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+<HTML>
+<HEAD>
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=windows-1252">
+<META NAME="Generator" CONTENT="Microsoft Word 97">
+<TITLE>Introduction to HDF5</TITLE>
+</HEAD>
+<BODY LINK="#0000ff" VLINK="#800080" bgcolor="#FFFFFF">
+
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+Introduction to HDF5&nbsp;<br>
+<a href="../H5.user.html">HDF5 User Guide</a>&nbsp;
+<!--
+<a href="../Glossary.html">Glossary</a><br>
+-->
+</td>
+<td valign=top align=right>
+<a href="../RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+<a href="../index.html">Other HDF5 documents and links</a>&nbsp;
+</td></tr>
+</table>
+</center>
+<hr>
+
+
+<h1 ALIGN="CENTER">Introduction to HDF5 -- Example Codes</h1></a>
+
+
+<a name="IEx-TOC">
+<hr>
+<center>
+<table border=0 width=90%>
+<tr><th colspan=3>Table of Contents</th></tr></a>
+<tr><td valign=top align=left width=42%>
+
+ <font size=-1>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <A href="#CreateExample">1: Creating and writing a
+ dataset</A><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <A href="#CheckAndReadExample">2. Reading a hyperslab</A><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <A href="#WriteSelected">3. Writing selected data</A><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <A href="#Compound">4. Working with compound datatypes</A><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <A href="#CreateExtendWrite">5. Creating and writing an extendible</a> <br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <A href="#CreateExtendWrite">dataset</A><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <A href="#ReadExtended">6. Reading data</A><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <A href="#CreateGroups">7. Creating groups</A><br>
+ </font>
+
+</td><td width=6%>&nbsp;&nbsp;</td><td valign=top align=left width=42%>
+
+ <font size=-1>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <A href="#ReadWriteAttributes">8. Writing and reading
+ attributes</A><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <a href="#CreateWriteRefObj">9. Creating and writing references</a><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <a href="#CreateWriteRefObj">to objects</a><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <a href="#ReadRefObj">10. Reading references to objects</a><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <a href="#CreateWriteRefReg">11. Creating and writing references</a><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <a href="#CreateWriteRefReg">to dataset regions</a><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <a href="#ReadRefReg">12. Reading references to dataset</a><br>
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ &nbsp;&nbsp&nbsp;&nbsp;&nbsp;&nbsp&nbsp;&nbsp;
+ <a href="#ReadRefReg">regions</a>
+ </font>
+</td></tr>
+</table>
+</center>
+<p>
+
+<hr>
+
+
+
+<H4><A NAME="CreateExample">Example 1: How to create a homogeneous multi-dimensional dataset</A> and write it to a file.</A></H4>
+<P>This example creates a 2-dimensional HDF 5 dataset of little endian 32-bit integers.
+<PRE>
+<!-- Insert Example 1, h5_write.c, here. -->
+/*
+ * This example writes data to the HDF5 file.
+ * Data conversion is performed during write operation.
+ */
+
+#include <hdf5.h>
+
+#define FILE "SDS.h5"
+#define DATASETNAME "IntArray"
+#define NX 5 /* dataset dimensions */
+#define NY 6
+#define RANK 2
+
+int
+main (void)
+{
+ hid_t file, dataset; /* file and dataset handles */
+ hid_t datatype, dataspace; /* handles */
+ hsize_t dimsf[2]; /* dataset dimensions */
+ herr_t status;
+ int data[NX][NY]; /* data to write */
+ int i, j;
+
+ /*
+ * Data and output buffer initialization.
+ */
+ for (j = 0; j < NX; j++) {
+ for (i = 0; i < NY; i++)
+ data[j][i] = i + j;
+ }
+ /*
+ * 0 1 2 3 4 5
+ * 1 2 3 4 5 6
+ * 2 3 4 5 6 7
+ * 3 4 5 6 7 8
+ * 4 5 6 7 8 9
+ */
+
+ /*
+ * Create a new file using H5F_ACC_TRUNC access,
+ * default file creation properties, and default file
+ * access properties.
+ */
+ file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+ /*
+ * Describe the size of the array and create the data space for fixed
+ * size dataset.
+ */
+ dimsf[0] = NX;
+ dimsf[1] = NY;
+ dataspace = H5Screate_simple(RANK, dimsf, NULL);
+
+ /*
+ * Define datatype for the data in the file.
+ * We will store little endian INT numbers.
+ */
+ datatype = H5Tcopy(H5T_NATIVE_INT);
+ status = H5Tset_order(datatype, H5T_ORDER_LE);
+
+ /*
+ * Create a new dataset within the file using defined dataspace and
+ * datatype and default dataset creation properties.
+ */
+ dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace,
+ H5P_DEFAULT);
+
+ /*
+ * Write the data to the dataset using default transfer properties.
+ */
+ status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, data);
+
+ /*
+ * Close/release resources.
+ */
+ H5Sclose(dataspace);
+ H5Tclose(datatype);
+ H5Dclose(dataset);
+ H5Fclose(file);
+
+ return 0;
+}
+</pre>
+
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<A NAME="CheckAndReadExample">&nbsp;</a>
+<H4><A NAME="_Toc429885326">Example 2.</A> How to read a hyperslab from file into memory.</A></H4>
+<P>This example reads a hyperslab from a 2-d HDF5 dataset into a 3-d dataset in memory.
+<PRE>
+<!-- Insert Example 2, h5_read.c, here. -->
+/*
+ * This example reads hyperslab from the SDS.h5 file
+ * created by h5_write.c program into two-dimensional
+ * plane of the three-dimensional array.
+ * Information about dataset in the SDS.h5 file is obtained.
+ */
+
+#include "hdf5.h"
+
+#define FILE "SDS.h5"
+#define DATASETNAME "IntArray"
+#define NX_SUB 3 /* hyperslab dimensions */
+#define NY_SUB 4
+#define NX 7 /* output buffer dimensions */
+#define NY 7
+#define NZ 3
+#define RANK 2
+#define RANK_OUT 3
+
+int
+main (void)
+{
+ hid_t file, dataset; /* handles */
+ hid_t datatype, dataspace;
+ hid_t memspace;
+ H5T_class_t class; /* datatype class */
+ H5T_order_t order; /* data order */
+ size_t size; /*
+ * size of the data element
+ * stored in file
+ */
+ hsize_t dimsm[3]; /* memory space dimensions */
+ hsize_t dims_out[2]; /* dataset dimensions */
+ herr_t status;
+
+ int data_out[NX][NY][NZ ]; /* output buffer */
+
+ hsize_t count[2]; /* size of the hyperslab in the file */
+ hssize_t offset[2]; /* hyperslab offset in the file */
+ hsize_t count_out[3]; /* size of the hyperslab in memory */
+ hssize_t offset_out[3]; /* hyperslab offset in memory */
+ int i, j, k, status_n, rank;
+
+ for (j = 0; j < NX; j++) {
+ for (i = 0; i < NY; i++) {
+ for (k = 0; k < NZ ; k++)
+ data_out[j][i][k] = 0;
+ }
+ }
+
+ /*
+ * Open the file and the dataset.
+ */
+ file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
+ dataset = H5Dopen(file, DATASETNAME);
+
+ /*
+ * Get datatype and dataspace handles and then query
+ * dataset class, order, size, rank and dimensions.
+ */
+ datatype = H5Dget_type(dataset); /* datatype handle */
+ class = H5Tget_class(datatype);
+ if (class == H5T_INTEGER) printf("Data set has INTEGER type \n");
+ order = H5Tget_order(datatype);
+ if (order == H5T_ORDER_LE) printf("Little endian order \n");
+
+ size = H5Tget_size(datatype);
+ printf(" Data size is %d \n", size);
+
+ dataspace = H5Dget_space(dataset); /* dataspace handle */
+ rank = H5Sget_simple_extent_ndims(dataspace);
+ status_n = H5Sget_simple_extent_dims(dataspace, dims_out, NULL);
+ printf("rank %d, dimensions %lu x %lu \n", rank,
+ (unsigned long)(dims_out[0]), (unsigned long)(dims_out[1]));
+
+ /*
+ * Define hyperslab in the dataset.
+ */
+ offset[0] = 1;
+ offset[1] = 2;
+ count[0] = NX_SUB;
+ count[1] = NY_SUB;
+ status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL,
+ count, NULL);
+
+ /*
+ * Define the memory dataspace.
+ */
+ dimsm[0] = NX;
+ dimsm[1] = NY;
+ dimsm[2] = NZ ;
+ memspace = H5Screate_simple(RANK_OUT,dimsm,NULL);
+
+ /*
+ * Define memory hyperslab.
+ */
+ offset_out[0] = 3;
+ offset_out[1] = 0;
+ offset_out[2] = 0;
+ count_out[0] = NX_SUB;
+ count_out[1] = NY_SUB;
+ count_out[2] = 1;
+ status = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, offset_out, NULL,
+ count_out, NULL);
+
+ /*
+ * Read data from hyperslab in the file into the hyperslab in
+ * memory and display.
+ */
+ status = H5Dread(dataset, H5T_NATIVE_INT, memspace, dataspace,
+ H5P_DEFAULT, data_out);
+ for (j = 0; j < NX; j++) {
+ for (i = 0; i < NY; i++) printf("%d ", data_out[j][i][0]);
+ printf("\n");
+ }
+ /*
+ * 0 0 0 0 0 0 0
+ * 0 0 0 0 0 0 0
+ * 0 0 0 0 0 0 0
+ * 3 4 5 6 0 0 0
+ * 4 5 6 7 0 0 0
+ * 5 6 7 8 0 0 0
+ * 0 0 0 0 0 0 0
+ */
+
+ /*
+ * Close/release resources.
+ */
+ H5Tclose(datatype);
+ H5Dclose(dataset);
+ H5Sclose(dataspace);
+ H5Sclose(memspace);
+ H5Fclose(file);
+
+ return 0;
+}
+</pre>
+
+
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<H4><A NAME="_Toc429885331"><A NAME="WriteSelected"></A>Example 3. Writing selected data from memory to a file.</A></H4>
+<P>This example shows how to use the selection capabilities of HDF5 to write selected data to a file. It includes the examples discussed in the text.
+
+<pre>
+<!-- Insert Example 3, h5_select.c, here. -->
+/*
+ * This program shows how the H5Sselect_hyperslab and H5Sselect_elements
+ * functions are used to write selected data from memory to the file.
+ * Program takes 48 elements from the linear buffer and writes them into
+ * the matrix using 3x2 blocks, (4,3) stride and (2,4) count.
+ * Then four elements of the matrix are overwritten with the new values and
+ * file is closed. Program reopens the file and reads and displays the result.
+ */
+
+#include <hdf5.h>
+
+#define FILE "Select.h5"
+
+#define MSPACE1_RANK 1 /* Rank of the first dataset in memory */
+#define MSPACE1_DIM 50 /* Dataset size in memory */
+
+#define MSPACE2_RANK 1 /* Rank of the second dataset in memory */
+#define MSPACE2_DIM 4 /* Dataset size in memory */
+
+#define FSPACE_RANK 2 /* Dataset rank as it is stored in the file */
+#define FSPACE_DIM1 8 /* Dimension sizes of the dataset as it is
+ stored in the file */
+#define FSPACE_DIM2 12
+
+ /* We will read dataset back from the file
+ to the dataset in memory with these
+ dataspace parameters. */
+#define MSPACE_RANK 2
+#define MSPACE_DIM1 8
+#define MSPACE_DIM2 12
+
+#define NPOINTS 4 /* Number of points that will be selected
+ and overwritten */
+int main (void)
+{
+
+ hid_t file, dataset; /* File and dataset identifiers */
+ hid_t mid1, mid2, fid; /* Dataspace identifiers */
+ hsize_t dim1[] = {MSPACE1_DIM}; /* Dimension size of the first dataset
+ (in memory) */
+ hsize_t dim2[] = {MSPACE2_DIM}; /* Dimension size of the second dataset
+ (in memory */
+ hsize_t fdim[] = {FSPACE_DIM1, FSPACE_DIM2};
+ /* Dimension sizes of the dataset (on disk) */
+
+ hssize_t start[2]; /* Start of hyperslab */
+ hsize_t stride[2]; /* Stride of hyperslab */
+ hsize_t count[2]; /* Block count */
+ hsize_t block[2]; /* Block sizes */
+
+ hssize_t coord[NPOINTS][FSPACE_RANK]; /* Array to store selected points
+ from the file dataspace */
+ herr_t ret;
+ uint i,j;
+ int matrix[MSPACE_DIM1][MSPACE_DIM2];
+ int vector[MSPACE1_DIM];
+ int values[] = {53, 59, 61, 67}; /* New values to be written */
+
+ /*
+ * Buffers' initialization.
+ */
+ vector[0] = vector[MSPACE1_DIM - 1] = -1;
+ for (i = 1; i < MSPACE1_DIM - 1; i++) vector[i] = i;
+
+ for (i = 0; i < MSPACE_DIM1; i++) {
+ for (j = 0; j < MSPACE_DIM2; j++)
+ matrix[i][j] = 0;
+ }
+
+ /*
+ * Create a file.
+ */
+ file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+ /*
+ * Create dataspace for the dataset in the file.
+ */
+ fid = H5Screate_simple(FSPACE_RANK, fdim, NULL);
+
+ /*
+ * Create dataset and write it into the file.
+ */
+ dataset = H5Dcreate(file, "Matrix in file", H5T_NATIVE_INT, fid, H5P_DEFAULT);
+ ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, matrix);
+
+ /*
+ * Select hyperslab for the dataset in the file, using 3x2 blocks,
+ * (4,3) stride and (2,4) count starting at the position (0,1).
+ */
+ start[0] = 0; start[1] = 1;
+ stride[0] = 4; stride[1] = 3;
+ count[0] = 2; count[1] = 4;
+ block[0] = 3; block[1] = 2;
+ ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block);
+
+ /*
+ * Create dataspace for the first dataset.
+ */
+ mid1 = H5Screate_simple(MSPACE1_RANK, dim1, NULL);
+
+ /*
+ * Select hyperslab.
+ * We will use 48 elements of the vector buffer starting at the second element.
+ * Selected elements are 1 2 3 . . . 48
+ */
+ start[0] = 1;
+ stride[0] = 1;
+ count[0] = 48;
+ block[0] = 1;
+ ret = H5Sselect_hyperslab(mid1, H5S_SELECT_SET, start, stride, count, block);
+
+ /*
+ * Write selection from the vector buffer to the dataset in the file.
+ *
+ * File dataset should look like this:
+ * 0 1 2 0 3 4 0 5 6 0 7 8
+ * 0 9 10 0 11 12 0 13 14 0 15 16
+ * 0 17 18 0 19 20 0 21 22 0 23 24
+ * 0 0 0 0 0 0 0 0 0 0 0 0
+ * 0 25 26 0 27 28 0 29 30 0 31 32
+ * 0 33 34 0 35 36 0 37 38 0 39 40
+ * 0 41 42 0 43 44 0 45 46 0 47 48
+ * 0 0 0 0 0 0 0 0 0 0 0 0
+ */
+ ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid1, fid, H5P_DEFAULT, vector);
+
+ /*
+ * Reset the selection for the file dataspace fid.
+ */
+ ret = H5Sselect_none(fid);
+
+ /*
+ * Create dataspace for the second dataset.
+ */
+ mid2 = H5Screate_simple(MSPACE2_RANK, dim2, NULL);
+
+ /*
+ * Select sequence of NPOINTS points in the file dataspace.
+ */
+ coord[0][0] = 0; coord[0][1] = 0;
+ coord[1][0] = 3; coord[1][1] = 3;
+ coord[2][0] = 3; coord[2][1] = 5;
+ coord[3][0] = 5; coord[3][1] = 6;
+
+ ret = H5Sselect_elements(fid, H5S_SELECT_SET, NPOINTS,
+ (const hssize_t **)coord);
+
+ /*
+ * Write new selection of points to the dataset.
+ */
+ ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid2, fid, H5P_DEFAULT, values);
+
+ /*
+ * File dataset should look like this:
+ * 53 1 2 0 3 4 0 5 6 0 7 8
+ * 0 9 10 0 11 12 0 13 14 0 15 16
+ * 0 17 18 0 19 20 0 21 22 0 23 24
+ * 0 0 0 59 0 61 0 0 0 0 0 0
+ * 0 25 26 0 27 28 0 29 30 0 31 32
+ * 0 33 34 0 35 36 67 37 38 0 39 40
+ * 0 41 42 0 43 44 0 45 46 0 47 48
+ * 0 0 0 0 0 0 0 0 0 0 0 0
+ *
+ */
+
+ /*
+ * Close memory file and memory dataspaces.
+ */
+ ret = H5Sclose(mid1);
+ ret = H5Sclose(mid2);
+ ret = H5Sclose(fid);
+
+ /*
+ * Close dataset.
+ */
+ ret = H5Dclose(dataset);
+
+ /*
+ * Close the file.
+ */
+ ret = H5Fclose(file);
+
+ /*
+ * Open the file.
+ */
+ file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
+
+ /*
+ * Open the dataset.
+ */
+ dataset = dataset = H5Dopen(file,"Matrix in file");
+
+ /*
+ * Read data back to the buffer matrix.
+ */
+ ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, matrix);
+
+ /*
+ * Display the result.
+ */
+ for (i=0; i < MSPACE_DIM1; i++) {
+ for(j=0; j < MSPACE_DIM2; j++) printf("%3d ", matrix[i][j]);
+ printf("\n");
+ }
+
+ return 0;
+}
+</pre>
+
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<H4><A NAME="Compound"><A NAME="_Toc429885327"></A>Example 4. Working with compound datatypes.</A></H4>
+<P>This example shows how to create a compound datatype, write an array which has the compound datatype to the file, and read back subsets of fields.
+<PRE>
+<!-- Insert Example 4, h5_compound.c, here. -->
+/*
+ * This example shows how to create a compound datatype,
+ * write an array which has the compound datatype to the file,
+ * and read back fields' subsets.
+ */
+
+#include "hdf5.h"
+
+#define FILE "SDScompound.h5"
+#define DATASETNAME "ArrayOfStructures"
+#define LENGTH 10
+#define RANK 1
+
+int
+main(void)
+{
+
+ /* First structure and dataset*/
+ typedef struct s1_t {
+ int a;
+ float b;
+ double c;
+ } s1_t;
+ s1_t s1[LENGTH];
+ hid_t s1_tid; /* File datatype identifier */
+
+ /* Second structure (subset of s1_t) and dataset*/
+ typedef struct s2_t {
+ double c;
+ int a;
+ } s2_t;
+ s2_t s2[LENGTH];
+ hid_t s2_tid; /* Memory datatype handle */
+
+ /* Third "structure" ( will be used to read float field of s1) */
+ hid_t s3_tid; /* Memory datatype handle */
+ float s3[LENGTH];
+
+ int i;
+ hid_t file, dataset, space; /* Handles */
+ herr_t status;
+ hsize_t dim[] = {LENGTH}; /* Dataspace dimensions */
+
+
+ /*
+ * Initialize the data
+ */
+ for (i = 0; i< LENGTH; i++) {
+ s1[i].a = i;
+ s1[i].b = i*i;
+ s1[i].c = 1./(i+1);
+ }
+
+ /*
+ * Create the data space.
+ */
+ space = H5Screate_simple(RANK, dim, NULL);
+
+ /*
+ * Create the file.
+ */
+ file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+ /*
+ * Create the memory datatype.
+ */
+ s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
+ H5Tinsert(s1_tid, "a_name", HOFFSET(s1_t, a), H5T_NATIVE_INT);
+ H5Tinsert(s1_tid, "c_name", HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE);
+ H5Tinsert(s1_tid, "b_name", HOFFSET(s1_t, b), H5T_NATIVE_FLOAT);
+
+ /*
+ * Create the dataset.
+ */
+ dataset = H5Dcreate(file, DATASETNAME, s1_tid, space, H5P_DEFAULT);
+
+ /*
+ * Wtite data to the dataset;
+ */
+ status = H5Dwrite(dataset, s1_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s1);
+
+ /*
+ * Release resources
+ */
+ H5Tclose(s1_tid);
+ H5Sclose(space);
+ H5Dclose(dataset);
+ H5Fclose(file);
+
+ /*
+ * Open the file and the dataset.
+ */
+ file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
+
+ dataset = H5Dopen(file, DATASETNAME);
+
+ /*
+ * Create a datatype for s2
+ */
+ s2_tid = H5Tcreate(H5T_COMPOUND, sizeof(s2_t));
+
+ H5Tinsert(s2_tid, "c_name", HOFFSET(s2_t, c), H5T_NATIVE_DOUBLE);
+ H5Tinsert(s2_tid, "a_name", HOFFSET(s2_t, a), H5T_NATIVE_INT);
+
+ /*
+ * Read two fields c and a from s1 dataset. Fields in the file
+ * are found by their names "c_name" and "a_name".
+ */
+ status = H5Dread(dataset, s2_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s2);
+
+ /*
+ * Display the fields
+ */
+ printf("\n");
+ printf("Field c : \n");
+ for( i = 0; i < LENGTH; i++) printf("%.4f ", s2[i].c);
+ printf("\n");
+
+ printf("\n");
+ printf("Field a : \n");
+ for( i = 0; i < LENGTH; i++) printf("%d ", s2[i].a);
+ printf("\n");
+
+ /*
+ * Create a datatype for s3.
+ */
+ s3_tid = H5Tcreate(H5T_COMPOUND, sizeof(float));
+
+ status = H5Tinsert(s3_tid, "b_name", 0, H5T_NATIVE_FLOAT);
+
+ /*
+ * Read field b from s1 dataset. Field in the file is found by its name.
+ */
+ status = H5Dread(dataset, s3_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, s3);
+
+ /*
+ * Display the field
+ */
+ printf("\n");
+ printf("Field b : \n");
+ for( i = 0; i < LENGTH; i++) printf("%.4f ", s3[i]);
+ printf("\n");
+
+ /*
+ * Release resources
+ */
+ H5Tclose(s2_tid);
+ H5Tclose(s3_tid);
+ H5Dclose(dataset);
+ H5Fclose(file);
+
+ return 0;
+}
+</pre>
+
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<H4><A NAME="CreateExtendWrite"><A NAME="_Toc429885328"></A>Example 5. Creating and writing an extendible dataset.</A></H4>
+<P>This example shows how to create a 3x3 extendible dataset, to extend the dataset to 10x3, then to extend it again to 10x5.
+<PRE>
+<!-- Insert Example 5, h5_extend_write.c, here. -->
+/*
+ * This example shows how to work with extendible dataset.
+ * In the current version of the library dataset MUST be
+ * chunked.
+ *
+ */
+
+#include "hdf5.h"
+
+#define FILE "SDSextendible.h5"
+#define DATASETNAME "ExtendibleArray"
+#define RANK 2
+#define NX 10
+#define NY 5
+
+int
+main (void)
+{
+ hid_t file; /* handles */
+ hid_t dataspace, dataset;
+ hid_t filespace;
+ hid_t cparms;
+ hsize_t dims[2] = { 3, 3}; /*
+ * dataset dimensions
+ * at the creation time
+ */
+ hsize_t dims1[2] = { 3, 3}; /* data1 dimensions */
+ hsize_t dims2[2] = { 7, 1}; /* data2 dimensions */
+ hsize_t dims3[2] = { 2, 2}; /* data3 dimensions */
+
+ hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
+ hsize_t chunk_dims[2] ={2, 5};
+ hsize_t size[2];
+ hssize_t offset[2];
+
+ herr_t status;
+
+ int data1[3][3] = { {1, 1, 1}, /* data to write */
+ {1, 1, 1},
+ {1, 1, 1} };
+
+ int data2[7] = { 2, 2, 2, 2, 2, 2, 2};
+
+ int data3[2][2] = { {3, 3},
+ {3, 3} };
+
+ /*
+ * Create the data space with unlimited dimensions.
+ */
+ dataspace = H5Screate_simple(RANK, dims, maxdims);
+
+ /*
+ * Create a new file. If file exists its contents will be overwritten.
+ */
+ file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+ /*
+ * Modify dataset creation properties, i.e. enable chunking.
+ */
+ cparms = H5Pcreate (H5P_DATASET_CREATE);
+ status = H5Pset_chunk( cparms, RANK, chunk_dims);
+
+ /*
+ * Create a new dataset within the file using cparms
+ * creation properties.
+ */
+ dataset = H5Dcreate(file, DATASETNAME, H5T_NATIVE_INT, dataspace,
+ cparms);
+
+ /*
+ * Extend the dataset. This call assures that dataset is at least 3 x 3.
+ */
+ size[0] = 3;
+ size[1] = 3;
+ status = H5Dextend (dataset, size);
+
+ /*
+ * Select a hyperslab.
+ */
+ filespace = H5Dget_space (dataset);
+ offset[0] = 0;
+ offset[1] = 0;
+ status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
+ dims1, NULL);
+
+ /*
+ * Write the data to the hyperslab.
+ */
+ status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
+ H5P_DEFAULT, data1);
+
+ /*
+ * Extend the dataset. Dataset becomes 10 x 3.
+ */
+ dims[0] = dims1[0] + dims2[0];
+ size[0] = dims[0];
+ size[1] = dims[1];
+ status = H5Dextend (dataset, size);
+
+ /*
+ * Select a hyperslab.
+ */
+ filespace = H5Dget_space (dataset);
+ offset[0] = 3;
+ offset[1] = 0;
+ status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
+ dims2, NULL);
+
+ /*
+ * Define memory space
+ */
+ dataspace = H5Screate_simple(RANK, dims2, NULL);
+
+ /*
+ * Write the data to the hyperslab.
+ */
+ status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
+ H5P_DEFAULT, data2);
+
+ /*
+ * Extend the dataset. Dataset becomes 10 x 5.
+ */
+ dims[1] = dims1[1] + dims3[1];
+ size[0] = dims[0];
+ size[1] = dims[1];
+ status = H5Dextend (dataset, size);
+
+ /*
+ * Select a hyperslab
+ */
+ filespace = H5Dget_space (dataset);
+ offset[0] = 0;
+ offset[1] = 3;
+ status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
+ dims3, NULL);
+
+ /*
+ * Define memory space.
+ */
+ dataspace = H5Screate_simple(RANK, dims3, NULL);
+
+ /*
+ * Write the data to the hyperslab.
+ */
+ status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
+ H5P_DEFAULT, data3);
+
+ /*
+ * Resulting dataset
+ *
+ * 3 3 3 2 2
+ * 3 3 3 2 2
+ * 3 3 3 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ */
+ /*
+ * Close/release resources.
+ */
+ H5Dclose(dataset);
+ H5Sclose(dataspace);
+ H5Sclose(filespace);
+ H5Fclose(file);
+
+ return 0;
+}
+</pre>
+
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<H4><A NAME="ReadExtended"><A NAME="_Toc429885329"></A>Example 6. Reading data.</A></H4>
+<P>This example shows how to read information the chunked dataset written by <A HREF="#CreateExtendWrite">Example 5</A>.
+<PRE>
+<!-- Insert Example 6, h5_chunk_read.c, here. -->
+/*
+ * This example shows how to read data from a chunked dataset.
+ * We will read from the file created by h5_extend_write.c
+ */
+
+#include "hdf5.h"
+
+#define FILE "SDSextendible.h5"
+#define DATASETNAME "ExtendibleArray"
+#define RANK 2
+#define RANKC 1
+#define NX 10
+#define NY 5
+
+int
+main (void)
+{
+ hid_t file; /* handles */
+ hid_t dataset;
+ hid_t filespace;
+ hid_t memspace;
+ hid_t cparms;
+ hsize_t dims[2]; /* dataset and chunk dimensions*/
+ hsize_t chunk_dims[2];
+ hsize_t col_dims[1];
+ hsize_t count[2];
+ hssize_t offset[2];
+
+ herr_t status, status_n;
+
+ int data_out[NX][NY]; /* buffer for dataset to be read */
+ int chunk_out[2][5]; /* buffer for chunk to be read */
+ int column[10]; /* buffer for column to be read */
+ int rank, rank_chunk;
+ hsize_t i, j;
+
+
+
+ /*
+ * Open the file and the dataset.
+ */
+ file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
+ dataset = H5Dopen(file, DATASETNAME);
+
+ /*
+ * Get dataset rank and dimension.
+ */
+
+ filespace = H5Dget_space(dataset); /* Get filespace handle first. */
+ rank = H5Sget_simple_extent_ndims(filespace);
+ status_n = H5Sget_simple_extent_dims(filespace, dims, NULL);
+ printf("dataset rank %d, dimensions %lu x %lu\n",
+ rank, (unsigned long)(dims[0]), (unsigned long)(dims[1]));
+
+ /*
+ * Get creation properties list.
+ */
+ cparms = H5Dget_create_plist(dataset); /* Get properties handle first. */
+
+ /*
+ * Check if dataset is chunked.
+ */
+ if (H5D_CHUNKED == H5Pget_layout(cparms)) {
+
+ /*
+ * Get chunking information: rank and dimensions
+ */
+ rank_chunk = H5Pget_chunk(cparms, 2, chunk_dims);
+ printf("chunk rank %d, dimensions %lu x %lu\n", rank_chunk,
+ (unsigned long)(chunk_dims[0]), (unsigned long)(chunk_dims[1]));
+ }
+
+ /*
+ * Define the memory space to read dataset.
+ */
+ memspace = H5Screate_simple(RANK,dims,NULL);
+
+ /*
+ * Read dataset back and display.
+ */
+ status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace,
+ H5P_DEFAULT, data_out);
+ printf("\n");
+ printf("Dataset: \n");
+ for (j = 0; j < dims[0]; j++) {
+ for (i = 0; i < dims[1]; i++) printf("%d ", data_out[j][i]);
+ printf("\n");
+ }
+
+ /*
+ * dataset rank 2, dimensions 10 x 5
+ * chunk rank 2, dimensions 2 x 5
+
+ * Dataset:
+ * 1 1 1 3 3
+ * 1 1 1 3 3
+ * 1 1 1 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ * 2 0 0 0 0
+ */
+
+ /*
+ * Read the third column from the dataset.
+ * First define memory dataspace, then define hyperslab
+ * and read it into column array.
+ */
+ col_dims[0] = 10;
+ memspace = H5Screate_simple(RANKC, col_dims, NULL);
+
+ /*
+ * Define the column (hyperslab) to read.
+ */
+ offset[0] = 0;
+ offset[1] = 2;
+ count[0] = 10;
+ count[1] = 1;
+ status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
+ count, NULL);
+ status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace,
+ H5P_DEFAULT, column);
+ printf("\n");
+ printf("Third column: \n");
+ for (i = 0; i < 10; i++) {
+ printf("%d \n", column[i]);
+ }
+
+ /*
+ * Third column:
+ * 1
+ * 1
+ * 1
+ * 0
+ * 0
+ * 0
+ * 0
+ * 0
+ * 0
+ * 0
+ */
+
+ /*
+ * Define the memory space to read a chunk.
+ */
+ memspace = H5Screate_simple(rank_chunk,chunk_dims,NULL);
+
+ /*
+ * Define chunk in the file (hyperslab) to read.
+ */
+ offset[0] = 2;
+ offset[1] = 0;
+ count[0] = chunk_dims[0];
+ count[1] = chunk_dims[1];
+ status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
+ count, NULL);
+
+ /*
+ * Read chunk back and display.
+ */
+ status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace,
+ H5P_DEFAULT, chunk_out);
+ printf("\n");
+ printf("Chunk: \n");
+ for (j = 0; j < chunk_dims[0]; j++) {
+ for (i = 0; i < chunk_dims[1]; i++) printf("%d ", chunk_out[j][i]);
+ printf("\n");
+ }
+ /*
+ * Chunk:
+ * 1 1 1 0 0
+ * 2 0 0 0 0
+ */
+
+ /*
+ * Close/release resources.
+ */
+ H5Pclose(cparms);
+ H5Dclose(dataset);
+ H5Sclose(filespace);
+ H5Sclose(memspace);
+ H5Fclose(file);
+
+ return 0;
+)
+
+</pre>
+
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<H4><A NAME="CreateGroups"><A NAME="_Toc429885330"></A>Example 7. Creating groups.</A></H4>
+<P>This example shows how to create and access a group in an
+HDF5 file and to place a dataset within this group.
+It also illustrates the usage of the <code>H5Giterate</code>,
+<code>H5Glink</code>, and <code>H5Gunlink</code> functions.
+
+<PRE>
+<!-- Insert Example 7, h5_group.c, here. -->
+/*
+ * This example creates a group in the file and dataset in the group.
+ * Hard link to the group object is created and the dataset is accessed
+ * under different names.
+ * Iterator function is used to find the object names in the root group.
+ */
+
+
+#include "hdf5.h"
+
+
+#define FILE "group.h5"
+#define RANK 2
+
+
+herr_t file_info(hid_t loc_id, const char *name, void *opdata);
+ /* Operator function */
+int
+main(void)
+{
+
+ hid_t file;
+ hid_t grp;
+ hid_t dataset, dataspace;
+ hid_t plist;
+
+ herr_t status;
+ hsize_t dims[2];
+ hsize_t cdims[2];
+
+ int idx;
+
+ /*
+ * Create a file.
+ */
+ file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+ /*
+ * Create a group in the file.
+ */
+ grp = H5Gcreate(file, "/Data", 0);
+
+ /*
+ * Create dataset "Compressed Data" in the group using absolute
+ * name. Dataset creation property list is modified to use
+ * GZIP compression with the compression effort set to 6.
+ * Note that compression can be used only when dataset is chunked.
+ */
+ dims[0] = 1000;
+ dims[1] = 20;
+ cdims[0] = 20;
+ cdims[1] = 20;
+ dataspace = H5Screate_simple(RANK, dims, NULL);
+ plist = H5Pcreate(H5P_DATASET_CREATE);
+ H5Pset_chunk(plist, 2, cdims);
+ H5Pset_deflate( plist, 6);
+ dataset = H5Dcreate(file, "/Data/Compressed_Data", H5T_NATIVE_INT,
+ dataspace, plist);
+
+ /*
+ * Close the dataset and the file.
+ */
+ H5Sclose(dataspace);
+ H5Dclose(dataset);
+ H5Fclose(file);
+
+ /*
+ * Now reopen the file and group in the file.
+ */
+ file = H5Fopen(FILE, H5F_ACC_RDWR, H5P_DEFAULT);
+ grp = H5Gopen(file, "Data");
+
+ /*
+ * Access "Compressed_Data" dataset in the group.
+ */
+ dataset = H5Dopen(grp, "Compressed_Data");
+ if( dataset < 0) printf(" Dataset is not found. \n");
+ printf("\"/Data/Compressed_Data\" dataset is open \n");
+
+ /*
+ * Close the dataset.
+ */
+ status = H5Dclose(dataset);
+
+ /*
+ * Create hard link to the Data group.
+ */
+ status = H5Glink(file, H5G_LINK_HARD, "Data", "Data_new");
+
+ /*
+ * We can access "Compressed_Data" dataset using created
+ * hard link "Data_new".
+ */
+ dataset = H5Dopen(file, "/Data_new/Compressed_Data");
+ if( dataset < 0) printf(" Dataset is not found. \n");
+ printf("\"/Data_new/Compressed_Data\" dataset is open \n");
+
+ /*
+ * Close the dataset.
+ */
+ status = H5Dclose(dataset);
+
+ /*
+ * Use iterator to see the names of the objects in the file
+ * root directory.
+ */
+ idx = H5Giterate(file, "/", NULL, file_info, NULL);
+
+ /*
+ * Unlink name "Data" and use iterator to see the names
+ * of the objects in the file root direvtory.
+ */
+ if (H5Gunlink(file, "Data") < 0)
+ printf(" H5Gunlink failed \n");
+ else
+ printf("\"Data\" is unlinked \n");
+
+ idx = H5Giterate(file, "/", NULL, file_info, NULL);
+
+
+ /*
+ * Close the file.
+ */
+
+ status = H5Fclose(file);
+
+ return 0;
+}
+/*
+ * Operator function.
+ */
+herr_t
+file_info(hid_t loc_id, const char *name, void *opdata)
+{
+ hid_t grp;
+ /*
+ * Open the group using its name.
+ */
+ grp = H5Gopen(loc_id, name);
+
+ /*
+ * Display group name.
+ */
+ printf("\n");
+ printf("Name : ");
+ puts(name);
+
+ H5Gclose(grp);
+ return 0;
+ }
+</pre>
+
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<H4><A NAME="_Toc429885332"><A NAME="ReadWriteAttributes">Example 8</A>. Writing and reading attributes.</A></H4>
+<P>This example shows how to create HDF5 attributes, to attach them to a dataset, and to read through all of the attributes of a dataset.
+
+<pre>
+<!-- Insert Example 8, h5_attribute.c, here. -->
+/*
+ * This program illustrates the usage of the H5A Interface functions.
+ * It creates and writes a dataset, and then creates and writes array,
+ * scalar, and string attributes of the dataset.
+ * Program reopens the file, attaches to the scalar attribute using
+ * attribute name and reads and displays its value. Then index of the
+ * third attribute is used to read and display attribute values.
+ * The H5Aiterate function is used to iterate through the dataset attributes,
+ * and display their names. The function is also reads and displays the values
+ * of the array attribute.
+ */
+
+#include <stdlib.h>
+#include <hdf5.h>
+
+#define FILE "Attributes.h5"
+
+#define RANK 1 /* Rank and size of the dataset */
+#define SIZE 7
+
+#define ARANK 2 /* Rank and dimension sizes of the first dataset attribute */
+#define ADIM1 2
+#define ADIM2 3
+#define ANAME "Float attribute" /* Name of the array attribute */
+#define ANAMES "Character attribute" /* Name of the string attribute */
+
+herr_t attr_info(hid_t loc_id, const char *name, void *opdata);
+ /* Operator function */
+
+int
+main (void)
+{
+
+ hid_t file, dataset; /* File and dataset identifiers */
+
+ hid_t fid; /* Dataspace identifier */
+ hid_t attr1, attr2, attr3; /* Attribute identifiers */
+ hid_t attr;
+ hid_t aid1, aid2, aid3; /* Attribute dataspace identifiers */
+ hid_t atype; /* Attribute type */
+
+ hsize_t fdim[] = {SIZE};
+ hsize_t adim[] = {ADIM1, ADIM2}; /* Dimensions of the first attribute */
+
+ float matrix[ADIM1][ADIM2]; /* Attribute data */
+
+ herr_t ret; /* Return value */
+ uint i,j; /* Counters */
+ int idx; /* Attribute index */
+ char string_out[80]; /* Buffer to read string attribute back */
+ int point_out; /* Buffer to read scalar attribute back */
+
+ /*
+ * Data initialization.
+ */
+ int vector[] = {1, 2, 3, 4, 5, 6, 7}; /* Dataset data */
+ int point = 1; /* Value of the scalar attribute */
+ char string[] = "ABCD"; /* Value of the string attribute */
+
+
+ for (i=0; i < ADIM1; i++) { /* Values of the array attribute */
+ for (j=0; j < ADIM2; j++)
+ matrix[i][j] = -1.;
+ }
+
+ /*
+ * Create a file.
+ */
+ file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+ /*
+ * Create the dataspace for the dataset in the file.
+ */
+ fid = H5Screate(H5S_SIMPLE);
+ ret = H5Sset_extent_simple(fid, RANK, fdim, NULL);
+
+ /*
+ * Create the dataset in the file.
+ */
+ dataset = H5Dcreate(file, "Dataset", H5T_NATIVE_INT, fid, H5P_DEFAULT);
+
+ /*
+ * Write data to the dataset.
+ */
+ ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT, vector);
+
+ /*
+ * Create dataspace for the first attribute.
+ */
+ aid1 = H5Screate(H5S_SIMPLE);
+ ret = H5Sset_extent_simple(aid1, ARANK, adim, NULL);
+
+ /*
+ * Create array attribute.
+ */
+ attr1 = H5Acreate(dataset, ANAME, H5T_NATIVE_FLOAT, aid1, H5P_DEFAULT);
+
+ /*
+ * Write array attribute.
+ */
+ ret = H5Awrite(attr1, H5T_NATIVE_FLOAT, matrix);
+
+ /*
+ * Create scalar attribute.
+ */
+ aid2 = H5Screate(H5S_SCALAR);
+ attr2 = H5Acreate(dataset, "Integer attribute", H5T_NATIVE_INT, aid2,
+ H5P_DEFAULT);
+
+ /*
+ * Write scalar attribute.
+ */
+ ret = H5Awrite(attr2, H5T_NATIVE_INT, &point);
+
+ /*
+ * Create string attribute.
+ */
+ aid3 = H5Screate(H5S_SCALAR);
+ atype = H5Tcopy(H5T_C_S1);
+ H5Tset_size(atype, 4);
+ attr3 = H5Acreate(dataset, ANAMES, atype, aid3, H5P_DEFAULT);
+
+ /*
+ * Write string attribute.
+ */
+ ret = H5Awrite(attr3, atype, string);
+
+ /*
+ * Close attribute and file dataspaces.
+ */
+ ret = H5Sclose(aid1);
+ ret = H5Sclose(aid2);
+ ret = H5Sclose(aid3);
+ ret = H5Sclose(fid);
+
+ /*
+ * Close the attributes.
+ */
+ ret = H5Aclose(attr1);
+ ret = H5Aclose(attr2);
+ ret = H5Aclose(attr3);
+
+ /*
+ * Close the dataset.
+ */
+ ret = H5Dclose(dataset);
+
+ /*
+ * Close the file.
+ */
+ ret = H5Fclose(file);
+
+ /*
+ * Reopen the file.
+ */
+ file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
+
+ /*
+ * Open the dataset.
+ */
+ dataset = H5Dopen(file,"Dataset");
+
+ /*
+ * Attach to the scalar attribute using attribute name, then read and
+ * display its value.
+ */
+ attr = H5Aopen_name(dataset,"Integer attribute");
+ ret = H5Aread(attr, H5T_NATIVE_INT, &point_out);
+ printf("The value of the attribute \"Integer attribute\" is %d \n", point_out);
+ ret = H5Aclose(attr);
+
+ /*
+ * Attach to the string attribute using its index, then read and display the value.
+ */
+ attr = H5Aopen_idx(dataset, 2);
+ atype = H5Tcopy(H5T_C_S1);
+ H5Tset_size(atype, 4);
+ ret = H5Aread(attr, atype, string_out);
+ printf("The value of the attribute with the index 2 is %s \n", string_out);
+ ret = H5Aclose(attr);
+ ret = H5Tclose(atype);
+
+ /*
+ * Get attribute info using iteration function.
+ */
+ idx = H5Aiterate(dataset, NULL, attr_info, NULL);
+
+ /*
+ * Close the dataset and the file.
+ */
+ H5Dclose(dataset);
+ H5Fclose(file);
+
+ return 0;
+}
+
+/*
+ * Operator function.
+ */
+herr_t
+attr_info(hid_t loc_id, const char *name, void *opdata)
+{
+ hid_t attr, atype, aspace; /* Attribute, datatype and dataspace identifiers */
+ int rank;
+ hsize_t sdim[64];
+ herr_t ret;
+ int i;
+ size_t npoints; /* Number of elements in the array attribute. */
+ float *float_array; /* Pointer to the array attribute. */
+ /*
+ * Open the attribute using its name.
+ */
+ attr = H5Aopen_name(loc_id, name);
+
+ /*
+ * Display attribute name.
+ */
+ printf("\n");
+ printf("Name : ");
+ puts(name);
+
+ /*
+ * Get attribute datatype, dataspace, rank, and dimensions.
+ */
+ atype = H5Aget_type(attr);
+ aspace = H5Aget_space(attr);
+ rank = H5Sget_simple_extent_ndims(aspace);
+ ret = H5Sget_simple_extent_dims(aspace, sdim, NULL);
+
+ /*
+ * Display rank and dimension sizes for the array attribute.
+ */
+
+ if(rank > 0) {
+ printf("Rank : %d \n", rank);
+ printf("Dimension sizes : ");
+ for (i=0; i< rank; i++) printf("%d ", (int)sdim[i]);
+ printf("\n");
+ }
+
+ /*
+ * Read array attribute and display its type and values.
+ */
+
+ if (H5T_FLOAT == H5Tget_class(atype)) {
+ printf("Type : FLOAT \n");
+ npoints = H5Sget_simple_extent_npoints(aspace);
+ float_array = (float *)malloc(sizeof(float)*(int)npoints);
+ ret = H5Aread(attr, atype, float_array);
+ printf("Values : ");
+ for( i = 0; i < (int)npoints; i++) printf("%f ", float_array[i]);
+ printf("\n");
+ free(float_array);
+ }
+
+ /*
+ * Release all identifiers.
+ */
+ H5Tclose(atype);
+ H5Sclose(aspace);
+ H5Aclose(attr);
+
+ return 0;
+}
+</pre>
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<H4><A NAME="CreateWriteRefObj">Example 9</A>. Creating and storing references to objects.</A></H4>
+This example creates a group and two datasets and a named datatype
+in the group. References to these four objects are stored in the dataset
+in the root group.
+
+<PRE>
+
+#include &lt;hdf5.h&gt;
+
+#define FILE1 "trefer1.h5"
+
+/* 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 dataset; /* Dataset ID */
+ hid_t group; /* Group ID */
+ hid_t sid1; /* Dataspace ID */
+ hid_t tid1; /* Datatype ID */
+ hsize_t dims1[] = {SPACE1_DIM1};
+ hobj_ref_t *wbuf; /* buffer to write to disk */
+ int *tu32; /* Temporary pointer to int data */
+ int i; /* counting variables */
+ const char *write_comment="Foo!"; /* Comments for group */
+ herr_t ret; /* Generic return value */
+
+/* Compound datatype */
+typedef struct s1_t {
+ unsigned int a;
+ unsigned int b;
+ float c;
+} s1_t;
+
+ /* Allocate write buffers */
+ wbuf=(hobj_ref_t *)malloc(sizeof(hobj_ref_t)*SPACE1_DIM1);
+ tu32=malloc(sizeof(int)*SPACE1_DIM1);
+
+ /* Create file */
+ fid1 = H5Fcreate(FILE1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+
+ /* Create dataspace for datasets */
+ sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
+
+ /* Create a group */
+ group=H5Gcreate(fid1,"Group1",-1);
+
+ /* Set group's comment */
+ ret=H5Gset_comment(group,".",write_comment);
+
+ /* Create a dataset (inside Group1) */
+ dataset=H5Dcreate(group,"Dataset1",H5T_STD_U32LE,sid1,H5P_DEFAULT);
+
+ for(i=0; i &lt; SPACE1_DIM1; i++)
+ tu32[i] = i*3;
+
+ /* Write selection to disk */
+ ret=H5Dwrite(dataset,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,tu32);
+
+ /* Close Dataset */
+ ret = H5Dclose(dataset);
+
+ /* Create another dataset (inside Group1) */
+ dataset=H5Dcreate(group,"Dataset2",H5T_NATIVE_UCHAR,sid1,H5P_DEFAULT);
+
+ /* Close Dataset */
+ ret = H5Dclose(dataset);
+
+ /* Create a datatype to refer to */
+ tid1 = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
+
+ /* Insert fields */
+ ret=H5Tinsert (tid1, "a", HOFFSET(s1_t,a), H5T_NATIVE_INT);
+
+ ret=H5Tinsert (tid1, "b", HOFFSET(s1_t,b), H5T_NATIVE_INT);
+
+ ret=H5Tinsert (tid1, "c", HOFFSET(s1_t,c), H5T_NATIVE_FLOAT);
+
+ /* Save datatype for later */
+ ret=H5Tcommit (group, "Datatype1", tid1);
+
+ /* Close datatype */
+ ret = H5Tclose(tid1);
+
+ /* Close group */
+ ret = H5Gclose(group);
+
+ /* Create a dataset to store references */
+ dataset=H5Dcreate(fid1,"Dataset3",H5T_STD_REF_OBJ,sid1,H5P_DEFAULT);
+
+ /* Create reference to dataset */
+ ret = H5Rcreate(&wbuf[0],fid1,"/Group1/Dataset1",H5R_OBJECT,-1);
+
+ /* Create reference to dataset */
+ ret = H5Rcreate(&wbuf[1],fid1,"/Group1/Dataset2",H5R_OBJECT,-1);
+
+ /* Create reference to group */
+ ret = H5Rcreate(&wbuf[2],fid1,"/Group1",H5R_OBJECT,-1);
+
+ /* Create reference to named datatype */
+ ret = H5Rcreate(&wbuf[3],fid1,"/Group1/Datatype1",H5R_OBJECT,-1);
+
+ /* Write selection to disk */
+ ret=H5Dwrite(dataset,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,wbuf);
+
+ /* Close disk dataspace */
+ ret = H5Sclose(sid1);
+
+ /* Close Dataset */
+ ret = H5Dclose(dataset);
+
+ /* Close file */
+ ret = H5Fclose(fid1);
+ free(wbuf);
+ free(tu32);
+ return 0;
+}
+
+</PRE>
+
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<H4><A NAME="ReadRefObj">Example 10</A>. Reading references to objects.</A></H4>
+This example opens and reads dataset <code>Dataset3</code> from
+the file created in Example 9. Then the program dereferences the references
+to dataset <code>Dataset1</code>, the group and the named datatype,
+and opens those objects.
+The program reads and displays the dataset's data, the group's comment, and
+the number of members of the compound datatype.
+
+
+<PRE>
+
+#include &lt;stdlib.h&gt;
+#include &lt;hdf5.h&gt;
+
+#define FILE1 "trefer1.h5"
+
+/* dataset with fixed dimensions */
+#define SPACE1_NAME "Space1"
+#define SPACE1_RANK 1
+#define SPACE1_DIM1 4
+
+int
+main(void)
+{
+ hid_t fid1; /* HDF5 File IDs */
+ hid_t dataset, /* Dataset ID */
+ dset2; /* Dereferenced dataset ID */
+ hid_t group; /* Group ID */
+ hid_t sid1; /* Dataspace ID */
+ hid_t tid1; /* Datatype ID */
+ hobj_ref_t *rbuf; /* buffer to read from disk */
+ int *tu32; /* temp. buffer read from disk */
+ int i; /* counting variables */
+ char read_comment[10];
+ herr_t ret; /* Generic return value */
+
+ /* Allocate read buffers */
+ rbuf = malloc(sizeof(hobj_ref_t)*SPACE1_DIM1);
+ tu32 = malloc(sizeof(int)*SPACE1_DIM1);
+
+ /* Open the file */
+ fid1 = H5Fopen(FILE1, H5F_ACC_RDWR, H5P_DEFAULT);
+
+ /* Open the dataset */
+ dataset=H5Dopen(fid1,"/Dataset3");
+
+ /* Read selection from disk */
+ ret=H5Dread(dataset,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,rbuf);
+
+ /* Open dataset object */
+ dset2 = H5Rdereference(dataset,H5R_OBJECT,&rbuf[0]);
+
+ /* Check information in referenced dataset */
+ sid1 = H5Dget_space(dset2);
+
+ ret=H5Sget_simple_extent_npoints(sid1);
+
+ /* Read from disk */
+ ret=H5Dread(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,tu32);
+ printf("Dataset data : \n");
+ for (i=0; i &lt; SPACE1_DIM1 ; i++) printf (" %d ", tu32[i]);
+ printf("\n");
+ printf("\n");
+
+ /* Close dereferenced Dataset */
+ ret = H5Dclose(dset2);
+
+ /* Open group object */
+ group = H5Rdereference(dataset,H5R_OBJECT,&rbuf[2]);
+
+ /* Get group's comment */
+ ret=H5Gget_comment(group,".",10,read_comment);
+ printf("Group comment is %s \n", read_comment);
+ printf(" \n");
+ /* Close group */
+ ret = H5Gclose(group);
+
+ /* Open datatype object */
+ tid1 = H5Rdereference(dataset,H5R_OBJECT,&rbuf[3]);
+
+ /* Verify correct datatype */
+ {
+ H5T_class_t tclass;
+
+ tclass= H5Tget_class(tid1);
+ if ((tclass == H5T_COMPOUND))
+ printf ("Number of compound datatype members is %d \n", H5Tget_nmembers(tid1));
+ printf(" \n");
+ }
+
+ /* Close datatype */
+ ret = H5Tclose(tid1);
+
+ /* Close Dataset */
+ ret = H5Dclose(dataset);
+
+ /* Close file */
+ ret = H5Fclose(fid1);
+
+ /* Free memory buffers */
+ free(rbuf);
+ free(tu32);
+ return 0;
+}
+
+</PRE>
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<H4><A NAME="CreateWriteRefReg">Example 11</A>. Creating and writing a reference to a region.</A></H4>
+
+This example 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.
+
+<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>
+
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<H4><A NAME="ReadRefReg">Example 12</A>. Reading a reference to a region.</A></H4>
+
+This 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:
+a hyperslab selection and a point selection. 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.
+
+<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>
+
+
+<P>&nbsp;
+<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font>
+
+
+<hr>
+<center>
+<table border=0 width=98%>
+<tr><td valign=top align=left>
+Introduction to HDF5&nbsp;<br>
+<a href="../H5.user.html">HDF5 User Guide</a>&nbsp;
+<!--
+<a href="../Glossary.html">Glossary</a><br>
+-->
+</td>
+<td valign=top align=right>
+<a href="../RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
+<a href="../index.html">Other HDF5 documents and links</a>&nbsp;
+</td></tr>
+</table>
+</center>
+<hr>
+
+
+<address>
+<table width=100% border=0>
+<tr><td align=left valign=top>
+<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
+<br>
+Last modified: 30 January 2001
+<br>
+Describes HDF5 Release 1.4, February 2001
+
+</td><td align=right valign=top>
+<a href="Copyright.html">Copyright</a>&nbsp;&nbsp;
+</td></tr>
+</table>
+
+
+</BODY>
+</HTML>