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diff --git a/doc/html/Intro/IntroExamples.html b/doc/html/Intro/IntroExamples.html deleted file mode 100644 index 6511683..0000000 --- a/doc/html/Intro/IntroExamples.html +++ /dev/null @@ -1,2128 +0,0 @@ -<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> <br> -<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User Guide</a> -<!-- -<a href="Glossary.html">Glossary</a><br> ---> -</td> -<td valign=top align=right> -<a href="../RM_H5Front.html">HDF5 Reference Manual</a> <br> -<a href="../index.html">Other HDF5 documents and links</a> -</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> -     - <A href="#CreateExample">1: Creating and writing a - dataset</A><br> -     - <A href="#CheckAndReadExample">2. Reading a hyperslab</A><br> -     - <A href="#WriteSelected">3. Writing selected data</A><br> -     - <A href="#Compound">4. Working with compound datatypes</A><br> -     - <A href="#CreateExtendWrite">5. Creating and writing an extendible</a> <br> -     -     - <A href="#CreateExtendWrite">dataset</A><br> -     - <A href="#ReadExtended">6. Reading data</A><br> -     - <A href="#CreateGroups">7. Creating groups</A><br> - </font> - -</td><td width=6%> </td><td valign=top align=left width=42%> - - <font size=-1> -     - <A href="#ReadWriteAttributes">8. Writing and reading - attributes</A><br> -     - <a href="#CreateWriteRefObj">9. Creating and writing references</a><br> -     -     - <a href="#CreateWriteRefObj">to objects</a><br> -     - <a href="#ReadRefObj">10. Reading references to objects</a><br> -     - <a href="#CreateWriteRefReg">11. Creating and writing references</a><br> -     -     - <a href="#CreateWriteRefReg">to dataset regions</a><br> -     - <a href="#ReadRefReg">12. Reading references to dataset</a><br> -     -     - <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> -<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font> - - -<A NAME="CheckAndReadExample"> </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> -<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> -<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> -<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> -<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> -<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> -<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> -<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 <hdf5.h> - -#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 < 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> -<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 <stdlib.h> -#include <hdf5.h> - -#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 < 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> -<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 <stdlib.h> -#include <hdf5.h> - -#define FILE2 "trefer2.h5" -#define SPACE1_NAME "Space1" -#define SPACE1_RANK 1 -#define SPACE1_DIM1 4 - -/* Dataset with fixed dimensions */ -#define SPACE2_NAME "Space2" -#define SPACE2_RANK 2 -#define SPACE2_DIM1 10 -#define SPACE2_DIM2 10 - -/* Element selection information */ -#define POINT1_NPOINTS 10 - -int -main(void) -{ - hid_t fid1; /* HDF5 File IDs */ - hid_t dset1, /* Dataset ID */ - dset2; /* Dereferenced dataset ID */ - hid_t sid1, /* Dataspace ID #1 */ - sid2; /* Dataspace ID #2 */ - hsize_t dims1[] = {SPACE1_DIM1}, - dims2[] = {SPACE2_DIM1, SPACE2_DIM2}; - 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 < 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> -<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 <stdlib.h> -#include <hdf5.h> - -#define FILE2 "trefer2.h5" -#define NPOINTS 10 - -/* 1-D dataset with fixed dimensions */ -#define SPACE1_NAME "Space1" -#define SPACE1_RANK 1 -#define SPACE1_DIM1 4 - -/* 2-D dataset with fixed dimensions */ -#define SPACE2_NAME "Space2" -#define SPACE2_RANK 2 -#define SPACE2_DIM1 10 -#define SPACE2_DIM2 10 - -int -main(void) -{ - hid_t fid1; /* HDF5 File IDs */ - hid_t dset1, /* Dataset ID */ - dset2; /* Dereferenced dataset ID */ - hid_t sid1, /* Dataspace ID #1 */ - sid2; /* Dataspace ID #2 */ - hsize_t * coords; /* Coordinate buffer */ - hsize_t low[SPACE2_RANK]; /* Selection bounds */ - hsize_t high[SPACE2_RANK]; /* Selection bounds */ - hdset_reg_ref_t *rbuf; /* buffer to to read disk */ - int *drbuf; /* Buffer for reading numeric data from disk */ - int i, j; /* counting variables */ - herr_t ret; /* Generic return value */ - - /* Output message about test being performed */ - - /* Allocate write & read buffers */ - rbuf=malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1); - drbuf=calloc(sizeof(int),SPACE2_DIM1*SPACE2_DIM2); - - /* Open the file */ - fid1 = H5Fopen(FILE2, H5F_ACC_RDWR, H5P_DEFAULT); - - /* Open the dataset */ - dset1=H5Dopen(fid1,"/Dataset1"); - - /* Read selection from disk */ - ret=H5Dread(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,rbuf); - - /* Try to open objects */ - dset2 = H5Rdereference(dset1,H5R_DATASET_REGION,&rbuf[0]); - - /* Check information in referenced dataset */ - sid1 = H5Dget_space(dset2); - - ret=H5Sget_simple_extent_npoints(sid1); - printf(" Number of elements in the dataset is : %d\n",ret); - - /* Read from disk */ - ret=H5Dread(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,drbuf); - - for(i=0; i < SPACE2_DIM1; i++) { - for (j=0; j < SPACE2_DIM2; j++) printf (" %d ", drbuf[i*SPACE2_DIM2+j]); - printf("\n"); } - - /* Get the hyperslab selection */ - sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[0]); - - /* Verify correct hyperslab selected */ - ret = H5Sget_select_npoints(sid2); - printf(" Number of elements in the hyperslab is : %d \n", ret); - ret = H5Sget_select_hyper_nblocks(sid2); - coords=malloc(ret*SPACE2_RANK*sizeof(hsize_t)*2); /* allocate space for the hyperslab blocks */ - ret = H5Sget_select_hyper_blocklist(sid2,0,ret,coords); - printf(" Hyperslab coordinates are : \n"); - printf (" ( %lu , %lu ) ( %lu , %lu ) \n", \ -(unsigned long)coords[0],(unsigned long)coords[1],(unsigned long)coords[2],(unsigned long)coords[3]); - free(coords); - ret = H5Sget_select_bounds(sid2,low,high); - - /* Close region space */ - ret = H5Sclose(sid2); - - /* Get the element selection */ - sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[1]); - - /* Verify correct elements selected */ - ret = H5Sget_select_elem_npoints(sid2); - printf(" Number of selected elements is : %d\n", ret); - - /* Allocate space for the element points */ - coords= malloc(ret*SPACE2_RANK*sizeof(hsize_t)); - ret = H5Sget_select_elem_pointlist(sid2,0,ret,coords); - printf(" Coordinates of selected elements are : \n"); - for (i=0; i < 2*NPOINTS; i=i+2) - printf(" ( %lu , %lu ) \n", (unsigned long)coords[i],(unsigned long)coords[i+1]); - - free(coords); - ret = H5Sget_select_bounds(sid2,low,high); - - /* Close region space */ - ret = H5Sclose(sid2); - - /* Close first space */ - ret = H5Sclose(sid1); - - /* Close dereferenced Dataset */ - ret = H5Dclose(dset2); - - /* Close Dataset */ - ret = H5Dclose(dset1); - - /* Close file */ - ret = H5Fclose(fid1); - - /* Free memory buffers */ - free(rbuf); - free(drbuf); - return 0; -} - -</PRE> - - -<P> -<p align=right><font size=-1><a href="#IEx-TOC">(Return to TOC)</a></font> - - -<!-- #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> <br> -<a href="http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/index.html">HDF5 User Guide</a> -<!-- -<a href="Glossary.html">Glossary</a><br> ---> -</td> -<td valign=top align=right> -<a href="../RM_H5Front.html">HDF5 Reference Manual</a> <br> -<a href="../index.html">Other HDF5 documents and links</a> -</td></tr> -</table> -</center> -<hr> -<!-- #EndLibraryItem --><address> -<table width=100% border=0> -<tr><td align=left valign=top> - -<!-- #BeginLibraryItem "/ed_libs/Footer.lbi" --><address> -<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a> -<br> -Describes HDF5 Release 1.7, the unreleased development branch; working toward HDF5 Release 1.8.0 -</address><!-- #EndLibraryItem --> - -Last modified: 3 August 2004 - -</td><td align=right valign=top> -<a href="../Copyright.html">Copyright</a> -</td></tr> -</table> - - -</BODY> -</HTML> |