546 lines
18 KiB
HTML
546 lines
18 KiB
HTML
<HTML><HEAD>
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<TITLE>HDF5 Tutorial - References to Dataset Regions
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</TITLE>
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</HEAD>
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<body bgcolor="#ffffff">
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<!-- BEGIN MAIN BODY -->
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<A HREF="http://www.ncsa.uiuc.edu/"><img border=0
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src="http://www.ncsa.uiuc.edu/Images/NCSAhome/footerlogo.gif"
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width=78 height=27 alt="NCSA"><P></A>
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[ <A HREF="title.html"><I>HDF5 Tutorial Top</I></A> ]
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<H1><BIG><BIG><BIG><FONT COLOR="#c101cd"> References to Dataset Regions</FONT>
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</BIG></BIG></BIG></H1>
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<hr noshade size=1>
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<BODY>
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<H2>Contents:</H2>
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<UL>
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<LI> <A HREF="#def">References to Dataset Regions</A>
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<LI> <A HREF="#def1">Creating and Storing References to Dataset Regions</A>
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<LI> Programming Example
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<UL>
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<LI> <A HREF="#desc1">Description</A>
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<LI> <A HREF="#rem1">Remarks</A>
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<LI> <A HREF="#fc1">File Contents</A>
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</UL>
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<LI> <A HREF="#def2">Reading References to Dataset Regions</A>
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<LI> Programming Example
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<UL>
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<LI> <A HREF="#desc2">Description</A>
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<LI> <A HREF="#rem2">Remarks</A>
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</UL>
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</UL>
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<HR>
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<A NAME="def">
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<H2>References to Dataset Regions</H2>
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Previously you learned about creating, reading, and writing
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dataset selections. Here you will learn how to store dataset
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selections in a file, and how to read them back using references
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to the dataset regions.
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<P>
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A dataset region reference points to the dataset selection by storing the
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relative file address of the dataset header and the global heap offset of
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the referenced selection. The selection referenced is located by retrieving
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the coordinates of the areas in the selection from the global heap. This
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internal mechanism of storing and retrieving dataset selections is transparent
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to the user. A reference to the dataset selection ( region ) is constant for
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the life of the dataset.
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<A NAME="def1">
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<H2>Creating and Storing References to Dataset Regions</H2>
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The following steps are involved in creating and storing references to
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the dataset regions:
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<OL>
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<LI> Create a dataset to store the dataset regions (selections).
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<P>
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<LI> Create selections in the dataset(s). Dataset(s) should already exist in the
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file.
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<P>
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<LI> Create references to the selections and store them in a buffer.
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<P>
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<LI> Write references to the dataset regions in the file.
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<P>
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<LI> Close all objects.
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</OL>
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<H2> Programming Example</H2>
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<A NAME="desc1">
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<H3><U>Description</U></H3>
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The example below creates a dataset in the file. Then it creates a
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dataset to store references to the dataset regions (selections).
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The first selection is a 6 x 6 hyperslab. The second selection is a point
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selection in the same dataset.
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References to both selections are created and stored in the buffer, and then
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written to the dataset in the file.
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[<A HREF="examples/h5_ref2regw.c">Download h5_ref2regw.c</A>]
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<PRE>
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++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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#include <stdlib.h>
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#include <hdf5.h>
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#define FILE2 "trefer2.h5"
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#define SPACE1_NAME "Space1"
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#define SPACE1_RANK 1
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#define SPACE1_DIM1 4
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/* Dataset with fixed dimensions */
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#define SPACE2_NAME "Space2"
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#define SPACE2_RANK 2
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#define SPACE2_DIM1 10
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#define SPACE2_DIM2 10
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/* Element selection information */
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#define POINT1_NPOINTS 10
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int
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main(void)
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{
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hid_t fid1; /* HDF5 File IDs */
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hid_t dset1, /* Dataset ID */
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dset2; /* Dereferenced dataset ID */
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hid_t sid1, /* Dataspace ID #1 */
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sid2; /* Dataspace ID #2 */
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hsize_t dims1[] = {SPACE1_DIM1},
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dims2[] = {SPACE2_DIM1, SPACE2_DIM2};
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hssize_t start[SPACE2_RANK]; /* Starting location of hyperslab */
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hsize_t stride[SPACE2_RANK]; /* Stride of hyperslab */
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hsize_t count[SPACE2_RANK]; /* Element count of hyperslab */
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hsize_t block[SPACE2_RANK]; /* Block size of hyperslab */
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hssize_t coord1[POINT1_NPOINTS][SPACE2_RANK];
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/* Coordinates for point selection */
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hdset_reg_ref_t *wbuf; /* buffer to write to disk */
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int *dwbuf; /* Buffer for writing numeric data to disk */
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int i; /* counting variables */
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herr_t ret; /* Generic return value */
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/* Allocate write & read buffers */
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wbuf=calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1);
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dwbuf=malloc(sizeof(int)*SPACE2_DIM1*SPACE2_DIM2);
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/* Create file */
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fid1 = H5Fcreate(FILE2, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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/* Create dataspace for datasets */
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sid2 = H5Screate_simple(SPACE2_RANK, dims2, NULL);
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/* Create a dataset */
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dset2=H5Dcreate(fid1,"Dataset2",H5T_STD_U8LE,sid2,H5P_DEFAULT);
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for(i=0; i < SPACE2_DIM1*SPACE2_DIM2; i++)
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dwbuf[i]=i*3;
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/* Write selection to disk */
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ret=H5Dwrite(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,dwbuf);
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/* Close Dataset */
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ret = H5Dclose(dset2);
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/* Create dataspace for the reference dataset */
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sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
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/* Create a dataset */
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dset1=H5Dcreate(fid1,"Dataset1",H5T_STD_REF_DSETREG,sid1,H5P_DEFAULT);
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/* Create references */
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/* Select 6x6 hyperslab for first reference */
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start[0]=2; start[1]=2;
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stride[0]=1; stride[1]=1;
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count[0]=6; count[1]=6;
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block[0]=1; block[1]=1;
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ret = H5Sselect_hyperslab(sid2,H5S_SELECT_SET,start,stride,count,block);
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/* Store first dataset region */
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ret = H5Rcreate(&wbuf[0],fid1,"/Dataset2",H5R_DATASET_REGION,sid2);
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/* Select sequence of ten points for second reference */
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coord1[0][0]=6; coord1[0][1]=9;
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coord1[1][0]=2; coord1[1][1]=2;
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coord1[2][0]=8; coord1[2][1]=4;
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coord1[3][0]=1; coord1[3][1]=6;
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coord1[4][0]=2; coord1[4][1]=8;
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coord1[5][0]=3; coord1[5][1]=2;
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coord1[6][0]=0; coord1[6][1]=4;
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coord1[7][0]=9; coord1[7][1]=0;
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coord1[8][0]=7; coord1[8][1]=1;
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coord1[9][0]=3; coord1[9][1]=3;
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ret = H5Sselect_elements(sid2,H5S_SELECT_SET,POINT1_NPOINTS,(const hssize_t **)coord1);
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/* Store second dataset region */
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ret = H5Rcreate(&wbuf[1],fid1,"/Dataset2",H5R_DATASET_REGION,sid2);
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/* Write selection to disk */
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ret=H5Dwrite(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,wbuf);
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/* Close all objects */
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ret = H5Sclose(sid1);
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ret = H5Dclose(dset1);
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ret = H5Sclose(sid2);
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/* Close file */
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ret = H5Fclose(fid1);
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free(wbuf);
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free(dwbuf);
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return 0;
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}
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++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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</PRE>
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<A NAME="rem1">
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<H3><U>Remarks</U></H3>
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<UL>
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<LI> The code,
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<PRE>
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dset1=H5Dcreate(fid1,"Dataset1",H5T_STD_REF_DSETREG,sid1,H5P_DEFAULT);
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</PRE>
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creates a dataset to store references to the dataset(s) regions(selections).
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Notice that the H5T_STD_REF_DSETREG data type is used.
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<P>
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<LI> This program uses hyperslab and point selections. We used the dataspace
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handle <I>sid2</I> for the calls to H5Sselect_hyperslab and
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H5Sselect_elements. The handle was created when dataset "Dataset2" was
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created and it describes the dataset's dataspace. We did not close it when
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the dataset was closed to decrease the number of function calls used
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in the example.
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In a real application program, one should open the dataset and determine
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its dataspace using the H5Dget_space function.
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<P>
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<LI> H5Rcreate is used to create a dataset region reference and store it in a
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buffer. The signature of the function is:
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<PRE>
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herr_t H5Rcreate(void *buf, hid_t loc_id, const char *name,
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H5R_type_t ref_type, hid_t space_id)
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</PRE>
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<UL>
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<LI> The first argument specifies the buffer to store the reference.
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<LI> The second and third arguments specify the name of the referenced
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dataset. In our example the file identifier <I>fid1</I> and the
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absolute name of the dataset "/Dataset2" were used to identify the
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dataset. The reference to the region of this dataset is stored in
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the buffer <I>buf</I>.
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<LI> The fourth argument specifies the type of the reference. Since we are
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creating references to the dataset regions, the H5R_DATASET_REGION
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data type is used.
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<LI> The fifth argument is a dataspace identifier of the referenced dataset.
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</UL>
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</UL>
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<A NAME="fc1">
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<H3><U>File Contents</U></H3>
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The contents of the file "trefer2.h5" created by this program are as follows:
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<PRE>
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HDF5 "trefer2.h5" {
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GROUP "/" {
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DATASET "Dataset1" {
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DATATYPE { H5T_REFERENCE }
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DATASPACE { SIMPLE ( 4 ) / ( 4 ) }
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DATA {
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DATASET 0:744 {(2,2)-(7,7)}, DATASET 0:744 {(6,9), (2,2), (8,4), (1,6),
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(2,8), (3,2), (0,4), (9,0), (7,1), (3,3)}, NULL, NULL
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}
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}
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DATASET "Dataset2" {
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DATATYPE { H5T_STD_U8LE }
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DATASPACE { SIMPLE ( 10, 10 ) / ( 10, 10 ) }
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DATA {
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0, 3, 6, 9, 12, 15, 18, 21, 24, 27,
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30, 33, 36, 39, 42, 45, 48, 51, 54, 57,
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60, 63, 66, 69, 72, 75, 78, 81, 84, 87,
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90, 93, 96, 99, 102, 105, 108, 111, 114, 117,
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120, 123, 126, 129, 132, 135, 138, 141, 144, 147,
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150, 153, 156, 159, 162, 165, 168, 171, 174, 177,
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180, 183, 186, 189, 192, 195, 198, 201, 204, 207,
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210, 213, 216, 219, 222, 225, 228, 231, 234, 237,
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240, 243, 246, 249, 252, 255, 255, 255, 255, 255,
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255, 255, 255, 255, 255, 255, 255, 255, 255, 255
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}
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}
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}
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}
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</PRE>
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Notice how raw data of the dataset with the dataset regions is displayed.
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Each element of the raw data consists of a reference to the dataset
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(DATASET number1:number2) and its selected region.
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If the selection is a hyperslab, the corner coordinates of the hyperslab
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are displayed.
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For the point selection, the coordinates of each point are displayed.
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Since only two selections were stored, the third and fourth elements of the
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dataset "Dataset1" are set to NULL. This was done by the buffer
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inizialization in the program.
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<A NAME="def2">
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<H2>Reading References to Dataset Regions</H2>
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The following steps are involved in reading references to the dataset
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regions and referenced dataset regions (selections).
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<OL>
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<LI> Open and read the dataset containing references to the dataset regions.
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The data type H5T_STD_REF_DSETREG must be used during read operation.
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<P>
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<LI>Use H5Rdereference to obtain the dataset identifier from the read
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dataset region reference.
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<PRE> <B>OR</B>
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</PRE>
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Use H5Rget_region to obtain the dataspace identifier for the dataset
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containing the selection from the read dataset region reference.
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<P>
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<LI> With the dataspace identifier, the H5S interface functions,
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H5Sget_select_*, can be used to obtain information about the
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selection.
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<P>
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<LI> Close all objects when they are no longer needed.
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</OL>
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<H2> Programming Example</H2>
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<A NAME="desc2">
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<H3><U>Description</U></H3>
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The following example reads a dataset containing dataset region references.
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It reads data from the dereferenced dataset and displays the number of
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elements and raw data. Then it reads two selections:
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hyperslab and point. The program queries a number of points in the
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hyperslab and the coordinates and displays them. Then it queries a number of
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selected points and their coordinates and displays the information.<BR>
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[ <A HREF="examples/h5_ref2regr.c">Download h5_ref2regr.c</A> ]
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<PRE>
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++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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#include <stdlib.h>
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#include <hdf5.h>
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#define FILE2 "trefer2.h5"
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#define NPOINTS 10
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/* 1-D dataset with fixed dimensions */
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#define SPACE1_NAME "Space1"
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#define SPACE1_RANK 1
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#define SPACE1_DIM1 4
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/* 2-D dataset with fixed dimensions */
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#define SPACE2_NAME "Space2"
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#define SPACE2_RANK 2
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#define SPACE2_DIM1 10
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#define SPACE2_DIM2 10
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int
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main(void)
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{
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hid_t fid1; /* HDF5 File IDs */
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hid_t dset1, /* Dataset ID */
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dset2; /* Dereferenced dataset ID */
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hid_t sid1, /* Dataspace ID #1 */
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sid2; /* Dataspace ID #2 */
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hsize_t * coords; /* Coordinate buffer */
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hsize_t low[SPACE2_RANK]; /* Selection bounds */
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hsize_t high[SPACE2_RANK]; /* Selection bounds */
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hdset_reg_ref_t *rbuf; /* buffer to to read disk */
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int *drbuf; /* Buffer for reading numeric data from disk */
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int i, j; /* counting variables */
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herr_t ret; /* Generic return value */
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/* Output message about test being performed */
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/* Allocate write & read buffers */
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rbuf=malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1);
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drbuf=calloc(sizeof(int),SPACE2_DIM1*SPACE2_DIM2);
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/* Open the file */
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fid1 = H5Fopen(FILE2, H5F_ACC_RDWR, H5P_DEFAULT);
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/* Open the dataset */
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dset1=H5Dopen(fid1,"/Dataset1");
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/* Read selection from disk */
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ret=H5Dread(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,rbuf);
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/* Try to open objects */
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dset2 = H5Rdereference(dset1,H5R_DATASET_REGION,&rbuf[0]);
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/* Check information in referenced dataset */
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sid1 = H5Dget_space(dset2);
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ret=H5Sget_simple_extent_npoints(sid1);
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printf(" Number of elements in the dataset is : %d\n",ret);
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/* Read from disk */
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ret=H5Dread(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,drbuf);
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for(i=0; i < SPACE2_DIM1; i++) {
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for (j=0; j < SPACE2_DIM2; j++) printf (" %d ", drbuf[i*SPACE2_DIM2+j]);
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printf("\n"); }
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/* Get the hyperslab selection */
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sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[0]);
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/* Verify correct hyperslab selected */
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ret = H5Sget_select_npoints(sid2);
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printf(" Number of elements in the hyperslab is : %d \n", ret);
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ret = H5Sget_select_hyper_nblocks(sid2);
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coords=malloc(ret*SPACE2_RANK*sizeof(hsize_t)*2); /* allocate space for the hyperslab blocks */
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ret = H5Sget_select_hyper_blocklist(sid2,0,ret,coords);
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printf(" Hyperslab coordinates are : \n");
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printf (" ( %lu , %lu ) ( %lu , %lu ) \n", \
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(unsigned long)coords[0],(unsigned long)coords[1],(unsigned long)coords[2],(unsigned long)coords[3]);
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free(coords);
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ret = H5Sget_select_bounds(sid2,low,high);
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/* Close region space */
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ret = H5Sclose(sid2);
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/* Get the element selection */
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sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[1]);
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/* Verify correct elements selected */
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ret = H5Sget_select_elem_npoints(sid2);
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printf(" Number of selected elements is : %d\n", ret);
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/* Allocate space for the element points */
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coords= malloc(ret*SPACE2_RANK*sizeof(hsize_t));
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ret = H5Sget_select_elem_pointlist(sid2,0,ret,coords);
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printf(" Coordinates of selected elements are : \n");
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for (i=0; i < 2*NPOINTS; i=i+2)
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printf(" ( %lu , %lu ) \n", (unsigned long)coords[i],(unsigned long)coords[i+1]);
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free(coords);
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ret = H5Sget_select_bounds(sid2,low,high);
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/* Close region space */
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ret = H5Sclose(sid2);
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/* Close first space */
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ret = H5Sclose(sid1);
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/* Close dereferenced Dataset */
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ret = H5Dclose(dset2);
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/* Close Dataset */
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ret = H5Dclose(dset1);
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/* Close file */
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ret = H5Fclose(fid1);
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/* Free memory buffers */
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free(rbuf);
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free(drbuf);
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return 0;
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}
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++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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</PRE>
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Output of this program is :
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<PRE>
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Number of elements in the dataset is : 100
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0 3 6 9 12 15 18 21 24 27
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30 33 36 39 42 45 48 51 54 57
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60 63 66 69 72 75 78 81 84 87
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90 93 96 99 102 105 108 111 114 117
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120 123 126 129 132 135 138 141 144 147
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|
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 )
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|
Number of selected elements is : 10
|
|
Coordinates of selected elements are :
|
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( 6 , 9 )
|
|
( 2 , 2 )
|
|
( 8 , 4 )
|
|
( 1 , 6 )
|
|
( 2 , 8 )
|
|
( 3 , 2 )
|
|
( 0 , 4 )
|
|
( 9 , 0 )
|
|
( 7 , 1 )
|
|
( 3 , 3 )
|
|
|
|
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|
|
</PRE>
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|
<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>
|
|
|
|
|
|
<!-- BEGIN FOOTER INFO -->
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<P><hr noshade size=1>
|
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<font face="arial,helvetica" size="-1">
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<a href="http://www.ncsa.uiuc.edu/"><img border=0
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src="http://www.ncsa.uiuc.edu/Images/NCSAhome/footerlogo.gif"
|
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width=78 height=27 alt="NCSA"><br>
|
|
The National Center for Supercomputing Applications</A><br>
|
|
<a href="http://www.uiuc.edu/">University of Illinois
|
|
at Urbana-Champaign</a><br>
|
|
<br>
|
|
<!-- <A HREF="helpdesk.mail.html"> -->
|
|
<A HREF="mailto:hdfhelp@ncsa.uiuc.edu">
|
|
hdfhelp@ncsa.uiuc.edu</A>
|
|
<BR> <H6>Last Modified: August 27, 1999</H6><BR>
|
|
<!-- modified by Barbara Jones - bljones@ncsa.uiuc.edu -->
|
|
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|
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|
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