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authorFrank Baker <fbaker@hdfgroup.org>2005-07-19 17:28:56 (GMT)
committerFrank Baker <fbaker@hdfgroup.org>2005-07-19 17:28:56 (GMT)
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Description: All HDF5 user documentation has been moved to a separate hdf5doc/ repository, managed under Subversion. With this 'cvs commit', all files are stripped from hdf5/doc/. THIS CHANGE IS APPLIED ONLY TO THE HDF5 DEVELOPMENT BRANCH, post Release 1.6.x; it is not applied to the release branches.
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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>
-
-<!-- #BeginLibraryItem "/ed_libs/styles_Intro.lbi" -->
-<!--
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Copyright by the Board of Trustees of the University of Illinois. *
- * All rights reserved. *
- * *
- * This file is part of HDF5. The full HDF5 copyright notice, including *
- * terms governing use, modification, and redistribution, is contained in *
- * the files COPYING and Copyright.html. COPYING can be found at the root *
- * of the source code distribution tree; Copyright.html can be found at the *
- * root level of an installed copy of the electronic HDF5 document set and *
- * is linked from the top-level documents page. It can also be found at *
- * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
- * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- -->
-
-<link href="../ed_styles/IntroElect.css" rel="stylesheet" type="text/css">
-<!-- #EndLibraryItem --></HEAD>
-<BODY LINK="#0000ff" VLINK="#800080" bgcolor="#FFFFFF">
-
-
-<!-- #BeginLibraryItem "/ed_libs/NavBar_Intro.lbi" --><hr>
-<center>
-<table border=0 width=98%>
-<tr><td valign=top align=left>
-<a href="../H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
-<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.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>
-<!-- #EndLibraryItem --><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 */
- hsize_t offset[2]; /* hyperslab offset in the file */
- hsize_t count_out[3]; /* size of the hyperslab in memory */
- hsize_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) */
-
- hsize_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 */
-
- hsize_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 hsize_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];
- hsize_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
- *
- * 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
- */
- /*
- * 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];
- hsize_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};
- hsize_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 */
- hsize_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 hsize_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>
-
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-Describes HDF5 Release 1.7, the unreleased development branch; working toward HDF5 Release 1.8.0
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-Last modified: 3 August 2004
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