Dget_space function.
<P>
<LI> H5Rcreate is used to create a dataset region reference and store it in a
buffer. The signature of the function is:
<PRE>
herr_t H5Rcreate(void *buf, hid_t loc_id, const char *name,
H5R_type_t ref_type, hid_t space_id)
</PRE>
<UL>
<LI> The first argument specifies the buffer to store the reference.
<LI> The second and third arguments specify the name of the referenced
dataset. In our example the file identifier <I>fid1</I> and the
absolute name of the dataset "/Dataset2" were used to identify the
dataset. The reference to the region of this dataset is stored in
the buffer <I>buf</I>.
<LI> The fourth argument specifies the type of the reference. Since we are
creating references to the dataset regions, the H5R_DATASET_REGION
data type is used.
<LI> The fifth argument is a dataspace identifier of the referenced dataset.
</UL>
</UL>
<A NAME="fc1">
<H3><U>File Contents</U></H3>
The contents of the file "trefer2.h5" created by this program are as follows:
<PRE>
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
}
}
}
}
</PRE>
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.
<A NAME="def2">
<H2>Reading References to Dataset Regions</H2>
The following steps are involved in reading references to the dataset
regions and referenced dataset regions (selections).
<OL>
<LI> Open and read the dataset containing references to the dataset regions.
The data type H5T_STD_REF_DSETREG must be used during read operation.
<P>
<LI>Use H5Rdereference to obtain the dataset identifier from the read
dataset region reference.
<PRE> <B>OR</B>
</PRE>
Use H5Rget_region to obtain the dataspace identifier for the dataset
containing the selection from the read dataset region reference.
<P>
<LI> With the dataspace identifier, the H5S interface functions,
H5Sget_select_*, can be used to obtain information about the
selection.
<P>
<LI> Close all objects when they are no longer needed.
</OL>
<H2> Programming Example</H2>
<A NAME="desc2">
<H3><U>Description</U></H3>
The following example reads a dataset containing dataset region references.
It reads data from the dereferenced dataset and displays the number of
elements and raw data. Then it reads two selections:
hyperslab and point. The program queries a number of points in the
hyperslab and the coordinates and displays them. Then it queries a number of
selected points and their coordinates and displays the information.<BR>
[ <A HREF="examples/h5_ref2regr.c">Download h5_ref2regr.c</A> ]
<PRE>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#include &lt;stdlib.h&gt;
#include &lt;hdf5.h&gt;
#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 &lt; SPACE2_DIM1; i++) {
for (j=0; j &lt; 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 &lt; 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;
}
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
</PRE>
Output of this program is :
<PRE>
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 )
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
</PRE>
<A NAME="rem2">
<H3><U>Remarks</U></H3>
<UL>
<LI> The dataset with the region references was read by H5Dread with
the H5T_STD_REF_DSETREG data type specified.
<P>
<LI> The read reference can be used to obtain the dataset identifier as we
did with the following call:
<PRE>
dset2 = H5Rdereference (dset1,H5R_DATASET_REGION,&rbuf[0]);
</PRE>
or to obtain spacial information ( dataspace and selection ) with the call
to H5Rget_region:
<PRE>
sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[0]);
</PRE>
The reference to the dataset region has information for both the dataset
itself and its selection. In both functions:
<UL>
<LI> The first parameter is an identifier of the dataset with the region
references.
<LI> The second parameter specifies the type of reference stored. In
this example a reference to the dataset region is stored.
<LI> The third parameter is a buffer containing the reference of the
specified type.
</UL>
<P>
<LI> This example introduces several H5Sget_select* functions used to obtain
information about selections:
<UL>
<B>H5Sget_select_npoints:</B> returns the number of elements in the
hyperslab<BR>
<B>H5Sget_select_hyper_nblocks:</B> returns the number of blocks in
the hyperslab<BR>
<B>H5Sget_select_blocklist:</B> returns the "lower left" and "upper right"
coordinates of the blocks in the hyperslab selection<BR>
<B>H5Sget_select_bounds:</B> returns the coordinates of the "minimal"
block containing a hyperslab selection<BR>
<B>H5Sget_select_elem_npoints:</B> returns the number of points in the
element selection<BR>
<B>H5Sget_select_elem_points:</B> returns the coordinates of the element
selection
</UL>
</UL>
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