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<H1>Introduction to HDF5 1.0 Alpha2.0</H1>
<FONT FACE="Times"><P>This is a brief 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 the
<A HREF="index.html">HDF5 documentation</A>. </FONT>
<FONT FACE="Times">. Available documents include the following:</P>
<UL>
</FONT>
<I><LI><a href="H5.user.html">HDF5 User’s Guide</a></I>.
Where appropriate, this <I>Introduction</I> will refer to specific sections
of the <I>User’s Guide</I>.</LI>
<I><LI><a href="RM_H5Front.html">HDF5 Reference Manual</a></I>
</LI></UL>
<FONT FACE="Times"><P>Code examples, that have been tested and work with the
HDF5 library, are available in the source code tree when you install HDF5.</P>
<UL>
</FONT><LI>The directory<FONT FACE="Courier New" SIZE=2> hdf5/examples</FONT>
contains the examples used in this document.</LI>
<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.</LI></UL>
<H2>What is the HDF5 prototype?</H2>
<FONT FACE="Times"><P>HDF5 is a new, experimental version of HDF that is
designed to address some of the limitations of the current version of
HDF (HDF4.x) and to address current and anticipated requirements of modern
systems and applications. </P>
<P>This HDF5 prototype is not complete, but it should be sufficient show the
basic features of HDF5. We urge you to look at it and give us feedback on
what you like or do not like about it, and what features you would like to
see added to it.</P>
<B><P>Why HDF5?</B> The development of HDF5 is motivated by a number of
limitations in the current HDF format, as well as limitations in the library.
Some of these limitations are:</P>
<UL>
</FONT><LI>A single file cannot store more than 20,000 complex objects, and
a single file cannot be larger than 2 gigabytes </LI>
<LI>The data models are less consistent than they should be, there are more
object types than necessary, and datatypes are too restricted. </LI>
<LI>The library source is old and overly complex, does not support parallel I/O
effectively, and is difficult to use in threaded applications.</LI></UL>
<FONT FACE="Times"><P>When complete HDF5 will include the following improvements.</P>
<UL>
</FONT><LI>A new file format designed to address some of the deficiencies of
HDF4.x, particularly the need to store larger files and more objects per file. </LI>
<LI>A simpler, more comprehensive data model that includes only two basic
structures: a multidimensional array of record structures, and a grouping
structure. </LI>
<LI>A simpler, better-engineered library and API, with improved support for
parallel i/o, threads, and other requirements imposed by modern systems and
applications.</LI></UL>
<H2>Limitations of the current prototype</H2>
<FONT FACE="Times"><P>The prototype release includes most of the <I>basic</I>
functionality that is planned for the HDF5 library. However, the library does
not implement all of the features detailed in the format and API specifications.
Here is a listing of some of the limitations of the current release: </P>
<UL>
</FONT><LI>Data compression is supported, though only GZIP is implemented.
GZIP, or GNU Zip, is a compression function from the GNU Project.</LI>
<LI>Some functions for manipulating datasets, dataspaces, and groups have not
been implemented.</LI>
<FONT FACE="Times"><LI>Some number types, including user-defined number types
are not supported. Also number type conversion is limited.</LI></UL>
This is the second alpha release of HDF5.
Highlights of the changes since the first alpha release include:
<ul>
<li> Compressed datasets are supported.
<li> An improved Group API has been implemented.
<li> Attributes are now supported for datasets.
<li> A revised and improved Dataspace API has been implemented.
<li> Datatype conversion support is improved, especially for floating-point types.
<li> Support has been implemented for datasets and files over 2GB in size.
<li> Dataset storage in external files is supported.
<li> Support for parallel I/O of chunked datasets has been implemented.
<li> (A more detailed listing appears in the file hdf5/RELEASE in the alpha code installation.)
</ul>
<P>See the</FONT><CITE> <a href="RM_H5Front.html>HDF5 Reference Manual</a></CITE>
<FONT FACE="Times"> for a complete listing of all routines that have been
implemented.</P>
</FONT><H2>HDF5 file organization and data model.</H2>
<FONT FACE="Times"><P>HDF5 files are organized in a hierarchical structure,
with two primary structures: "groups" and "datasets."</P>
<UL>
</FONT><I><LI>HDF5 group: </I>a grouping structure containing instances of
zero or more groups or datasets, together with supporting metadata </LI>
<I><LI>HD5F dataset:</I> a multidimensional array of data elements, together
with supporting metadata. </LI></UL>
<FONT FACE="Times"><P>Working with groups and group members is similar in
many ways to working with directories and files in UNIX.
As with UNIX directories and files, objects in an HDF5 file are often
described by giving their full path names. </P>
</FONT><CODE><DL>
<DD>/</CODE> signifies the root group. </DD>
<CODE><DD>/foo</CODE> signifies a member of the root group called
<CODE>foo</CODE>.</DD>
<CODE><DD>/foo/zoo</CODE> signifies a member of the group <CODE>foo</CODE>,
which in turn is a member of the root group.</DD>
</DL>
<FONT FACE="Times"><P>Any HDF5 group, dataset, or named datatype may have an
associated <I>attribute list.</I> An HDF5 <I>attribute</I> is a user-defined
HDF5 structure that provides extra information about an HDF5 object.
Attributes are described in more detail below. </P>
</FONT><H3>HDF5 Groups</H3>
<FONT FACE="Times"><P>An<I> HDF5 group</I> is a structure containing zero or
more HDF5 objects. A group has two parts:</P>
<UL>
</FONT><LI>A <I>group header</I>, which contains a group name and a list of
group attributes. </LI>
<LI>A group symbol table, which is a list of the HDF5 objects that belong to
the group.</LI></UL>
<H3>HDF5 Datasets</H3>
<FONT FACE="Times"><P>A dataset is stored in a file in two parts: a header
and a data array. </P>
<P>The header contains information that is needed to interpret the array portion
of the dataset, as well as metadata, or pointers to metadata, that describes or
annotates the dataset. Header information includes the name of the object, its
dimensionality, its number-type, information about how the data itself is stored
on disk, and other information used by the library to speed up access to the
dataset or maintain the file's integrity.</P>
<P>There are four essential classes of information in any header: <I>name</I>,
<I>datatype</I>, <I>dataspace</I>, and <I>storage layout</I>:</P>
</FONT><B><DFN><P>Name.</B></DFN><FONT FACE="Times"> A dataset <I>name</I> is
a sequence of alphanumeric ASCII characters.</P>
</FONT><B><DFN><P>Datatype.</B></DFN><FONT FACE="Times"> HDF5 allows one to
define many different kinds of <B>datatypes</B>. There are two basic categories
of data types: "atomic" types and "compound" types. Atomic types are those that
are not decomposed at the data type interface level, such as integers and floats.
Compound types are made up of atomic types. </P>
<I><P>Atomic datatypes</I> include integers and floating-point numbers. Each
atomic type belongs to a particular class and has several properties: size,
order, precision, and offset. In this introduction, we consider only a few of
these properties.</P>
<P>Atomic datatypes include integer, float, date and time, string, bit field,
and opaque. <I>(Note: Only integer and float classes are available in the
current implementation.)</P>
</I><P>Properties of integer types include size, order (endian-ness), and
signed-ness (signed/unsigned).</P>
<P>Properties of float types include the size and location of the exponent
and mantissa, and the location of the sign bit.</P>
<P>The datatypes that are supported in the current implementation are: </P>
<UL>
</FONT><LI>Integer datatypes: 8-bit, 16-bit, 32-bit, and 64-bit integers in
both little and big-endian format. </LI>
<LI>Floating-point numbers: IEEE 32-bit and 64-bit floating-point numbers in
both little and big-endian format.</LI></UL>
<FONT FACE="Times"><P>A <I>compound datatype</I> is one in which a collection
of simple datatypes are represented as a single unit, similar to a "struct" in C.
The parts of a compound datatype are called <I>members.</I> The members of a
compound datatype may be of any datatype, including another compound datatype.
It is possible to read members from a compound type without reading the whole
type.</P>
<B><DFN><P>Dataspace.</B> </DFN>A dataset <I>dataspace </I>describes the
dimensionality of the dataset. The dimensions of a dataset can be fixed
(unchanging), or they may be <I>unlimited</I>, which means that they are
extendible (i.e. they can grow larger). </P>
<P>Properties of a dataspace consist of the <I>rank </I>(number of dimensions)
of the data array, and the <I>actual sizes of the dimensions</I> of the array,
and the <I>maximum sizes of the dimensions </I>of the array.
For a fixed-dimension dataset, the actual size is the same as the maximum size
of a dimension. When a dimension is unlimited, the maximum size is set to the
</FONT>value <CODE>H5P_UNLIMITED</CODE>.<FONT FACE="Times"> (An example below
shows how to create extendible datasets.)</P>
<P>A dataspace can also describe portions of a dataset, making it possible to
do partial I/O (hyperslab) operations.</P>
<P>Since I/O operations have two end-points, the raw data transfer functions
require two dataspace arguments: one describes the application memory dataspace
or subset thereof, and the other describes the file dataspace or subset thereof.</P>
<P>See <I><a href="Dataspaces.html">Dataspaces</a></I>
</FONT>
<FONT FACE="Times"> in the<I> HDF User’s Guide</I> for further information.</P>
</FONT><B><DFN><P>Storage layout.</B></DFN><FONT FACE="Times"> The HDF5 format
makes it possible to store data in a variety of ways. The default storage
layout format is <I>contiguous</I>, meaning that data is stored in the same
linear way that it is organized in memory. Two other storage layout formats
are currently defined for HDF5: <I>compact, </I>and<I> chunked. </I>In the
future, other storage layouts may be added.<I> </P>
<P>Compact</I> storage is used when the amount of data is small and can be
stored directly in the object header. <I>(Note: Compact storage is not supported
in this prototype.)</I> </P>
<I><P>Chunked</I> storage involves dividing the dataset into equal-sized "chunks"
that are stored separately. Chunking has three important benefits. </P>
<OL>
<LI>It makes it possible to achieve good performance when accessing subsets of
the datasets, even when the subset to be chosen is orthogonal to the normal
storage order of the dataset. </LI>
<LI>It makes it possible to compress large datasets and still achieve good
performance when accessing subsets of the dataset. </LI>
<LI>It makes it possible efficiently to extend the dimensions of a dataset in
any direction.</LI></OL>
<P>See <I><a href="Datasets.html">Datasets</a></I> </FONT>
<FONT FACE="Times"> in the<I> HDF User’s Guide</I> for further information.</P>
</FONT><H3>HDF5 attributes</H3>
<FONT FACE="Times"><P>The Attribute API (H5A) is primarily designed to easily
allow small datasets to be attached to primary datasets as metadata information.
Additional goals for the H5A interface include keeping storage requirement for
each attribute to a minimum and easily sharing attributes among datasets. </P>
<P>Because attributes are intended to be small objects, large datasets intended
as additional information for a primary dataset should be stored as supplemental
datasets in a group with the primary dataset. Attributes can then be attached to
the group containing everything to indicate a particular type of dataset with
supplemental datasets is located in the group. How small is "small" is not
defined by the library and is up to the user's interpretation. </P>
<P>Attributes are not seperate objects in the file, they are always contained
in the object header of the object they are attached to. The I/O functions
defined in the H5A interface are required to read or write attribute information,
not the H5D I/O routines. </P>
<P>See <I><a href="Attributes.html">Attributes</a></I>
</FONT>
<FONT FACE="Times"> in the<I> HDF User’s Guide</I> for further information.</P>
</FONT><H2>The HDF5 Applications Programming Interface (API)</H2>
<FONT FACE="Times"><P>The current HDF5 API is implemented only in C. The API
provides routines for creating HDF5 files, creating and writing groups, datasets,
and their attributes to HDF5 files, and reading groups, datasets and their
attributes from HDF5 files.</P>
</FONT><H3>Naming conventions</H3>
<FONT FACE="Times"><P>All C routines on the HDF 5 library begin with a prefix of
the form "H5*", where "*" is a single letter indicating the object on which the
operation is to be performed:</P>
<UL>
</FONT><B><LI>H5F</B>: <B>F</B>ile-level access routines. <BR>
Example: <CODE>H5Fopen</CODE>, which opens an HDF5 file. </LI>
<B><LI>H5G</B>: <B>G</B>roup functions, for creating and operating on physical
groups of objects. <BR>
Example: <CODE>H5Gset</CODE><FONT FACE="Courier">,</FONT>which sets the working
group to the specified group. </LI>
<B><LI>H5T: </B>Data<B>T</B>ype functions, for creating and operating on simple
and compound datatypes to be used as the elements in data arrays.<B><BR>
</B>Example: <CODE>H5Tcopy</CODE><FONT FACE="Courier">,</FONT>which creates a
copy of an existing data type. </LI>
<B><LI>H5S: </B>Data<B>S</B>pace functions, which create and manipulate the
dataspace in which the elements of a data array are stored.<BR>
Example: <CODE>H5Screate_simple</CODE>, which creates simple dataspaces. </LI>
<B><LI>H5D: D</B>ataset functions, which manipulate the data within datasets and
determine how the data is to be stored in the file. <BR>
Example: <CODE>H5Dread</CODE>, which reads all or part of a dataset into a
buffer in memory. </LI>
<B><LI>H5P</B>: <B>P</B>roperty list functions, for manipulating object creation
and access properties. <BR>
Example: <CODE>H5Pset_chunk</CODE>, which sets the number of dimensions and the
size of a chunk.</LI>
<B><LI>H5A</B>: <B>A</B>ttribute access and manipulating routines. <BR>
Example: <CODE>H5Aget_name</CODE>, which retrieves name of an attribute.</LI>
<B><LI>H5SZ</B>: <B>C</B>ompression registration routine. <BR>
Example: <CODE>H5Zregister</CODE>, which registers new compression and
uncompression functions for use with the HDF5 library.</LI>
<B><LI>H5E</B>: <B>E</B>rror handling routines. <BR>
Example: <CODE>H5Eprint</CODE>, which prints the current error stack.</LI></UL>
<H3>Include files </H3>
<FONT FACE="Times"><P>There are a number definitions and declarations that
should be included with any HDF5 program. These definitions and declarations
are contained in several <I>include</I> files. The main include </FONT>file is
<CODE>hdf5.h</CODE>. This file<FONT FACE="Times"> includes all of the other
files that your program is likely to need. <I>Be sure to include hdf5.h in
any program that accesses HDF5.</P>
</I></FONT><H3>Predefined atomic datatypes</H3>
<P>The datatype interface provides a mechanism to describe the storage format
of individual data points of a data set and is designed to allow new features
to be easily added without disrupting applications that use the datatype
interface. A dataset (the H5D interface) is composed of a collection or raw
data points of homogeneous type organized according to the dataspace (the H5S
interface).</P>
<P>A <DFN>datatype</DFN> is a collection of data type properties, all of which
can be stored on disk, and which when taken as a whole, provide complete
information for data conversion to or from that data type. The interface
provides functions to set and query properties of a data type.</P>
<P>A <DFN>data point</DFN> is an instance of a <DFN>data type</DFN>, which
is an instance of a <DFN>type class</DFN>. We have defined a set of type
classes and properties which can be extended at a later time. The
<DFN>atomic type classes</DFN> are those which describe types which cannot
be decomposed at the data type interface level; all other classes are
<DFN>compound</DFN>.</P>
<P>To illustrate, let us consider a set of predefined atomic datatypes.
The library predefines a modest number of data types having names like
<CODE> H5T_<I>arch</I>_<I>base</I></CODE> where <I><CODE>arch</I> </CODE>is
an architecture name and <I><CODE>base</I></CODE> is a programming type name.
New types can be derived from the predifined types by copying the predefined
type (see <CODE>H5Tcopy()</CODE>) and then modifying the result.</P>
<P>The<CODE> NATIVE </CODE>architecture, for example, contains C-like data types
for the machine on which the library was compiled. The types were actually
defined by running the<CODE> H5detect </CODE>program when the library was
compiled. In order to be portable, applications should almost always use this
architecture to describe things in memory.</P>
<P>The <CODE>NATIVE</CODE> architecture has base names which do not follow the
same rules as the others. Instead, native type names are similar to the C type
names. Here are some examples:</P>
<P ALIGN="CENTER"><CENTER><TABLE BORDER CELLSPACING=1 CELLPADDING=7 WIDTH=462>
<TR><TD WIDTH="49%" VALIGN="TOP">
<B><P ALIGN="CENTER">Example</B></TD>
<TD WIDTH="51%" VALIGN="TOP">
<B><P ALIGN="CENTER">Corresponding C Type</B></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_CHAR</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<PRE>signed char</PRE></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_UCHAR</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>unsigned char</FONT></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_SHORT</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>short</FONT></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_USHORT</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>unsigned short</FONT></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_INT</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>int</FONT></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_UINT</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>unsigned</FONT></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_LONG</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>long</FONT></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_ULONG</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>unsigned long</FONT></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_LLONG</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>long long</FONT></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_ULLONG</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>unsigned long long</FONT></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_FLOAT</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<PRE>float</PRE></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_DOUBLE</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>double</FONT></TD>
</TR>
<TR><TD WIDTH="49%" VALIGN="TOP">
<FONT FACE="Courier New" SIZE=2><P>H5T_NATIVE_LDOUBLE</FONT></TD>
<TD WIDTH="51%" VALIGN="TOP">
<FONT SIZE=2><P>long double</FONT></TD>
</TR>
</TABLE>
</CENTER></P>
<FONT FACE="Times"><P>See <I><a href="Datatypes.html">Datatypes</a></I> at
</FONT>
in the<I> HDF User’s Guide</I> for further information.</P>
</FONT><H3>Programming models</H3>
<FONT FACE="Times"><P>In this section we describe how to program some basic
operations on files, including how to</P>
<UL>
</FONT><LI>create a file </LI>
<LI>create and initialize a dataset </LI>
<LI>discard objects when they are no longer needed </LI>
<LI>write a dataset to a new file </LI>
<LI>obtain information about a dataset </LI>
<LI>read a portion of a dataset </LI>
<LI>create and write compound datatypes </LI>
<LI>create and write extendible datasets </LI>
<LI>create and populate groups </LI></UL>
<H4>How to create an HDF5 file</H4>
<P>This programming model shows how to create a file and also how to close the
file.</P>
<OL>
<LI>Create the file using <CODE>H5Fcreate</CODE>. Obtain a file identifier.</LI>
<LI>Close the file with <CODE>H5Fclose</CODE>.</LI>
<P>The following code fragment implements the specified model. If there is a
possibility that the file already exists, the user must add the flag
<CODE>H5ACC_TRUNC</CODE> to the access mode to overwrite the previous file's
information. </P>
<CODE><PRE>hid_t file; /* handle */
/*
* Create a new file using H5ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
* Then close the file.
*/
file = H5Fcreate(FILE, H5ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
status = H5Fclose(file); </PRE>
</CODE>
</OL>
<H4>How to create and initialize the essential components of a dataset for
writing to a file.</H4>
<P>Recall that datatypes and dimensionality (dataspace) are independent objects,
which are created separately from any dataset that they might be attached to.
Because of this the creation of a dataset requires, at a minimum, separate
definitions of datatype, dimensionality, and dataset. Hence, to create a dataset
the following steps need to be taken:</P>
<ol>
<FONT FACE="Times"><LI VALUE=1>Create and initialize a dataspace for the
dataset to be written.</LI>
<LI>Define the datatype for the dataset to be written. </LI>
<LI>Create and initialize the dataset itself.</LI></OL>
</FONT><FONT FACE="Courier New"><P> </P>
</FONT><FONT FACE="Times"><P>The following code illustrates the creation of
these three components of a dataset object.</P>
</FONT><CODE><PRE>hid_t dataset, datatype, dataspace; /* declare handles */
/*
* 1. Create dataspace: Describe the size of the array and
* create the data space for fixed size dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Pcreate_simple(RANK, dimsf, NULL);
/*
/*
* 2. Define datatype for the data in the file.
* We will store little endian integer numbers.
*/
datatype = H5Tcopy(H5T_NATIVE_INT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
/*
* 3. Create a new dataset within the file using defined
* dataspace and datatype and default dataset creation
* properties.
* NOTE: H5T_NATIVE_INT can be used as datatype if conversion
* to little endian is not needed.
*/
dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace, H5P_DEFAULT);</PRE>
</CODE><H4>How to discard objects when they are no longer needed</H4>
<FONT FACE="Times"><P>The type, dataspace and dataset objects should be released
once they are no longer needed by a program. Since each is an independent object,
the must be released (or <I>closed</I>) separately. The following lines of code
close the type, dataspace, datasets, and file that were created in the preceding
section.</P>
</FONT><CODE><P>H5Tclose(datatype);</P>
<P>H5Dclose(dataset);</P>
<P>H5Sclose(dataspace);</P>
</CODE><H4>How to write a dataset to a new file</H4>
<FONT FACE="Times"><P>Having defined the datatype, dataset, and dataspace
parameters, you write out the data with a call to
</FONT><CODE>H5Dwrite</CODE><FONT FACE="Courier">.</P>
</FONT><CODE><PRE>/*
* Write the data to the dataset using default transfer
* properties.
*/
status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);</PRE>
</CODE><FONT FACE="Times"><P>The third and fourth parameters of
</FONT><CODE>H5Dwrite</CODE><FONT FACE="Times"> in the example describe the
dataspaces in memory and in the file, respectively. They are set to the value
</FONT><CODE>H5S_ALL</CODE><FONT FACE="Times"> to indicate that an entire
dataset is to be written. In a later section we look at how we would access
a portion of a dataset.</P>
</FONT><P><A HREF="#CreateExample"><FONT FACE="Times">Example 1</FONT></A>
<FONT FACE="Times"> contains a program that creates a file and a dataset, and
writes the dataset to the file. </P>
<P>Reading is analogous to writing. If, in the previous example, we wish to
read an entire dataset, we would use the same basic calls with the same
parameters. Of course, the routine </FONT><CODE>H5Dread</CODE><FONT FACE="Times">
would replace </FONT><CODE>H5Dwrite</CODE><FONT FACE="Courier">.
</FONT><FONT FACE="Times"> </P>
</FONT><H4>Getting information about a dataset</H4>
<FONT FACE="Times"><P>Although reading is analogous to writing, it is often
necessary to query a file to obtain information about a dataset. For instance,
we often need to know about the datatype associated with a dataset, as well
dataspace information (e.g. rank and dimensions). There are several "get"
routines for obtaining this information The following code segment illustrates
how we would get this kind of information: </P>
</FONT><CODE><PRE>/*
* 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 = H5Sextent_ndims(dataspace);
status_n = H5Sextent_dims(dataspace, dims_out);
printf("rank %d, dimensions %d x %d \n", rank, dims_out[0], dims_out[1]);</PRE>
</CODE><H4>Reading a portion of a dataset</H4>
<FONT FACE="Times"><P>In the previous discussion, we describe how to access an
entire dataset with one write (or read) operation. To read or write a
<I>portion</I> of a dataset, we need to provide more contextual information.</P>
<P>Consider the following example. Suppose there is 500x600 dataset in a file,
and we wish to read from the dataset a 100x200 hyperslab located beginning at
element </FONT><CODE><200,200></CODE><FONT FACE="Times">. In addition,
suppose we wish to read the hyperslab into an 200x400 array in memory beginning
at element </FONT><CODE><0,0></CODE><FONT FACE="Times"> in memory.
Visually, the transfer looks something like this: </P>
</FONT><P ALIGN="CENTER"><IMG SRC="dataset_pl.gif" WIDTH=417 HEIGHT=337></P>
<FONT FACE="Times" SIZE=6><P ALIGN="CENTER"> </P>
</FONT><FONT FACE="Times"><P>As the example illustrates, whenever we read part
of a dataset from a file we must provide two dataspaces: the dataspace of the
object in the file as well as the dataspace of the object in memory into which
we read. There are dataspace routines (</FONT><CODE>H5S...</CODE>
<FONT FACE="Times">) for doing this. </P>
<P>For example, suppose we want to read a 3x4 hyperslab from a dataset in a
file beginning at the element </FONT><CODE><1,2></CODE><FONT FACE="Times">
in the dataset. In order to do this, we must create a dataspace that describes
the overall rank and dimensions of the dataset in the file, as well as the
position and size of the hyperslab that we are extracting from that dataset.
The following code illustrates how this would be done. </P>
</FONT><CODE><PRE>/*
* Get overall rank and dimensions of dataspace.
*/
dataspace = H5Dget_space(dataset); /* get dataspace handle */
rank = H5Pextent_ndims(dataspace);
status_n = H5Pextent_dims(dataspace, dims_out);
/*
* Define hyperslab in the dataset.
*/
offset[0] = 1;
offset[1] = 2;
count[0] = 3;
count[1] = 4;
status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, count, NULL);</PRE>
</CODE><FONT FACE="Times"><P>This describes the dataspace from which we wish
to read. We need to define the dataspace in memory analogously. Suppose, for
instance, that we have in memory a 3 dimensional 7x7x3 array into which we
wish to read the 3x4 hyperslab described above beginning at the element
</FONT><CODE><3,0,0></CODE><FONT FACE="Times">. Since the in-memory
dataspace has three dimensions, we have to describe the hyperslab as an array
with three dimensions, with the last dimension being 1:
</FONT><CODE><3,4,1></CODE><FONT FACE="Times">.</P>
<P>Notice that now we must describe two things: the dimensions of the in-memory
array, and the size and position of the hyperslab that we wish to read in.
The following code illustrates how this would be done. </P>
</FONT><CODE><PRE>/*
* Define the memory dataspace.
*/
dimsm[0] = 7;
dimsm[1] = 7;
dimsm[2] = 3;
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] = 3;
count_out[1] = 4;
count_out[2] = 1;
status = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, offset_out, NULL, count_out, NULL);
/*</PRE>
</CODE><P><A HREF="#CheckAndReadExample"><FONT FACE="Times">Example 2</FONT></A>
<FONT FACE="Times"> contains a complete program that performs these operations.</P>
</FONT><H4>Creating compound datatypes</H4>
<B><P>Properties of compound datatypes. </B>A compound datatype is similar to
a struct in C or a common block in Fortran. It is a collection of one or more
atomic types or small arrays of such types. To create and use of a compound
datatype requires you need to refer to various <DFN>properties</DFN> of the
data compound datatype:</P>
<UL>
<LI>It is of class <DFN>compound</DFN><I>.</I> </LI>
<LI>It has a fixed total <DFN>size</DFN>, in bytes. </LI>
<LI>It consists of zero or more <DFN>members</DFN> (defined in any order) with
unique names and which occupy non-overlapping regions within the datum. </LI>
<LI>Each member has its own <DFN>datatype</DFN>. </LI>
<LI>Each member is referenced by an <DFN>index number</DFN> between zero and N-1,
where N is the number of members in the compound datatype. </LI>
<LI>Each member has a <DFN>name</DFN> which is unique among its siblings in a
compound data type. </LI>
<LI>Each member has a fixed <DFN>byte offset</DFN>, which is the first byte
(smallest byte address) of that member in a compound datatype. </LI>
<LI>Each member can be a small array of up to four dimensions.</LI></UL>
<FONT FACE="Times"><P>Properties of members of a compound data type are defined
when the member is added to the compound type and cannot be subsequently
modified.</P>
<B><P>Defining compound datatypes. </B>Compound datatypes must be built out of
other datatypes. First, one creates an empty compound data type and specifies
its total size. Then members are added to the compound data type in any order.</P>
<I><P>Member names. </I>Each member must have a descriptive name, which is the
key used to uniquely identify the member within the compound data type. A member
name in an HDF5 data type does not necessarily have to be the same as the name
of the corresponding member in the C struct in memory, although this is often
the case. Nor does one need to define all members of the C struct in the HDF5
compound data type (or vice versa). </P>
<I><P>Offsets. </I>Usually a C struct will be defined to hold a data point in
memory, and the offsets of the members in memory will be the offsets of the
struct members from the beginning of an instance of the struct. The library
defines the macro to compute the offset of a member within a struct:</P>
</FONT><CODE><P>HOFFSET(s,m)<FONT SIZE=5>. </FONT></CODE><FONT FACE="Times">This
macro computes the offset of member </FONT><FONT FACE="Courier"><EM>m</EM>
</FONT><FONT FACE="Times">within a struct variable <EM>s</EM>. </P>
<P>Here is an example in which a compound data type is created to describe
complex numbers whose type is defined by the </FONT><CODE>complex_t</CODE>
<FONT FACE="Times" SIZE=2> </FONT><FONT FACE="Times">struct. </P>
</FONT><CODE><PRE>typedef struct {
double re; /*real part */
double im; /*imaginary part */
} complex_t;
complex_t tmp; /*used only to compute offsets */
hid_t complex_id = H5Tcreate (H5T_COMPOUND, sizeof tmp);
H5Tinsert (complex_id, "real", HOFFSET(tmp,re),
H5T_NATIVE_DOUBLE);
H5Tinsert (complex_id, "imaginary", HOFFSET(tmp,im),
H5T_NATIVE_DOUBLE);</PRE>
</CODE><P><A HREF="#Compound">Example 3</A><FONT FACE="Times"> shows how to
create a compound data type, write an array that has the compound data type
to the file, and read back subsets of the members.</P>
</FONT><H4>Creating and writing extendible datasets</H4>
<FONT FACE="Times"><P>An <I>extendible</I> dataset is one whose dimensions
can grow. In HDF5, it is possible to define a dataset to have certain initial
dimensions, then later to increase the size of any of the initial dimensions. </P>
<P>For example, you can create and store the following 3x3 HDF5 dataset:</P>
</FONT><PRE> 1 1 1
1 1 1
1 1 1 </PRE>
<FONT FACE="Times"><P>then later to extend this into a 10x3 dataset by adding
7 rows, such as this:</P>
</FONT><PRE> 1 1 1
1 1 1
1 1 1
2 2 2
2 2 2
2 2 2
2 2 2
2 2 2
2 2 2
2 2 2</PRE>
<FONT FACE="Times"><P>then further extend it to a 10x5 dataset by adding two
columns, such as this:</P>
</FONT><PRE> 1 1 1 3 3
1 1 1 3 3
1 1 1 3 3
2 2 2 3 3
2 2 2 3 3
2 2 2 3 3
2 2 2 3 3
2 2 2 3 3
2 2 2 3 3
2 2 2 3 3</PRE>
<FONT FACE="Times"><P>The current version of HDF 5 requires you to use
<I>chunking</I> in order to define extendible datasets. Chunking makes
it possible to extend datasets efficiently, without having to reorganize
storage excessively. </P>
<P>Three operations are required in order to write an extendible dataset:</P>
<OL>
<LI>Declare the dataspace of the dataset to have <I>unlimited dimensions</I>
for all dimensions that might eventually be extended.</LI>
<LI>When creating the dataset, set the storage layout for the dataset to
<I>chunked</I>.</LI>
<LI>Extend the size of the dataset.</LI></OL>
<P>For example, suppose we wish to create a dataset similar to the one shown
above. We want to start with a 3x3 dataset, then later extend it in both
directions. </P>
<B><P>Declaring unlimited dimensions. </B>We could declare the dataspace
to have unlimited dimensions with the following code, which uses the predefined
constant </FONT><CODE>H5S_UNLIMITED</CODE><FONT FACE="Times"> to specify
unlimited dimensions.</P>
</FONT><PRE>hsize_t dims[2] = { 3, 3}; /* dataset dimensions
at the creation time */
hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
/*
* 1. Create the data space with unlimited dimensions.
*/
dataspace = H5Screate_simple(RANK, dims, maxdims); </PRE>
<B><P>Enabling chunking. </B>We can then modify the dataset storage layout
properties to enable chunking. We do this using the routine
<CODE>H5Pset_chunk</CODE><FONT SIZE=4>:</P>
</FONT><PRE>hid_t cparms;
hsize_t chunk_dims[2] ={2, 5};
/*
* 2. Modify dataset creation properties to enable chunking.
*/
cparms = H5Pcreate (H5P_DATASET_CREATE);
status = H5Pset_chunk( cparms, RANK, chunk_dims);
</PRE>
<B><P>Extending dataset size. </B>Finally, when we want to extend the size of
the dataset, we invoke <CODE>H5Dextend </CODE>to extend the size of the dataset.
In the following example, we extend the dataset along the first dimension, by
seven rows, so that the new dimensions are <CODE><10,3></CODE>:</P>
<PRE>/*
* Extend the dataset. Dataset becomes 10 x 3.
*/
dims[0] = dims[0] + 7;
size[0] = dims[0];
size[1] = dims[1];
status = H5Dextend (dataset, size);</PRE>
<FONT FACE="Courier New" SIZE=2><P> </P>
</FONT><P><A HREF="#CreateExtendWrite">Example 4</A> shows how to create a 3x3
extendible dataset, write the dataset, extend the dataset to 10x3, write the
dataset again, extend it again to 10x5, write the dataset again.</P>
<P><A HREF="#ReadExtended">Example 5</A> shows how to read the data written by
Example 4. </P>
<H3>Working with groups in a file</H3>
<P>Groups provide a mechanism for organizing datasets in an HDF5 file extendable
meaningful ways. The H5G API contains routines for working with groups. </P>
<B><P>To create a group</B>, use <CODE>H5Gcreate</CODE>. For example, the
following code creates two groups that are members of the root group. They
are called <CODE>/IntData</CODE> and <CODE>/FloatData</CODE>. The return value
(<CODE>dir</CODE>) is the group identifier.</P>
<CODE><PRE>/*
* Create two groups in a file.
*/
dir = H5Gcreate(file, "/IntData", 0);
status = H5Gclose(dir);
dir = H5Gcreate(file,"/FloatData", 0);
status = H5Gclose(dir);</PRE>
</CODE><P>The third parameter in <CODE>H5Gcreate</CODE> optionally specifies
how much file space to reserve to store the names that will appear in this group.
If a non-positive value is supplied then a default size is chosen.</P>
<CODE><P>H5Gclose</CODE> closes the group and releases the group identifier.</P>
<P> </P>
<B><P>Creating an object in a particular group. </B>Except for single-object
HDF5 files, every object in an HDF5 file must belong to a group, and hence has
a path name. Hence, we put an object in a particular group by giving its path
name when we create it. For example, the following code creates a dataset
<CODE>IntArray</CODE> in the group <CODE>/IntData</CODE>:</P>
<CODE><PRE>/*
* Create dataset in the /IntData group by specifying full path.
*/
dims[0] = 2;
dims[1] = 3;
dataspace = H5Pcreate_simple(2, dims, NULL);
dataset = H5Dcreate(file, "/IntData/IntArray", H5T_NATIVE_INT, dataspace, H5C_DEFAULT); </PRE>
</CODE><B><P>Changing the current group. </B>The HDF5 Group API supports the
idea of a <DFN>current group</DFN>. This is analogous to the
<DFN>current working directory</DFN> idea in UNIX. You can set the current
group in HDF5 with the routine <CODE>H5Gset</CODE>. The following code shows
how to set a current group, then create a certain dataset (<CODE>FloatData</CODE>)
in that group. </P>
<CODE><PRE>/*
* Set current group to /FloatData.
*/
status = H5Gset (file, "/FloatData");
/*
* Create two datasets
*/
dims[0] = 5;
dims[1] = 10;
dataspace = H5Screate_simple(2, dims, NULL);
dataset = H5Dcreate(file, "FloatArray", H5T_NATIVE_FLOAT, dataspace, H5P_DEFAULT); </PRE>
</CODE><P><A HREF="#CreateGroups">Example 6</A> shows how to create an
HDF5 file with two group, and to place some datasets within those groups.</P>
<P> </P>
<H3> </H3>
<H3>Example code</H3>
<H4><A NAME="CreateExample">Example 1: How to create a homogeneous
multi-dimensional dataset</A> and write it to a file.</H4>
<P>This example creates a 2-dimensional HDF 5 dataset of little endian
32-bit integers.</P>
<PRE><A NAME="CheckAndReadExample">
/*
* 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
main ()
{
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);
} </PRE>
<FONT FACE="Courier New" SIZE=2><P> </P>
</FONT><H4>Example 2.</A> How to read a hyperslab from file into memory.</H4>
<P>This example reads a hyperslab from a 2-d HDF5 dataset into a 3-d dataset
in memory.</P>
<PRE>
/*
* This example reads hyperslab from the SDS.h5 file
* created by h5_write.c program into two-dimensional
* plane of the tree-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
main ()
{
hid_t file, dataset; /* handles */
hid_t datatype, dataspace;
hid_t memspace;
H5T_class_t class; /* data type 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 = H5Sextent_ndims(dataspace);
status_n = H5Sextent_dims(dataspace, dims_out, NULL);
printf("rank %d, dimensions %d x %d \n", rank, dims_out[0], dims_out[1]);
/*
* Define hyperslab in the datatset.
*/
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);
} </PRE>
<FONT FACE="Times" SIZE=2><P> </P>
</FONT><H4><A NAME="Compound"></A>Example 3. Working with compound datatypes.</H4>
<P>This example shows how to create a compound data type, write an array which
has the compound data type to the file, and read back subsets of fields.</P>
<PRE>
/*
* This example shows how to create a compound data type,
* write an array which has the compound data type to the file,
* and read back fields' subsets.
*/
#include "hdf5.h"
#define FILE "SDScompound.h5"
#define DATASETNAME "ArrayOfStructures"
#define LENGTH 10
#define RANK 1
main()
{
/* 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 hadle */
/* 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, datatype, 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 data type.
*/
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 data type 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 data type 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);
}</PRE>
<FONT FACE="Times" SIZE=2><P> </P>
</FONT><H4><A NAME="CreateExtendWrite"></A>Example 4. Creating and writing an extendible dataset.</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.</P>
<PRE>
/*
* 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
main ()
{
hid_t file; /* handles */
hid_t datatype, 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 ulimited 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);
} </PRE>
<FONT FACE="Courier New" SIZE=2><P> </P>
</FONT><H4><A NAME="ReadExtended"></A>Example 5. Reading data.</H4>
<P>This example shows how to read information the chunked dataset written
by <A HREF="#CreateExtendWrite">Example 4</A>.</P>
<PRE>
/*
* 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
main ()
{
hid_t file; /* handles */
hid_t datatype, dataset;
hid_t filespace;
hid_t memspace;
hid_t cparms;
H5T_class_t class; /* data type class */
size_t elem_size; /* size of the data element
stored in file */
hsize_t dims[2]; /* dataset and chunk dimensions */
hsize_t chunk_dims[2];
hsize_t col_dims[1];
size_t size[2];
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 i, j, rank, rank_chunk;
/*
* 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 = H5Sextent_ndims(filespace);
status_n = H5Sextent_dims(filespace, dims, NULL);
printf("dataset rank %d, dimensions %d x %d \n", rank, dims[0], 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 %d x %d \n", rank_chunk,
chunk_dims[0], 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);
} </PRE>
<FONT FACE="Courier New" SIZE=2><P> </P>
</FONT><H4><A NAME="CreateGroups"></A>Example 6. Creating groups.</H4>
<P>This example shows how to create an HDF5 file with two groups, and to
place some datasets within those groups.</P>
<PRE>
/*
* This example shows how to create groups within the file and
* datasets within the file and groups.
*/
#include "hdf5.h"
#define FILE "DIR.h5"
#define RANK 2
main()
{
hid_t file, dir;
hid_t dataset, dataspace;
herr_t status;
hsize_t dims[2];
hsize_t size[1];
/*
* Create a file.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create two groups in a file.
*/
dir = H5Gcreate(file, "/IntData", 0);
status = H5Gclose(dir);
dir = H5Gcreate(file,"/FloatData", 0);
status = H5Gclose(dir);
/*
* Create dataspace for the character string
*/
size[0] = 80;
dataspace = H5Screate_simple(1, size, NULL);
/*
* Create dataset "String" in the root group.
*/
dataset = H5Dcreate(file, "String", H5T_NATIVE_CHAR, dataspace, H5P_DEFAULT);
H5Dclose(dataset);
/*
* Create dataset "String" in the /IntData group.
*/
dataset = H5Dcreate(file, "/IntData/String", H5T_NATIVE_CHAR, dataspace,
H5P_DEFAULT);
H5Dclose(dataset);
/*
* Create dataset "String" in the /FloatData group.
*/
dataset = H5Dcreate(file, "/FloatData/String", H5T_NATIVE_CHAR, dataspace,
H5P_DEFAULT);
H5Sclose(dataspace);
H5Dclose(dataset);
/*
* Create IntArray dataset in the /IntData group by specifying full path.
*/
dims[0] = 2;
dims[1] = 3;
dataspace = H5Screate_simple(RANK, dims, NULL);
dataset = H5Dcreate(file, "/IntData/IntArray", H5T_NATIVE_INT, dataspace,
H5P_DEFAULT);
H5Sclose(dataspace);
H5Dclose(dataset);
/*
* Set current group to /IntData and attach to the dataset String.
*/
status = H5Gset (file, "/IntData");
dataset = H5Dopen(file, "String");
if (dataset > 0) printf("String dataset in /IntData group is found\n");
H5Dclose(dataset);
/*
* Set current group to /FloatData.
*/
status = H5Gset (file, "/FloatData");
/*
* Create two datasets FlatArray and DoubleArray.
*/
dims[0] = 5;
dims[1] = 10;
dataspace = H5Screate_simple(RANK, dims, NULL);
dataset = H5Dcreate(file, "FloatArray", H5T_NATIVE_FLOAT, dataspace, H5P_DEFAULT);
H5Sclose(dataspace);
H5Dclose(dataset);
dims[0] = 4;
dims[1] = 6;
dataspace = H5Screate_simple(RANK, dims, NULL);
dataset = H5Dcreate(file, "DoubleArray", H5T_NATIVE_DOUBLE, dataspace,
H5P_DEFAULT);
H5Sclose(dataspace);
H5Dclose(dataset);
/*
* Attach to /FloatData/String dataset.
*/
dataset = H5Dopen(file, "/FloatData/String");
if (dataset > 0) printf("/FloatData/String dataset is found\n");
H5Dclose(dataset);
H5Fclose(file);
}</PRE>
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<address>
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
<br>
Last modified: 14 July 1998
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