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| -rw-r--r-- | doc/html/H5.intro.html | 1975 |
1 files changed, 27 insertions, 1948 deletions
diff --git a/doc/html/H5.intro.html b/doc/html/H5.intro.html index b2c5c8e..4fa3246 100644 --- a/doc/html/H5.intro.html +++ b/doc/html/H5.intro.html @@ -28,7 +28,7 @@ Introduction to HDF5 <br> <a name="Intro-Intro"> -<h1 ALIGN="CENTER">Introduction to HDF5 Release 1.2</h1></a> +<h1 ALIGN="CENTER">Introduction to HDF5 Release 1.4</h1></a> </FONT><FONT FACE="Times"><P>This is an introduction to the HDF5 data model and programming model. Being a <I>Getting Started</I> or <I>QuickStart</I> document, this </FONT><I>Introduction to HDF5</I> <FONT FACE="Times">is intended to provide enough information for you to develop a basic understanding of how HDF5 works and is meant to be used. Knowledge of the current version of HDF will make it easier to follow the text, but it is not required. More complete information of the sort you will need to actually use HDF5 is available in <A HREF="index.html">the HDF5 documentation</FONT></a><FONT FACE="Times">. Available documents include the following: @@ -39,7 +39,8 @@ Introduction to HDF5 <br> <FONT FACE="Times"><P>Code examples are available in the source code tree when you install HDF5. <UL> -</FONT><LI>The directories <code>hdf5/examples</code> and +</FONT><LI>The directories <code>hdf5/examples</code>, +<code>hdf5/doc/html/examples/</code>, and <code>hdf5/doc/html/Tutor/examples/</code> contain the examples used in this document. <LI>The directory<FONT FACE="Courier" SIZE=2> hdf5/test</FONT> contains the development tests used by the HDF5 developers. Since these codes are intended to fully exercise the system, they provide more diverse and sophisticated examples of what HDF5 can do.</UL> @@ -51,7 +52,7 @@ used in this document. <tr><th colspan=3>Table of Contents</th></tr></a> <tr><td valign=top align=left width=42%> - <a href="#Intro-Intro">Introduction to HDF5 Release 1.2</a><p> + <a href="#Intro-Intro">Introduction to HDF5 Release 1.4</a><p> <a href="#Intro-WhatIs">1. What Is HDF5?</a><br> <font size=-1>   <a href="#Intro-Why">Why HDF5?</a><br> @@ -121,46 +122,46 @@ used in this document.     <A href="#Intro-PMWorkRefRegions">regions</A><p> </font> - <a href="#Intro-Examples">4. Example Codes</a><br> + <a href="Intro/IntroExamples.html" target="ExampleWin">Introduction to HDF5 -- Example Codes</a><br> <font size=-1>     - <A href="#CreateExample">1: Creating and writing a + <A href="Intro/IntroExamples.html#CreateExample" target="ExampleWin">1: Creating and writing a dataset</A><br>     - <A href="#CheckAndReadExample">2. Reading a hyperslab</A><br> + <A href="Intro/IntroExamples.html#CheckAndReadExample" target="ExampleWin">2. Reading a hyperslab</A><br>     - <A href="#WriteSelected">3. Writing selected data</A><br> + <A href="Intro/IntroExamples.html#WriteSelected" target="ExampleWin">3. Writing selected data</A><br>     - <A href="#Compound">4. Working with compound datatypes</A><br> + <A href="Intro/IntroExamples.html#Compound" target="ExampleWin">4. Working with compound datatypes</A><br>     - <A href="#CreateExtendWrite">5. Creating and writing an extendible</a> <br> + <A href="Intro/IntroExamples.html#CreateExtendWrite" target="ExampleWin">5. Creating and writing an extendible</a> <br>         - <A href="#CreateExtendWrite">dataset</A><br> + <A href="Intro/IntroExamples.html#CreateExtendWrite" target="ExampleWin">dataset</A><br>     - <A href="#ReadExtended">6. Reading data</A><br> + <A href="Intro/IntroExamples.html#ReadExtended" target="ExampleWin">6. Reading data</A><br>     - <A href="#CreateGroups">7. Creating groups</A><br> + <A href="Intro/IntroExamples.html#CreateGroups" target="ExampleWin">7. Creating groups</A><br>     - <A href="#ReadWriteAttributes">8. Writing and reading + <A href="Intro/IntroExamples.html#ReadWriteAttributes" target="ExampleWin">8. Writing and reading attributes</A><br>     - <a href="#CreateWriteRefObj">9. Creating and writing references</a><br> + <a href="Intro/IntroExamples.html#CreateWriteRefObj" target="ExampleWin">9. Creating and writing references</a><br>         - <a href="#CreateWriteRefObj">to objects</a><br> + <a href="Intro/IntroExamples.html#CreateWriteRefObj" target="ExampleWin">to objects</a><br>     - <a href="#ReadRefObj">10. Reading references to objects</a><br> + <a href="Intro/IntroExamples.html#ReadRefObj" target="ExampleWin">10. Reading references to objects</a><br>     - <a href="#CreateWriteRefReg">11. Creating and writing references</a><br> + <a href="Intro/IntroExamples.html#CreateWriteRefReg" target="ExampleWin">11. Creating and writing references</a><br>         - <a href="#CreateWriteRefReg">to dataset regions</a><br> + <a href="Intro/IntroExamples.html#CreateWriteRefReg" target="ExampleWin">to dataset regions</a><br>     - <a href="#ReadRefReg">12. Reading references to dataset</a><br> + <a href="Intro/IntroExamples.html#ReadRefReg" target="ExampleWin">12. Reading references to dataset</a><br>         - <a href="#ReadRefReg">regions</a> + <a href="Intro/IntroExamples.html#ReadRefReg" target="ExampleWin">regions</a> </font> </td></tr> </table> @@ -230,7 +231,7 @@ in the source code installation. At a higher level, those changes include: <li>Over 30 new API functions </UL> -<P>The changes in bugfix releases, numbered Release 1.2.<i>x</i>, +<P>The changes in bugfix releases, numbered Release 1.4.<i>x</i>, will be listed in the <code>RELEASE</code>, <code>HISTORY</code>, and <code>README</code> files distributed with the source code. @@ -3060,1937 +3061,15 @@ The output of this program is : <hr> -<H2><A NAME="Intro-Examples">4. Example Codes</A></H2> +<H2>4. Example Codes</H2> +For the example codes, see +<a href="Intro/IntroExamples.html" target="ExampleWin"><cite>Introduction to HDF5 -- Example Codes</cite></a>. -<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> - - - -<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 */ - hssize_t offset[2]; /* hyperslab offset in the file */ - hsize_t count_out[3]; /* size of the hyperslab in memory */ - hssize_t offset_out[3]; /* hyperslab offset in memory */ - int i, j, k, status_n, rank; - - for (j = 0; j < NX; j++) { - for (i = 0; i < NY; i++) { - for (k = 0; k < NZ ; k++) - data_out[j][i][k] = 0; - } - } - - /* - * Open the file and the dataset. - */ - file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT); - dataset = H5Dopen(file, DATASETNAME); - - /* - * Get datatype and dataspace handles and then query - * dataset class, order, size, rank and dimensions. - */ - datatype = H5Dget_type(dataset); /* datatype handle */ - class = H5Tget_class(datatype); - if (class == H5T_INTEGER) printf("Data set has INTEGER type \n"); - order = H5Tget_order(datatype); - if (order == H5T_ORDER_LE) printf("Little endian order \n"); - - size = H5Tget_size(datatype); - printf(" Data size is %d \n", size); - - dataspace = H5Dget_space(dataset); /* dataspace handle */ - rank = H5Sget_simple_extent_ndims(dataspace); - status_n = H5Sget_simple_extent_dims(dataspace, dims_out, NULL); - printf("rank %d, dimensions %lu x %lu \n", rank, - (unsigned long)(dims_out[0]), (unsigned long)(dims_out[1])); - - /* - * Define hyperslab in the dataset. - */ - offset[0] = 1; - offset[1] = 2; - count[0] = NX_SUB; - count[1] = NY_SUB; - status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, - count, NULL); - - /* - * Define the memory dataspace. - */ - dimsm[0] = NX; - dimsm[1] = NY; - dimsm[2] = NZ ; - memspace = H5Screate_simple(RANK_OUT,dimsm,NULL); - - /* - * Define memory hyperslab. - */ - offset_out[0] = 3; - offset_out[1] = 0; - offset_out[2] = 0; - count_out[0] = NX_SUB; - count_out[1] = NY_SUB; - count_out[2] = 1; - status = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, offset_out, NULL, - count_out, NULL); - - /* - * Read data from hyperslab in the file into the hyperslab in - * memory and display. - */ - status = H5Dread(dataset, H5T_NATIVE_INT, memspace, dataspace, - H5P_DEFAULT, data_out); - for (j = 0; j < NX; j++) { - for (i = 0; i < NY; i++) printf("%d ", data_out[j][i][0]); - printf("\n"); - } - /* - * 0 0 0 0 0 0 0 - * 0 0 0 0 0 0 0 - * 0 0 0 0 0 0 0 - * 3 4 5 6 0 0 0 - * 4 5 6 7 0 0 0 - * 5 6 7 8 0 0 0 - * 0 0 0 0 0 0 0 - */ - - /* - * Close/release resources. - */ - H5Tclose(datatype); - H5Dclose(dataset); - H5Sclose(dataspace); - H5Sclose(memspace); - H5Fclose(file); - - return 0; -} -</pre> - - - - -<H4><A NAME="_Toc429885331"><A NAME="WriteSelected"></A>Example 3. Writing selected data from memory to a file.</A></H4> -<P>This example shows how to use the selection capabilities of HDF5 to write selected data to a file. It includes the examples discussed in the text. - -<pre> -<!-- Insert Example 3, h5_select.c, here. --> -/* - * This program shows how the H5Sselect_hyperslab and H5Sselect_elements - * functions are used to write selected data from memory to the file. - * Program takes 48 elements from the linear buffer and writes them into - * the matrix using 3x2 blocks, (4,3) stride and (2,4) count. - * Then four elements of the matrix are overwritten with the new values and - * file is closed. Program reopens the file and reads and displays the result. - */ - -#include <hdf5.h> - -#define FILE "Select.h5" - -#define MSPACE1_RANK 1 /* Rank of the first dataset in memory */ -#define MSPACE1_DIM 50 /* Dataset size in memory */ - -#define MSPACE2_RANK 1 /* Rank of the second dataset in memory */ -#define MSPACE2_DIM 4 /* Dataset size in memory */ - -#define FSPACE_RANK 2 /* Dataset rank as it is stored in the file */ -#define FSPACE_DIM1 8 /* Dimension sizes of the dataset as it is - stored in the file */ -#define FSPACE_DIM2 12 - - /* We will read dataset back from the file - to the dataset in memory with these - dataspace parameters. */ -#define MSPACE_RANK 2 -#define MSPACE_DIM1 8 -#define MSPACE_DIM2 12 - -#define NPOINTS 4 /* Number of points that will be selected - and overwritten */ -int main (void) -{ - - hid_t file, dataset; /* File and dataset identifiers */ - hid_t mid1, mid2, fid; /* Dataspace identifiers */ - hsize_t dim1[] = {MSPACE1_DIM}; /* Dimension size of the first dataset - (in memory) */ - hsize_t dim2[] = {MSPACE2_DIM}; /* Dimension size of the second dataset - (in memory */ - hsize_t fdim[] = {FSPACE_DIM1, FSPACE_DIM2}; - /* Dimension sizes of the dataset (on disk) */ - - hssize_t start[2]; /* Start of hyperslab */ - hsize_t stride[2]; /* Stride of hyperslab */ - hsize_t count[2]; /* Block count */ - hsize_t block[2]; /* Block sizes */ - - hssize_t coord[NPOINTS][FSPACE_RANK]; /* Array to store selected points - from the file dataspace */ - herr_t ret; - uint i,j; - int matrix[MSPACE_DIM1][MSPACE_DIM2]; - int vector[MSPACE1_DIM]; - int values[] = {53, 59, 61, 67}; /* New values to be written */ - - /* - * Buffers' initialization. - */ - vector[0] = vector[MSPACE1_DIM - 1] = -1; - for (i = 1; i < MSPACE1_DIM - 1; i++) vector[i] = i; - - for (i = 0; i < MSPACE_DIM1; i++) { - for (j = 0; j < MSPACE_DIM2; j++) - matrix[i][j] = 0; - } - - /* - * Create a file. - */ - file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Create dataspace for the dataset in the file. - */ - fid = H5Screate_simple(FSPACE_RANK, fdim, NULL); - - /* - * Create dataset and write it into the file. - */ - dataset = H5Dcreate(file, "Matrix in file", H5T_NATIVE_INT, fid, H5P_DEFAULT); - ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, matrix); - - /* - * Select hyperslab for the dataset in the file, using 3x2 blocks, - * (4,3) stride and (2,4) count starting at the position (0,1). - */ - start[0] = 0; start[1] = 1; - stride[0] = 4; stride[1] = 3; - count[0] = 2; count[1] = 4; - block[0] = 3; block[1] = 2; - ret = H5Sselect_hyperslab(fid, H5S_SELECT_SET, start, stride, count, block); - - /* - * Create dataspace for the first dataset. - */ - mid1 = H5Screate_simple(MSPACE1_RANK, dim1, NULL); - - /* - * Select hyperslab. - * We will use 48 elements of the vector buffer starting at the second element. - * Selected elements are 1 2 3 . . . 48 - */ - start[0] = 1; - stride[0] = 1; - count[0] = 48; - block[0] = 1; - ret = H5Sselect_hyperslab(mid1, H5S_SELECT_SET, start, stride, count, block); - - /* - * Write selection from the vector buffer to the dataset in the file. - * - * File dataset should look like this: - * 0 1 2 0 3 4 0 5 6 0 7 8 - * 0 9 10 0 11 12 0 13 14 0 15 16 - * 0 17 18 0 19 20 0 21 22 0 23 24 - * 0 0 0 0 0 0 0 0 0 0 0 0 - * 0 25 26 0 27 28 0 29 30 0 31 32 - * 0 33 34 0 35 36 0 37 38 0 39 40 - * 0 41 42 0 43 44 0 45 46 0 47 48 - * 0 0 0 0 0 0 0 0 0 0 0 0 - */ - ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid1, fid, H5P_DEFAULT, vector); - - /* - * Reset the selection for the file dataspace fid. - */ - ret = H5Sselect_none(fid); - - /* - * Create dataspace for the second dataset. - */ - mid2 = H5Screate_simple(MSPACE2_RANK, dim2, NULL); - - /* - * Select sequence of NPOINTS points in the file dataspace. - */ - coord[0][0] = 0; coord[0][1] = 0; - coord[1][0] = 3; coord[1][1] = 3; - coord[2][0] = 3; coord[2][1] = 5; - coord[3][0] = 5; coord[3][1] = 6; - - ret = H5Sselect_elements(fid, H5S_SELECT_SET, NPOINTS, - (const hssize_t **)coord); - - /* - * Write new selection of points to the dataset. - */ - ret = H5Dwrite(dataset, H5T_NATIVE_INT, mid2, fid, H5P_DEFAULT, values); - - /* - * File dataset should look like this: - * 53 1 2 0 3 4 0 5 6 0 7 8 - * 0 9 10 0 11 12 0 13 14 0 15 16 - * 0 17 18 0 19 20 0 21 22 0 23 24 - * 0 0 0 59 0 61 0 0 0 0 0 0 - * 0 25 26 0 27 28 0 29 30 0 31 32 - * 0 33 34 0 35 36 67 37 38 0 39 40 - * 0 41 42 0 43 44 0 45 46 0 47 48 - * 0 0 0 0 0 0 0 0 0 0 0 0 - * - */ - - /* - * Close memory file and memory dataspaces. - */ - ret = H5Sclose(mid1); - ret = H5Sclose(mid2); - ret = H5Sclose(fid); - - /* - * Close dataset. - */ - ret = H5Dclose(dataset); - - /* - * Close the file. - */ - ret = H5Fclose(file); - - /* - * Open the file. - */ - file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT); - - /* - * Open the dataset. - */ - dataset = dataset = H5Dopen(file,"Matrix in file"); - - /* - * Read data back to the buffer matrix. - */ - ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, - H5P_DEFAULT, matrix); - - /* - * Display the result. - */ - for (i=0; i < MSPACE_DIM1; i++) { - for(j=0; j < MSPACE_DIM2; j++) printf("%3d ", matrix[i][j]); - printf("\n"); - } - - return 0; -} -</pre> - - - -<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> - - - -<H4><A NAME="CreateExtendWrite"><A NAME="_Toc429885328"></A>Example 5. Creating and writing an extendible dataset.</A></H4> -<P>This example shows how to create a 3x3 extendible dataset, to extend the dataset to 10x3, then to extend it again to 10x5. -<PRE> -<!-- Insert Example 5, h5_extend_write.c, here. --> -/* - * This example shows how to work with extendible dataset. - * In the current version of the library dataset MUST be - * chunked. - * - */ - -#include "hdf5.h" - -#define FILE "SDSextendible.h5" -#define DATASETNAME "ExtendibleArray" -#define RANK 2 -#define NX 10 -#define NY 5 - -int -main (void) -{ - hid_t file; /* handles */ - hid_t dataspace, dataset; - hid_t filespace; - hid_t cparms; - hsize_t dims[2] = { 3, 3}; /* - * dataset dimensions - * at the creation time - */ - hsize_t dims1[2] = { 3, 3}; /* data1 dimensions */ - hsize_t dims2[2] = { 7, 1}; /* data2 dimensions */ - hsize_t dims3[2] = { 2, 2}; /* data3 dimensions */ - - hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED}; - hsize_t chunk_dims[2] ={2, 5}; - hsize_t size[2]; - hssize_t offset[2]; - - herr_t status; - - int data1[3][3] = { {1, 1, 1}, /* data to write */ - {1, 1, 1}, - {1, 1, 1} }; - - int data2[7] = { 2, 2, 2, 2, 2, 2, 2}; - - int data3[2][2] = { {3, 3}, - {3, 3} }; - - /* - * Create the data space with unlimited dimensions. - */ - dataspace = H5Screate_simple(RANK, dims, maxdims); - - /* - * Create a new file. If file exists its contents will be overwritten. - */ - file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* - * Modify dataset creation properties, i.e. enable chunking. - */ - cparms = H5Pcreate (H5P_DATASET_CREATE); - status = H5Pset_chunk( cparms, RANK, chunk_dims); - - /* - * Create a new dataset within the file using cparms - * creation properties. - */ - dataset = H5Dcreate(file, DATASETNAME, H5T_NATIVE_INT, dataspace, - cparms); - - /* - * Extend the dataset. This call assures that dataset is at least 3 x 3. - */ - size[0] = 3; - size[1] = 3; - status = H5Dextend (dataset, size); - - /* - * Select a hyperslab. - */ - filespace = H5Dget_space (dataset); - offset[0] = 0; - offset[1] = 0; - status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, - dims1, NULL); - - /* - * Write the data to the hyperslab. - */ - status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace, - H5P_DEFAULT, data1); - - /* - * Extend the dataset. Dataset becomes 10 x 3. - */ - dims[0] = dims1[0] + dims2[0]; - size[0] = dims[0]; - size[1] = dims[1]; - status = H5Dextend (dataset, size); - - /* - * Select a hyperslab. - */ - filespace = H5Dget_space (dataset); - offset[0] = 3; - offset[1] = 0; - status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, - dims2, NULL); - - /* - * Define memory space - */ - dataspace = H5Screate_simple(RANK, dims2, NULL); - - /* - * Write the data to the hyperslab. - */ - status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace, - H5P_DEFAULT, data2); - - /* - * Extend the dataset. Dataset becomes 10 x 5. - */ - dims[1] = dims1[1] + dims3[1]; - size[0] = dims[0]; - size[1] = dims[1]; - status = H5Dextend (dataset, size); - - /* - * Select a hyperslab - */ - filespace = H5Dget_space (dataset); - offset[0] = 0; - offset[1] = 3; - status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, - dims3, NULL); - - /* - * Define memory space. - */ - dataspace = H5Screate_simple(RANK, dims3, NULL); - - /* - * Write the data to the hyperslab. - */ - status = H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace, - H5P_DEFAULT, data3); - - /* - * Resulting dataset - * - * 3 3 3 2 2 - * 3 3 3 2 2 - * 3 3 3 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - */ - /* - * Close/release resources. - */ - H5Dclose(dataset); - H5Sclose(dataspace); - H5Sclose(filespace); - H5Fclose(file); - - return 0; -} -</pre> - - - -<H4><A NAME="ReadExtended"><A NAME="_Toc429885329"></A>Example 6. Reading data.</A></H4> -<P>This example shows how to read information the chunked dataset written by <A HREF="#CreateExtendWrite">Example 5</A>. -<PRE> -<!-- Insert Example 6, h5_chunk_read.c, here. --> -/* - * This example shows how to read data from a chunked dataset. - * We will read from the file created by h5_extend_write.c - */ - -#include "hdf5.h" - -#define FILE "SDSextendible.h5" -#define DATASETNAME "ExtendibleArray" -#define RANK 2 -#define RANKC 1 -#define NX 10 -#define NY 5 - -int -main (void) -{ - hid_t file; /* handles */ - hid_t dataset; - hid_t filespace; - hid_t memspace; - hid_t cparms; - hsize_t dims[2]; /* dataset and chunk dimensions*/ - hsize_t chunk_dims[2]; - hsize_t col_dims[1]; - hsize_t count[2]; - hssize_t offset[2]; - - herr_t status, status_n; - - int data_out[NX][NY]; /* buffer for dataset to be read */ - int chunk_out[2][5]; /* buffer for chunk to be read */ - int column[10]; /* buffer for column to be read */ - int rank, rank_chunk; - hsize_t i, j; - - - - /* - * Open the file and the dataset. - */ - file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT); - dataset = H5Dopen(file, DATASETNAME); - - /* - * Get dataset rank and dimension. - */ - - filespace = H5Dget_space(dataset); /* Get filespace handle first. */ - rank = H5Sget_simple_extent_ndims(filespace); - status_n = H5Sget_simple_extent_dims(filespace, dims, NULL); - printf("dataset rank %d, dimensions %lu x %lu\n", - rank, (unsigned long)(dims[0]), (unsigned long)(dims[1])); - - /* - * Get creation properties list. - */ - cparms = H5Dget_create_plist(dataset); /* Get properties handle first. */ - - /* - * Check if dataset is chunked. - */ - if (H5D_CHUNKED == H5Pget_layout(cparms)) { - - /* - * Get chunking information: rank and dimensions - */ - rank_chunk = H5Pget_chunk(cparms, 2, chunk_dims); - printf("chunk rank %d, dimensions %lu x %lu\n", rank_chunk, - (unsigned long)(chunk_dims[0]), (unsigned long)(chunk_dims[1])); - } - - /* - * Define the memory space to read dataset. - */ - memspace = H5Screate_simple(RANK,dims,NULL); - - /* - * Read dataset back and display. - */ - status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, - H5P_DEFAULT, data_out); - printf("\n"); - printf("Dataset: \n"); - for (j = 0; j < dims[0]; j++) { - for (i = 0; i < dims[1]; i++) printf("%d ", data_out[j][i]); - printf("\n"); - } - - /* - * dataset rank 2, dimensions 10 x 5 - * chunk rank 2, dimensions 2 x 5 - - * Dataset: - * 1 1 1 3 3 - * 1 1 1 3 3 - * 1 1 1 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - * 2 0 0 0 0 - */ - - /* - * Read the third column from the dataset. - * First define memory dataspace, then define hyperslab - * and read it into column array. - */ - col_dims[0] = 10; - memspace = H5Screate_simple(RANKC, col_dims, NULL); - - /* - * Define the column (hyperslab) to read. - */ - offset[0] = 0; - offset[1] = 2; - count[0] = 10; - count[1] = 1; - status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, - count, NULL); - status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, - H5P_DEFAULT, column); - printf("\n"); - printf("Third column: \n"); - for (i = 0; i < 10; i++) { - printf("%d \n", column[i]); - } - - /* - * Third column: - * 1 - * 1 - * 1 - * 0 - * 0 - * 0 - * 0 - * 0 - * 0 - * 0 - */ - - /* - * Define the memory space to read a chunk. - */ - memspace = H5Screate_simple(rank_chunk,chunk_dims,NULL); - - /* - * Define chunk in the file (hyperslab) to read. - */ - offset[0] = 2; - offset[1] = 0; - count[0] = chunk_dims[0]; - count[1] = chunk_dims[1]; - status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, - count, NULL); - - /* - * Read chunk back and display. - */ - status = H5Dread(dataset, H5T_NATIVE_INT, memspace, filespace, - H5P_DEFAULT, chunk_out); - printf("\n"); - printf("Chunk: \n"); - for (j = 0; j < chunk_dims[0]; j++) { - for (i = 0; i < chunk_dims[1]; i++) printf("%d ", chunk_out[j][i]); - printf("\n"); - } - /* - * Chunk: - * 1 1 1 0 0 - * 2 0 0 0 0 - */ - - /* - * Close/release resources. - */ - H5Pclose(cparms); - H5Dclose(dataset); - H5Sclose(filespace); - H5Sclose(memspace); - H5Fclose(file); - - return 0; - -</pre> - - - -<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> - - - -<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> - - -<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> - - - -<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> - - -<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}; - hssize_t start[SPACE2_RANK]; /* Starting location of hyperslab */ - hsize_t stride[SPACE2_RANK]; /* Stride of hyperslab */ - hsize_t count[SPACE2_RANK]; /* Element count of hyperslab */ - hsize_t block[SPACE2_RANK]; /* Block size of hyperslab */ - hssize_t coord1[POINT1_NPOINTS][SPACE2_RANK]; - /* Coordinates for point selection */ - hdset_reg_ref_t *wbuf; /* buffer to write to disk */ - int *dwbuf; /* Buffer for writing numeric data to disk */ - int i; /* counting variables */ - herr_t ret; /* Generic return value */ - - - /* Allocate write & read buffers */ - wbuf=calloc(sizeof(hdset_reg_ref_t), SPACE1_DIM1); - dwbuf=malloc(sizeof(int)*SPACE2_DIM1*SPACE2_DIM2); - - /* Create file */ - fid1 = H5Fcreate(FILE2, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); - - /* Create dataspace for datasets */ - sid2 = H5Screate_simple(SPACE2_RANK, dims2, NULL); - - /* Create a dataset */ - dset2=H5Dcreate(fid1,"Dataset2",H5T_STD_U8LE,sid2,H5P_DEFAULT); - - for(i=0; i < SPACE2_DIM1*SPACE2_DIM2; i++) - dwbuf[i]=i*3; - - /* Write selection to disk */ - ret=H5Dwrite(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,dwbuf); - - /* Close Dataset */ - ret = H5Dclose(dset2); - - /* Create dataspace for the reference dataset */ - sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL); - - /* Create a dataset */ - dset1=H5Dcreate(fid1,"Dataset1",H5T_STD_REF_DSETREG,sid1,H5P_DEFAULT); - - /* Create references */ - - /* Select 6x6 hyperslab for first reference */ - start[0]=2; start[1]=2; - stride[0]=1; stride[1]=1; - count[0]=6; count[1]=6; - block[0]=1; block[1]=1; - ret = H5Sselect_hyperslab(sid2,H5S_SELECT_SET,start,stride,count,block); - - /* Store first dataset region */ - ret = H5Rcreate(&wbuf[0],fid1,"/Dataset2",H5R_DATASET_REGION,sid2); - - /* Select sequence of ten points for second reference */ - coord1[0][0]=6; coord1[0][1]=9; - coord1[1][0]=2; coord1[1][1]=2; - coord1[2][0]=8; coord1[2][1]=4; - coord1[3][0]=1; coord1[3][1]=6; - coord1[4][0]=2; coord1[4][1]=8; - coord1[5][0]=3; coord1[5][1]=2; - coord1[6][0]=0; coord1[6][1]=4; - coord1[7][0]=9; coord1[7][1]=0; - coord1[8][0]=7; coord1[8][1]=1; - coord1[9][0]=3; coord1[9][1]=3; - ret = H5Sselect_elements(sid2,H5S_SELECT_SET,POINT1_NPOINTS,(const hssize_t **)coord1); - - /* Store second dataset region */ - ret = H5Rcreate(&wbuf[1],fid1,"/Dataset2",H5R_DATASET_REGION,sid2); - - /* Write selection to disk */ - ret=H5Dwrite(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,wbuf); - - /* Close all objects */ - ret = H5Sclose(sid1); - ret = H5Dclose(dset1); - ret = H5Sclose(sid2); - - /* Close file */ - ret = H5Fclose(fid1); - - free(wbuf); - free(dwbuf); - return 0; -} - -</pre> - - -<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> <p align=right><font size=-1><a href="#Intro-TOC">(Return to TOC)</a></font> - <hr> <center> <table border=0 width=98%> @@ -5015,7 +3094,7 @@ Introduction to HDF5 <br> <tr><td align=left valign=top> <a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a> <br> -Last modified: 17 July 2000 +Last modified: 30 January 2001 <br> Describes HDF5 Release 1.4 Beta, December 2000 |