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<title>Chapter 6: HDF5 Datatypes</title>
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<tr valign="top"> \
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<a href="#Intro">1.</a></td>\
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<a href="#Intro">Introduction</a></td> \
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<td class="tocTableContentCell2"> \
<a href="#DtypesUsed">2.</a></td>\
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<a href="#DtypesUsed">How Datatypes Are Used</a></td>\
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<a href="#FileFunctSums">3.</a></td>\
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<a href="#Pmodel">The Programming Model</a></td>\
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<a href="#NonNumDtypes">5.</a></td>\
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<a href="#NonNumDtypes">Other Non-numeric Datatypes</a></td> \
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<a href="#Fvalues">6.</a></td>\
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<a href="#Fvalues">Fill Values</a></td>\
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<a href="#CCDtypes">7.</a></td>\
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<a href="#CCDtypes">Complex Combinations of Datatypes</a>\
</td>\
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<td class="tocTableContentCell2"> \
<a href="#LCDtypeObj">8.</a></td>\
<td class="tocTableContentCell3">\
<a href="#LCDtypeObj">Life Cycle of the Datatype Object</a>\
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<h2>Chapter 6<br /><font size="7">HDF5 Datatypes</font></h2>
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<a name="Intro">
<h3>6.1. Introduction</h3>
</a>
<h4>6.1.1. Introduction and Definitions</h4>
<p>An HDF5 dataset is an array of data elements, arranged according to the
specifications of the dataspace. In general, a data element is the smallest
addressable unit of storage in the HDF5 file. (Compound datatypes are the
exception to this rule.) The HDF5 datatype defines the storage format for a
single data element. See the figure below.</p>
<p>The model for HDF5 attributes is extremely similar to datasets:
an attribute has a dataspace and a datatype, as shown in the figure below.
The information in this chapter applies to both datasets and attributes.</p>
<table width="500" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig1.JPG">
</td>
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<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 1. Datatypes, dataspaces, and datasets</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>Abstractly, each data element within the dataset is a sequence of bits,
interpreted as a single value from a set of values (e.g., a number or a
character). For a given datatype, there is a standard or convention for
representing the values as bits, and when the bits are represented in
a particular storage the bits are laid out in a specific storage
scheme, e.g., as 8-bit bytes, with a specific ordering and alignment
of bytes within the storage array.</p>
<p>HDF5 datatypes implement a flexible, extensible, and portable mechanism
for specifying and discovering the storage layout of the data elements,
determining how to interpret the elements (e.g., as floating point numbers),
and for transferring data from different compatible layouts.</p>
<!-- NEW PAGE -->
<p>An HDF5 datatype describes one specific layout of bits. A dataset has a
single datatype which applies to every data element. When a dataset is
created, the storage datatype is defined. After the dataset or attribute
is created, the datatype cannot be changed.</p>
<ul>
<li>The datatype describes the storage layout of a single data element</li>
<li>All elements of the dataset must have the same type</li>
<li>The datatype of a dataset is immutable</li>
</ul>
<p>When data is transferred (e.g., a read or write), each end point of the
transfer has a datatype, which describes the correct storage for the elements.
The source and destination may have different (but compatible) layouts, in which
case the data elements are automatically transformed during the transfer.</p>
<p>HDF5 datatypes describe commonly used binary formats for numbers (integers
and floating point) and characters (ASCII). A given computing architecture and
programming language supports certain number and character representations.
For example, a computer may support 8-, 16-, 32-, and 64-bit signed integers,
stored in memory in little-endian byte order. These would presumably correspond
to the C programming language types ‘char’, ‘short’,
‘int’, and ‘long’.</p>
<p>When reading and writing from memory, the HDF5 library must know the
appropriate datatype that describes the architecture specific layout.
The HDF5 library provides the platform independent ‘NATIVE’
types, which are mapped to an appropriate datatype for each platform. So
the type ‘<code>H5T_NATIVE_INT</code>’ is an alias for
the appropriate descriptor for each platform.</p>
<p>Data in memory has a datatype:</p>
<ul>
<li>The storage layout in memory is architecture-specific</li>
<li>The HDF5 ‘NATIVE’ types are predefined aliases for the
architecture-specific memory layout</li>
<li>The memory datatype need not be the same as the stored datatype of
the dataset</li>
</ul>
<p>In addition to numbers and characters, an HDF5 datatype can describe more
abstract classes of types, including
<!-- date-times,
(TIME REFERENCES COMMENTED OUT 6 FEB 2006,
UNTIL TIME DATATYPE IS PROPERLY SUPPORTED IN THE LIBRARY) -->
enumerations, strings, bit strings, and references (pointers to objects
in the HDF5 file). HDF5 supports several classes of composite datatypes
which are combinations of one or more other datatypes. In addition to
the standard predefined datatypes, users can define new datatypes
within the datatype classes.</p>
<p>The HDF5 datatype model is very general and flexible:</p>
<ul>
<li>For common simple purposes, only predefined types will be needed</li>
<li>Datatypes can be combined to create complex structured datatypes</li>
<li>If needed, users can define custom atomic datatypes</li>
<li>Committed datatypes can be shared by datasets or attributes</li>
</ul>
<!-- NEW PAGE -->
<h4>6.1.2. HDF5 Datatype Model</h4>
<p>The HDF5 Library implements an object-oriented model of datatypes.
HDF5 datatypes are organized as a logical set of base types, or datatype
classes. Each datatype class defines a format for representing logical
values as a sequence of bits. For example the <code>H5T_INTEGER</code>
class is a format for representing twos complement integers of various
sizes.</p>
<p>A datatype class is defined as a set of one or more datatype properties.
A datatype property is a property of the bit string. The datatype properties
are defined by the logical model of the datatype class. For example, the
integer class (twos complement integers) has properties such as
“signed or unsigned”, “length”, and
“byte-order”. The float class (IEEE floating point
numbers) has these properties, plus “exponent bits”,
“exponent sign”, etc.</p>
<p>A datatype is derived from one datatype class: a given datatype has
a specific value for the datatype properties defined by the class.
For example, for 32-bit signed integers, stored big-endian, the HDF5
datatype is a sub-type of integer with the properties set to
<code>signed=1</code>, <code>size=4</code> (bytes), and
<code>byte-order=BE</code>.</p>
<p>The HDF5 datatype API (H5T functions) provides methods to create
datatypes of different datatype classes, to set the datatype properties
of a new datatype, and to discover the datatype properties of an
existing datatype.</p>
<p>The datatype for a dataset is stored in the HDF5 file as part of
the metadata for the dataset.</p>
<p>A datatype can be shared by more than one dataset in the file if the
datatype is saved to the file with a name. This shareable datatype is known
as a committed datatype. In the past, this kind of datatype was called
a named datatype. </p>
<p>When transferring data (e.g., a read or write), the data elements of
the source and destination storage must have compatible types. As a
general rule, data elements with the same datatype class are compatible
while elements from different datatype classes are not compatible. When
transferring data of one datatype to another compatible datatype, the
HDF5 Library uses the datatype properties of the source and
destination to automatically transform each data element. For
example, when reading from data stored as 32-bit signed integers,
big-endian into 32-bit signed integers, little-endian, the HDF5
Library will automatically swap the bytes.</p>
<p>Thus, data transfer operations (<code>H5Dread</code>,
<code>H5Dwrite</code>, <code>H5Aread</code>, <code>H5Awrite</code>) require
a datatype for both the source and the destination.</p>
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<table width="500" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig2.JPG">
</td></tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 2. The datatype model</b>
<hr color="green" size="3"/></td></tr>
</table>
<br />
<p>The HDF5 Library defines a set of predefined datatypes, corresponding to
commonly used storage formats, such as twos complement integers, IEEE Floating
point numbers, etc., 4- and 8-byte sizes, big-endian and little-endian
byte orders. In addition, a user can derive types with custom values
for the properties. For example, a user program may create a datatype
to describe a 6-bit integer, or a 600-bit floating point number.</p>
<p>In addition to atomic datatypes, the HDF5 Library supports
composite datatypes. A composite datatype is an aggregation of one
or more datatypes. Each class of composite datatypes has properties
that describe the organization of the composite datatype. See the
figure below. Composite datatypes include:</p>
<ul>
<li>Compound datatypes: structured records</li>
<li>Array: a multidimensional array of a datatype</li>
<li>Variable-length: a one-dimensional array of a datatype</li>
</ul>
<br />
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<table width="400" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig3.JPG">
</td></tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 3. Composite datatypes</b>
<hr color="green" size="3"/></td></tr>
</table>
<br />
<h4><em>6.1.2.1. Datatype Classes and Properties</em></h4>
<p>The figure below shows the HDF5 datatype classes. Each class is
defined to have a set of properties which describe the layout of the
data element and the interpretation of the bits. The table below
lists the properties for the datatype classes.</p>
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<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig4.JPG">
</td></tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 4. Datatype classes</b>
<hr color="green" size="3"/></td></tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="7" align="left" valign="bottom">
<b>Table 1. Datatype classes and their properties</b></td>
</tr>
<tr><td colspan="7"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="20%"><b>Class</b></td>
<td width="2%"> </td>
<td width="18%"><b>Description</b></td>
<td width="2%"> </td>
<td width="28%"><b>Properties</b></td>
<td width="2%"> </td>
<td width="28%"><b>Notes</b></td>
</tr>
<tr><td colspan="7"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Integer</td>
<td> </td>
<td>Twos complement integers</td>
<td> </td>
<td>Size (bytes), precision (bits), offset (bits),
pad, byte order, signed/unsigned</td>
<td> </td>
<td> </td>
</tr>
<tr><td colspan="7"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Float</td>
<td> </td>
<td>Floating Point numbers</td>
<td> </td>
<td>Size (bytes), precision (bits), offset (bits),
pad, byte order, sign position, exponent position, exponent size (bits),
exponent sign, exponent bias, mantissa position, mantissa (size) bits,
mantissa sign, mantissa normalization, internal padding</td>
<td> </td>
<td>See IEEE 754 for a definition of these properties. These
properties describe non-IEEE 754 floating point formats as well.</td>
</tr>
<tr><td colspan="7"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Character</td>
<td> </td>
<td>Array of 1-byte character encoding </td>
<td> </td>
<td>Size (characters), Character set, byte order,
pad/no pad, pad character</td>
<td> </td>
<td>Currently, ASCII and UTF-8 are supported.</td>
</tr>
<tr><td colspan="7"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Bitfield</td>
<td> </td>
<td>String of bits</td>
<td> </td>
<td>Size (bytes), precision (bits), offset (bits),
pad, byte order</td>
<td> </td>
<td>A sequence of bit values packed into one or more bytes.</td>
</tr>
<tr><td colspan="7"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Opaque</td>
<td> </td>
<td>Uninterpreted data</td>
<td> </td>
<td>Size (bytes), precision (bits), offset (bits),
pad, byte order, tag</td>
<td> </td>
<td>A sequence of bytes, stored and retrieved as a block. The
‘tag’ is a string that can be used to label
the value.</td>
</tr>
<tr><td colspan="7"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Enumeration</td>
<td> </td>
<td>A list of discrete values, with symbolic names
in the form of strings.</td>
<td> </td>
<td>Number of elements, element names, element values</td>
<td> </td>
<td>Enumeration is a list of pairs, (name, value). The name is
a string, the value is an unsigned integer.</td>
</tr>
<tr><td colspan="7"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Reference</td>
<td> </td>
<td>Reference to object or region within the HDF5 file</td>
<td> </td>
<td> </td>
<td> </td>
<td> See the Reference API, H5R</td>
</tr>
<tr><td colspan="7"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Array</td>
<td> </td>
<td>Array (1-4 dimensions) of data elements</td>
<td> </td>
<td>Number of dimensions, dimension sizes, base datatype</td>
<td> </td>
<td>The array is accessed atomically: no selection or sub-setting.</td>
</tr>
<!-- NEW PAGE -->
<tr><td colspan="7"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Variable-length</td>
<td> </td>
<td>A variable-length 1-dimensional array of data data elements</td>
<td> </td>
<td>Current size, base type</td>
<td> </td>
<td> </td>
</tr>
<tr><td colspan="7"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Compound</td>
<td> </td>
<td>A Datatype of a sequence of Datatypes</td>
<td> </td>
<td>Number of members, member names, member types,
member offset, member class, member size, byte order </td>
<td> </td>
<td> </td>
</tr>
<tr><td colspan="7"><hr color="green" size="3" /></td></tr>
</table>
<br />
<h4><em>6.1.2.2. Predefined Datatypes</em></h4>
<p>The HDF5 library predefines a modest number of commonly used datatypes.
These types have standard symbolic names of the form
<code>H5T_<em>arch_base</em></code> where <em>arch</em> is an architecture
name and <em>base</em> is a programming type name (Table 2). New types can
be derived from the predefined types by copying the predefined type (see
<code>H5Tcopy()</code>) and then modifying the result. </p>
<p>The base name of most types consists of a letter to indicate the class
(Table 3), a precision in bits, and an indication of the byte order (Table 4).</p>
<p>Table 5 shows examples of predefined datatypes.
The full list can be found in the “HDF5 Predefined Datatypes”
section of the <a href="../RM/RM_H5Front.html">
<cite>HDF5 Reference Manual</cite></a>.</p>
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<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 2. Architectures used in predefined datatypes</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="20%">
<b>Architecture<br />Name</b></td>
<td width="80%">
<b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>IEEE</code> </td>
<td>IEEE-754 standard floating point types in
various byte orders.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>STD</code> </td>
<td>
This is an architecture that contains semi-standard
datatypes like signed two’s complement integers, unsigned
integers, and bitfields in various byte orders.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>C <br /> FORTRAN</code> </td>
<td>Types which are specific to the C or Fortran
programming languages are defined in these architectures. For instance,
<code>H5T_C_S1</code> defines a base string type with null termination
which can be used to derive string types of other lengths.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>NATIVE</code> </td>
<td>This architecture contains C-like
datatypes 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.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>CRAY</code> </td>
<td>Cray architectures. These are
word-addressable, big-endian systems with non-IEEE floating point.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>INTEL</code> </td>
<td>All Intel and compatible CPU’s
including 80286, 80386, 80486, Pentium, Pentium-Pro, and Pentium-II.
These are little-endian systems with IEEE floating-point.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>MIPS</code> </td>
<td>All MIPS CPU’s commonly used in
SGI systems. These are big-endian systems with IEEE floating-point.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>ALPHA</code> </td>
<td>All DEC Alpha CPU’s,
little-endian systems with IEEE floating-point.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="200" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 3. Base types</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50">B</td>
<td width="150">Bitfield</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>F</td>
<td>Floating point</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>I</td>
<td>Signed integer</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>R</td>
<td>References</td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>S</td>
<td>Character string</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>U</td>
<td>Unsigned integer</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="200" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 4. Byte order</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50">BE</td>
<td width="150">Big-endian</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>LE</td>
<td>Little-endian</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 5. Some predefined datatypes</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="25%">
<b>Example</b></td>
<td width="75%">
<b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_IEEE_F64LE</code> </td>
<td>Eight-byte, little-endian, IEEE floating-point</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_IEEE_F32BE</code> </td>
<td>Four-byte, big-endian, IEEE floating point</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_STD_I32LE</code> </td>
<td>Four-byte, little-endian, signed two’s complement
integer</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_STD_U16BE</code> </td>
<td>Two-byte, big-endian, unsigned integer</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_C_S1</code> </td>
<td>One-byte, null-terminated string of eight-bit characters</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_INTEL_B64</code> </td>
<td>Eight-byte bit field on an Intel CPU</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_CRAY_F64</code> </td>
<td>Eight-byte Cray floating point</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_STD_ROBJ</code> </td>
<td>Reference to an entire object in a file</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<p>The HDF5 Library predefines a set of <code>NATIVE</code> datatypes which
are similar to C type names. The native types are set to be an alias for the
appropriate HDF5 datatype for each platform. For example,
<code>H5T_NATIVE_INT</code> corresponds to a C <code>int</code> type.
On an Intel based PC, this type is the same as <code>H5T_STD_I32LE</code>,
while on a MIPS system this would be equivalent to <code>H5T_STD_I32BE</code>.
Table 6 shows examples of <code>NATIVE</code> types and corresponding
C types for a common 32-bit workstation.</p>
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<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 6. Native and 32-bit C datatypes</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td><b>Example</b></td>
<td><b>Corresponding C Type</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_CHAR</code> </td>
<td>char</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_SCHAR</code> </td>
<td>signed char</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_UCHAR</code> </td>
<td>unsigned char</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_SHORT</code> </td>
<td>short</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_USHORT</code> </td>
<td>unsigned short</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_INT</code> </td>
<td>int</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_UINT</code> </td>
<td>unsigned</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_LONG</code> </td>
<td>long</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_ULONG</code> </td>
<td>unsigned long</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_LLONG</code> </td>
<td>long long</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_ULLONG</code> </td>
<td>unsigned long long</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_FLOAT</code> </td>
<td>float</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_DOUBLE</code> </td>
<td>double</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_LDOUBLE</code> </td>
<td>long double</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_HSIZE</code> </td>
<td>hsize_t</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_HSSIZE</code> </td>
<td>hssize_t</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_HERR</code> </td>
<td>herr_t</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_HBOOL</code> </td>
<td>hbool_t</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_B8</code> </td>
<td>8-bit unsigned integer or 8-bit buffer in memory</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_B16</code> </td>
<td>16-bit unsigned integer or 16-bit buffer in memory</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_B32</code> </td>
<td>32-bit unsigned integer or 32-bit buffer in memory</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_NATIVE_B64</code> </td>
<td>64-bit unsigned integer or 64-bit buffer in memory</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
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<h3 class=pagebefore>6.2. How Datatypes are Used</h3>
</a>
<h4>6.2.1. The Datatype Object and the HDF5 Datatype API</h4>
<p>The HDF5 Library manages datatypes as objects. The HDF5 datatype API
manipulates the datatype objects through C function calls. New datatypes
can be created from scratch or copied from existing datatypes. When a
datatype is no longer needed its resources should be released by calling
<code>H5Tclose()</code>. </p>
<p>The datatype object is used in several roles in the HDF5 data model
and library. Essentially, a datatype is used whenever the format of
data elements is needed. There are four major uses of datatypes in
the HDF5 Library: at dataset creation, during data transfers, when
discovering the contents of a file, and for specifying user-defined
datatypes. See the table below.</p>
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 7. Datatype uses</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>Use</b></td>
<td>
<b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Dataset creation</td>
<td>The datatype of the data elements must be
declared when the dataset is created.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Data transfer</td>
<td>The datatype (format) of the data elements
must be defined for both the source and destination.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Discovery</td>
<td>The datatype of a dataset can be
interrogated to retrieve a complete description of the storage layout.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Creating user-defined datatypes</td>
<td>Users can define their own datatypes by
creating datatype objects and setting their properties.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<h4>6.2.2. Dataset Creation</h4>
<p>All the data elements of a dataset have the same datatype. When a dataset
is created, the datatype for the data elements must be specified. The
datatype of a dataset can never be changed. The example below shows
the use of a datatype to create a dataset called “/dset”. In
this example, the dataset will be stored as 32-bit signed integers in
big-endian order.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t dt;
dt = H5Tcopy(H5T_STD_I32BE);
dataset_id = H5Dcreate(file_id, “/dset”, dt, dataspace_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 1. Using a datatype to create a dataset </b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<h4>6.2.3. Data Transfer (Read and Write)</h4>
<p>Probably the most common use of datatypes is to write or read data from a
dataset or attribute. In these operations, each data element is transferred
from the source to the destination (possibly rearranging the order of the
elements). Since the source and destination do not need to be identical
(i.e., one is disk and the other is memory) the transfer requires both the
format of the source element and the destination element. Therefore, data
transfers use two datatype objects, for the source and destination.</p>
<p>When data is written, the source is memory and the destination is disk
(file). The memory datatype describes the format of the data element in the
machine memory, and the file datatype describes the desired format of the data
element on disk. Similarly, when reading, the source datatype describes the
format of the data element on disk, and the destination datatype describes the
format in memory.</p>
<p>In the most common cases, the file datatype is the datatype specified
when the dataset was created, and the memory datatype should be the
appropriate NATIVE type.</p>
<p>The examples below show samples of writing data to and reading data
from a dataset. The data in memory is declared C type ‘int’,
and the datatype <code>H5T_NATIVE_INT</code> corresponds to this type.
The datatype of the dataset should be of datatype class
<code>H5T_INTEGER</code>.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
int dset_data[DATA_SIZE];
status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, dset_data);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 2. Writing to a dataset</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
int dset_data[DATA_SIZE];
status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, dset_data);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 3. Reading from a dataset</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<h4>6.2.4. Discovery of Data Format</h4>
<p>The HDF5 Library enables a program to determine the datatype class and
properties for any datatype. In order to discover the storage format of data
in a dataset, the datatype is obtained, and the properties are determined
by queries to the datatype object. The example below shows code that
analyzes the datatype for an integer and prints out a description of
its storage properties (byte order, signed, size.)</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
switch (H5Tget_class(type)) {
case H5T_INTEGER:
ord = H5Tget_order(type);
sgn = H5Tget_sign(type);
printf(“Integer ByteOrder= ”);
switch (ord) {
case H5T_ORDER_LE:
printf(“LE”);
break;
case H5T_ORDER_BE:
printf(“BE”);
break;
}
printf(“ Sign= ”);
switch (sgn) {
case H5T_SGN_NONE:
printf(“false”);
break;
case H5T_SGN_2:
printf(“true”);
break;
}
printf(“ Size= ”);
sz = H5Tget_size(type);
printf(“%d”, sz);
printf(“\n”);
break;</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 4. Discovering datatype properties</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<h4>6.2.5. Creating and Using User-defined Datatypes</h4>
<p>Most programs will primarily use the predefined datatypes described above,
possibly in composite datatypes such as compound or array datatypes.
However, the HDF5 datatype model is extremely general; a user program can
define a great variety of atomic datatypes (storage layouts). In particular,
the datatype properties can define signed and unsigned integers of any size
and byte order, and floating point numbers with different formats, size, and
byte order. The HDF5 datatype API provides methods to set these properties.</p>
<p>User-defined types can be used to define the layout of data in memory,
e.g., to match some platform specific number format or application
defined bit-field. The user-defined type can also describe data in
the file, e.g., some application-defined format. The user-defined
types can be translated to and from standard types of the same class,
as described above.</p>
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<a name="FileFunctSums">
<h3 class=pagebefore>6.3. Datatype (H5T) Function Summaries</h3>
</a>
<p>Functions that can be used with datatypes (H5T functions) and property
list functions that can be used with datatypes (H5P functions) are listed
below.</p>
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 1. General datatype operations
</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top"><td width="25%"><b>C Function<br />Fortran Function</b></td>
<td width="2%"> </td>
<td width="73%"><b>Purpose</b></td>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tcreate<br />h5tcreate_f</code>
</td><td> </td>
<td>
Creates a new datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Topen<br />h5topen_f</code>
</td><td> </td>
<td>
Opens a committed datatype. The C function is a
macro: see <a href="../RM/APICompatMacros.html">“API
Compatibility Macros in HDF5.”</a>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tcommit<br />h5tcommit_f</code>
</td><td> </td>
<td>
Commits a transient datatype to a file. The datatype is now a
committed datatype. The C function is a
macro: see <a href="../RM/APICompatMacros.html">“API
Compatibility Macros in HDF5.”</a>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tcommit_anon<br />h5tcommit_anon_f</code>
</td><td> </td>
<td>
Commits a transient datatype to a file. The datatype is now a
committed datatype, but it is not linked into the file structure.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tcommitted<br />h5tcommitted_f</code>
</td><td> </td>
<td>
Determines whether a datatype is a committed or a transient type.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tcopy<br />h5tcopy_f</code>
</td><td> </td>
<td>
Copies an existing datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tequal<br />h5tequal_f</code>
</td><td> </td>
<td>
Determines whether two datatype identifiers refer to the same datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tlock<br />(none)</code>
</td><td> </td>
<td>
Locks a datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_class<br />h5tget_class_f</code>
</td><td> </td>
<td>
Returns the datatype class identifier.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_create_plist<br />h5tget_create_plist_f</code>
</td><td> </td>
<td>
Returns a copy of a datatype creation property list.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_size<br />h5tget_size_f</code>
</td><td> </td>
<td>
Returns the size of a datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_super<br />h5tget_super_f</code>
</td><td> </td>
<td>
Returns the base datatype from which a datatype is derived.
</td>
</tr>
<!-- NEW PAGE -->
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_native_type<br />h5tget_native_type_f</code>
</td><td> </td>
<td>
Returns the native datatype of a specified datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tdetect_class<br />(none)</code>
</td><td> </td>
<td>
Determines whether a datatype is of the given datatype class.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_order<br />h5tget_order_f</code>
</td><td> </td>
<td>
Returns the byte order of a datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_order<br />h5tset_order_f</code>
</td><td> </td>
<td>
Sets the byte ordering of a datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tdecode<br />h5tdecode_f</code>
</td><td> </td>
<td>
Decode a binary object description of datatype and return a new
object identifier.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tencode<br />h5tencode</code>
</td><td> </td>
<td>
Encode a datatype object description into a binary buffer.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tclose<br />h5tclose_f</code>
</td><td> </td>
<td>
Releases a datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 2. Conversion functions
</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>C Function<br />Fortran Function</b>
</td><td> </td>
<td>
<b>Purpose</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tconvert<br />h5tconvert_f</code>
</td><td> </td>
<td>
Converts data between specified datatypes.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tcompiler_conv<br />h5tcompiler_conv_f</code>
</td><td> </td>
<td>
Check whether the librarys default conversion is hard conversion.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tfind<br />(none)</code>
</td><td> </td>
<td>
Finds a conversion function.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tregister<br />(none)</code>
</td><td> </td>
<td>
Registers a conversion function.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tunregister<br />(none)</code>
</td><td> </td>
<td>
Removes a conversion function from all conversion paths.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 3. Atomic datatype properties
</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>C Function<br />Fortran Function</b>
</td><td> </td>
<td>
<b>Purpose</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_size<br />h5tset_size_f</code>
</td><td> </td>
<td>
Sets the total size for an atomic datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_precision<br />h5tget_precision_f</code>
</td><td> </td>
<td>
Returns the precision of an atomic datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_precision<br />h5tset_precision_f</code>
</td><td> </td>
<td>
Sets the precision of an atomic datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_offset<br />h5tget_offset_f</code>
</td><td> </td>
<td>
Retrieves the bit offset of the first significant bit.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_offset<br />h5tset_offset_f</code>
</td><td> </td>
<td>
Sets the bit offset of the first significant bit.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_pad<br />h5tget_pad_f</code>
</td><td> </td>
<td>
Retrieves the padding type of the least and most-significant bit
padding.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_pad<br />h5tset_pad_f</code>
</td><td> </td>
<td>
Sets the least and most-significant bits padding types.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_sign<br />h5tget_sign_f</code>
</td><td> </td>
<td>
Retrieves the sign type for an integer type.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_sign<br />h5tset_sign_f</code>
</td><td> </td>
<td>
Sets the sign property for an integer type.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_fields<br />h5tget_fields_f</code>
</td><td> </td>
<td>
Retrieves floating point datatype bit field information.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_fields<br />h5tset_fields_f</code>
</td><td> </td>
<td>
Sets locations and sizes of floating point bit fields.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_ebias<br />h5tget_ebias_f</code>
</td><td> </td>
<td>
Retrieves the exponent bias of a floating-point type.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_ebias<br />h5tset_ebias_f</code>
</td><td> </td>
<td>
Sets the exponent bias of a floating-point type.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_norm<br />h5tget_norm_f</code>
</td><td> </td>
<td>
Retrieves mantissa normalization of a floating-point datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_norm<br />h5tset_norm_f</code>
</td><td> </td>
<td>
Sets the mantissa normalization of a floating-point datatype.
</td>
</tr>
<!-- NEW PAGE -->
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_inpad<br />h5tget_inpad_f</code>
</td><td> </td>
<td>
Retrieves the internal padding type for unused bits in floating-point
datatypes.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_inpad<br />h5tset_inpad_f</code>
</td><td> </td>
<td>
Fills unused internal floating point bits.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_cset<br />h5tget_cset_f</code>
</td><td> </td>
<td>
Retrieves the character set type of a string datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_cset<br />h5tset_cset_f</code>
</td><td> </td>
<td>
Sets character set to be used.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_strpad<br />h5tget_strpad_f</code>
</td><td> </td>
<td>
Retrieves the storage mechanism for a string datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_strpad<br />h5tset_strpad_f</code>
</td><td> </td>
<td>
Defines the storage mechanism for character strings.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 4. Enumeration datatypes
</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>C Function<br />Fortran Function</b>
</td><td> </td>
<td>
<b>Purpose</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tenum_create<br />h5tenum_create_f</code>
</td><td> </td>
<td>
Creates a new enumeration datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tenum_insert<br />h5tenum_insert_f</code>
</td><td> </td>
<td>
Inserts a new enumeration datatype member.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tenum_nameof<br />h5tenum_nameof_f</code>
</td><td> </td>
<td>
Returns the symbol name corresponding to a specified member of an
enumeration datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tenum_valueof<br />h5tenum_valueof_f</code>
</td><td> </td>
<td>
Returns the value corresponding to a specified member of an
enumeration datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_member_value<br />h5tget_member_value_f</code>
</td><td> </td>
<td>
Returns the value of an enumeration datatype member.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_nmembers<br />h5tget_nmembers_f</code>
</td><td> </td>
<td>
Retrieves the number of elements in a compound or enumeration datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_member_name<br />h5tget_member_name_f</code>
</td><td> </td>
<td>
Retrieves the name of a compound or enumeration datatype member.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_member_index<br />(none)</code>
</td><td> </td>
<td>
Retrieves the index of a compound or enumeration datatype member.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 5. Compound datatype properties
</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>C Function<br />Fortran Function</b>
</td><td> </td>
<td>
<b>Purpose</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_nmembers<br />h5tget_nmembers_f</code>
</td><td> </td>
<td>
Retrieves the number of elements in a compound or enumeration datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_member_class<br />h5tget_member_class_f</code>
</td><td> </td>
<td>
Returns datatype class of compound datatype member.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_member_name<br />h5tget_member_name_f</code>
</td><td> </td>
<td>
Retrieves the name of a compound or enumeration datatype member.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_member_index<br />h5tget_member_index_f</code>
</td><td> </td>
<td>
Retrieves the index of a compound or enumeration datatype member.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_member_offset<br />h5tget_member_offset_f</code>
</td><td> </td>
<td>
Retrieves the offset of a field of a compound datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_member_type<br />h5tget_member_type_f</code>
</td><td> </td>
<td>
Returns the datatype of the specified member.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tinsert<br />h5tinsert_f</code>
</td><td> </td>
<td>
Adds a new member to a compound datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tpack<br />h5tpack_f</code>
</td><td> </td>
<td>
Recursively removes padding from within a compound datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 6. Array datatypes
</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>C Function<br />Fortran Function</b>
</td><td> </td>
<td>
<b>Purpose</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tarray_create<br />h5tarray_create_f</code>
</td><td> </td>
<td>
Creates an array datatype object. The C function is a
macro: see <a href="../RM/APICompatMacros.html">“API
Compatibility Macros in HDF5.”</a>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_array_ndims<br />h5tget_array_ndims_f</code>
</td><td> </td>
<td>
Returns the rank of an array datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_array_dims<br />h5tget_array_dims_f</code>
</td><td> </td>
<td>
Returns sizes of array dimensions and dimension permutations.
The C function is a
macro: see <a href="../RM/APICompatMacros.html">“API
Compatibility Macros in HDF5.”</a>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 7. Variable-length datatypes
</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>C Function<br />Fortran Function</b>
</td><td> </td>
<td>
<b>Purpose</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tvlen_create<br />h5tvlen_create_f</code>
</td><td> </td>
<td>
Creates a new variable-length datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tis_variable_str<br />h5tis_variable_str_f</code>
</td><td> </td>
<td>
Determines whether datatype is a variable-length string.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 8. Opaque datatypes
</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>C Function<br />Fortran Function</b>
</td><td> </td>
<td>
<b>Purpose</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tset_tag<br />h5tset_tag_f</code>
</td><td> </td>
<td>
Tags an opaque datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Tget_tag<br />h5tget_tag_f</code>
</td><td> </td>
<td>
Gets the tag associated with an opaque datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 9. Conversions between datatype and text
</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>C Function<br />Fortran Function</b>
</td><td> </td>
<td>
<b>Purpose</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5LTtext_to_dtype<br />(none)</code>
</td><td> </td>
<td>
Creates a datatype from a text description.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5LTdtype_to_text<br />(none)</code>
</td><td> </td>
<td>
Generates a text description of a datatype.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 10. Datatype creation property list
functions (H5P)</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>C Function<br />Fortran Function</b>
</td><td> </td>
<td>
<b>Purpose</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Pset_char_encoding<br />h5pset_char_encoding_f</code>
</td><td> </td>
<td>
Sets the character encoding used to encode a string.
Use to set ASCII or UTF-8 character encoding for object names.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Pget_char_encoding<br />h5pget_char_encoding_f</code>
</td><td> </td>
<td>
Retrieves the character encoding used to create a string.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Function Listing 11. Datatype access property list
functions (H5P)</b></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td>
<b>C Function<br />Fortran Function</b>
</td><td> </td>
<td>
<b>Purpose</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Pset_type_conv_cb<br />(none)</code>
</td><td> </td>
<td>
Sets user-defined datatype conversion callback function.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>
<code>H5Pget_type_conv_cb<br />(none)</code>
</td><td> </td>
<td>
Gets user-defined datatype conversion callback function.
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
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<h3 class=pagebefore>6.4. The Programming Model</h3>
</a>
<h4>6.4.1. Introduction</h4>
<p>The HDF5 Library implements an object-oriented model of datatypes. HDF5
datatypes
are organized as a logical set of base types, or datatype classes. The HDF5
Library manages datatypes as objects. The HDF5 datatype API manipulates the
datatype objects through C function calls. The figure below shows the
abstract view
of the datatype object. The table below shows the methods (C functions)
that operate on datatype objects. New datatypes can be created from
scratch or copied from existing datatypes.</p>
<table width="550" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table align="center" border="1">
<tr>
<td valign="middle" align="center"><code>Datatype</code></td>
</tr>
<tr>
<td valign="middle" align="left">
<code> size:int?<br />
byteOrder:BOtype</code></td>
</tr>
<tr>
<td valign="middle" align="left">
<code> open(hid_t loc, char *, name):return hid_t<br />
copy(hid_t tid) return hid_t<br />
create(hid_class_t clss, size_t size)
return hid_t </code>
</td>
</tr>
</table>
</td></tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 5. The datatype object</b>
<hr color="green" size="3"/></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 8. General operations on datatype objects</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>API Function</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>hid_t H5Tcreate (H5T_class_t
<i>class</i>, size_t <i>size</i>)</code></td>
<td>Create a new datatype object of
datatype class <i>class</i>. The following datatype classes are
supported with this function:
<ul>
<li><code>H5T_COMPOUND</code></li>
<li><code>H5T_OPAQUE</code> </li>
<li><code>H5T_ENUM </code></li>
</ul>
Other datatypes are created with <code>H5Tcopy()</code>.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>hid_t H5Tcopy (hid_t <i>type</i>)
</code></td>
<td>Obtain a modifiable transient datatype
which is a copy of <i>type</i>. If <i>type</i> is a dataset
identifier then the type returned is a modifiable transient copy
of the datatype of the specified dataset. </td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>hid_t H5Topen (hid_t <i>location</i>, <br />
const char *<i>name</i>, H5P_DEFAULT)</code></td>
<td>Open a committed datatype. The
committed datatype returned by this function is read-only.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>htri_t H5Tequal (hid_t <i>type1</i>, <br />
hid_t <i>type2</i>)</code></td>
<td>Determines if two types are equal. </td>
</tr>
<!-- NEW PAGE -->
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tclose (hid_t <i>type</i>)
</code></td>
<td>Releases resources associated with a
datatype obtained from <code>H5Tcopy</code>, <code>H5Topen</code>, or
<code>H5Tcreate</code>. It is illegal to close an
immutable transient datatype (e.g., predefined types).</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tcommit (hid_t
<i>location</i>, const char *<i>name</i>, hid_t <i>type</i>,
H5P_DEFAULT, H5P_DEFAULT, <br />H5P_DEFAULT)</code></td>
<td>Commit a transient datatype (not immutable)
to a file to become a committed datatype. Committed datatypes can be shared.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>htri_t H5Tcommitted (hid_t
<i>type</i>)</code></td>
<td>Test whether the datatype is
transient or committed (named).</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tlock (hid_t
<i>type</i>)</code></td>
<td>Make a transient datatype immutable
(read-only and not closable). Predefined types are locked.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<p>In order to use a datatype, the object must be created
(<code>H5Tcreate</code>), or a reference obtained by cloning from an
existing type (<code>H5Tcopy</code>), or opened (<code>H5Topen</code>).
In addition, a reference to the datatype of a dataset or attribute
can be obtained with <code>H5Dget_type</code> or
<code>H5Aget_type</code>. For composite datatypes a reference
to the datatype for members or base types can be obtained
(<code>H5Tget_member_type</code>, <code>H5Tget_super</code>).
When the datatype object is no longer needed, the reference is
discarded with <code>H5Tclose</code>. </p>
<p>Two datatype objects can be tested to see if they are the same with
<code>H5Tequal</code>. This function returns true if the two datatype
references refer to the same datatype object. However, if two datatype
objects define equivalent datatypes (the same datatype class and
datatype properties), they will not be considered ‘equal’.</p>
<p>A datatype can be written to the file as a first class object
(<code>H5Tcommit</code>). This is a committed datatype and can be used
in the same way as any other datatype.</p>
<h4>6.4.2. Discovery of Datatype Properties</h4>
<p>Any HDF5 datatype object can be queried to discover all of its
datatype properties. For each datatype class, there are a set of
API functions to retrieve the datatype properties for this class. </p>
<h4>6.4.2.1. Properties of Atomic Datatypes</h4>
<p>Table 9 lists the functions to discover the properties of atomic
datatypes. Table 10 lists the queries relevant to specific numeric
types. Table 11 gives the properties for atomic string datatype, and
Table 12 gives the property of the opaque datatype.</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 9. Functions to discover properties of atomic datatypes</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Functions</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_class_t H5Tget_class (hid_t
<i>type</i>)</code></td>
<td>The datatype class: <code>H5T_INTEGER,
H5T_FLOAT, H5T_STRING, or H5T_BITFIELD, H5T_OPAQUE,
H5T_COMPOUND, H5T_REFERENCE, H5T_ENUM, H5T_VLEN, H5T_ARRAY</code></td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>size_t H5Tget_size
(hid_t <i>type</i>)</code></td>
<td>The total size of the element in bytes, including padding
which may appear on either side of the actual value.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_order_t H5Tget_order
(hid_t <i>type</i>)</code></td>
<td>The byte order describes how the bytes of the datatype are
laid out in memory. If the lowest memory address contains the
least significant byte of the datum then it is
said to be <i>little-endian</i> or <code>H5T_ORDER_LE</code>. If
the bytes are in the opposite order then they are said to be
<i>big-endian</i> or <code>H5T_ORDER_BE.</code></td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>size_t H5Tget_precision
(hid_t <i>type</i>)</code></td>
<td>The <code>precision</code> property identifies the number
of significant bits of a datatype and the
<code>offset</code> property (defined below) identifies its location.
Some datatypes occupy more bytes than what is needed to store the
value. For instance, a <code>short</code> on a Cray is 32 significant
bits in an eight-byte field.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>int H5Tget_offset (hid_t <i>type</i>)</code></td>
<td>The <code>offset</code> property defines the bit location
of the least significant bit of a bit
field whose length is <code>precision</code>.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tget_pad
(hid_t <i>type</i>, H5T_pad_t <i>*lsb</i>, H5T_pad_t
<i>*msb</i>)</code></td>
<td>Padding is the bits of a data element
which are not significant as defined by the <code>precision</code>
and <code>offset</code> properties. Padding in the low-numbered
bits is <i>lsb</i> padding and padding in the high-numbered
bits is <i>msb</i> padding. Padding bits can be set to zero
(<code>H5T_PAD_ZERO</code>) or one (<code>H5T_PAD_ONE</code>).</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 10. Functions to discover properties of atomic
numeric datatypes</b> </td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Functions</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_sign_t H5Tget_sign
(hid_t <i>type</i>)</code></td>
<td><b>(INTEGER)</b> Integer data can be signed two’s
complement (<code>H5T_SGN_2</code>)
or unsigned (<code>H5T_SGN_NONE</code>).</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tget_fields
(hid_t <i>type</i>, size_t *<i>spos</i>, size_t *<i>epos</i>,
size_t *<i>esize</i>, size_t *<i>mpos</i>,
size_t *<i>msize</i>)</code> </td>
<td><b>(FLOAT)</b> A floating-point
data element has bit fields which are the exponent and mantissa
as well as a mantissa sign bit. These properties define the
location (bit position of least significant bit of the field)
and size (in bits) of each field. The sign bit is always of
length one and none of the fields are allowed to overlap.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>size_t H5Tget_ebias
(hid_t <i>type</i>)</code></td>
<td><b>(FLOAT)</b> The exponent is stored as a non-negative
value which is <code>ebias</code> larger than the true exponent. </td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_norm_t H5Tget_norm
(hid_t <i>type</i>)</code></td>
<td><b>(FLOAT)</b> This property describes the normalization
method of the mantissa.
<ul>
<li><code>H5T_NORM_MSBSET</code>: the mantissa is shifted left
(if non-zero) until the first bit after the radix point is
set and the exponent is adjusted accordingly. All bits of
the mantissa after the radix point are stored. </li>
<li><code>H5T_NORM_IMPLIED</code>: the mantissa is shifted left \
(if non-zero) until the first bit after the radix point is set
and the exponent is adjusted accordingly. The first bit after
the radix point is not stored since it’s always set. </li>
<li><code>H5T_NORM_NONE</code>: the fractional part of the
mantissa is stored without normalizing it. </li>
</ul></td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_pad_t H5Tget_inpad
(hid_t <i>type</i>)</code></td>
<td><b>(FLOAT)</b> If any internal bits (that is, bits between
the sign bit, the mantissa field, and the exponent field but
within the precision field) are unused, then they will be
filled according to the value of this property. The padding can
be: <code>H5T_PAD_NONE</code>, <code>H5T_PAD_ZERO</code>
or <code>H5T_PAD_ONE</code>.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 11. Functions to discover properties of atomic
string datatypes</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Functions</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_cset_t H5Tget_cset
(hid_t <em>type</em>)</code></td>
<td>Two character sets are currently
supported: ASCII (<code>H5T_CSET_ASCII</code>) and UTF-8
(<code>H5T_CSET_UTF8</code>).</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_str_t H5Tget_strpad
(hid_t <em>type</em>)</code></td>
<td>The string datatype has a fixed
length, but the string may be shorter than the length. This
property defines the storage mechanism for the left over bytes.
The options are: <code>H5T_STR_NULLTERM</code>,
<code>H5T_STR_NULLPAD</code>, or <code>H5T_STR_SPACEPAD</code>.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 12. Functions to discover properties of atomic opaque
datatypes</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Functions</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>char *H5Tget_tag(hid_t type_id)</code></td>
<td>A user-defined string.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<h4><em>6.4.2.2. Properties of Composite Datatypes</em></h4>
<p>The composite datatype classes can also be analyzed to discover their
datatype properties and the datatypes that are members or base types
of the composite datatype. The member or base type can, in turn, be
analyzed. The table below lists the functions that can access the
datatype properties of the different composite datatypes.</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 13. Functions to discover properties of composite datatypes</b>
</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Functions</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>int H5Tget_nmembers(hid_t type_id)</code></td>
<td><b>(COMPOUND)</b>The number of fields in the compound
datatype.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>H5T_class_t H5Tget_member_class<br />
(hid_t cdtype_id, unsigned member_no)</code></td>
<td><b>(COMPOUND)</b> The datatype class of compound datatype
member <code>member_no</code>.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>char * H5Tget_member_name
(hid_t type_id, unsigned field_idx)</code></td>
<td><b>(COMPOUND)</b> The name of field <code>field_idx</code>
of a compound datatype.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>size_t H5Tget_member_offset
(hid_t type_id, unsigned memb_no)</code></td>
<td><b>(COMPOUND)</b> The byte offset
of the beginning of a field within a compound datatype.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>hid_t H5Tget_member_type
(hid_t type_id, unsigned field_idx)</code></td>
<td><b>(COMPOUND)</b> The datatype of the specified member.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>int H5Tget_array_ndims
(hid_t adtype_id)</code></td>
<td><b>(ARRAY)</b> The number of dimensions (rank) of the array
datatype object.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>int H5Tget_array_dims
(hid_t adtype_id, hsize_t *dims[])</code></td>
<td><b>(ARRAY)</b> The sizes of the dimensions and the dimension
permutations of the array datatype object.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>hid_t H5Tget_super(hid_t type)
</code></td>
<td><b>(ARRAY, VL, ENUM)</b>The base datatype from which the
datatype type is derived.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tenum_nameof(hid_t type <br />
void *value, char *name, size_t size)</code></td>
<td><b>(ENUM)</b> The symbol name
that corresponds to the specified value of the enumeration datatype</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tenum_valueof(hid_t type <br />
char *name, void *value)</code></td>
<td><b>(ENUM)</b> The value that corresponds to the specified
name of the enumeration datatype</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tget_member_value<br />
(hid_t type unsigned memb_no, <br />void *value)</code></td>
<td><b>(ENUM)</b> The value of the
enumeration datatype member <code>memb_no</code></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<!-- NEW PAGE -->
<h4>6.4.3. Definition of Datatypes</h4>
<p>The HDF5 Library enables user programs to create and modify datatypes. The
essential steps are:
<ol>
<li>a) Create a new datatype object of a specific composite datatype class,
or <br />
b) Copy an existing atomic datatype object</li>
<li>Set properties of the datatype object</li>
<li>Use the datatype object</li>
<li>Close the datatype object</li>
</ol>
<p>To create a user-defined atomic datatype, the procedure is to clone
a predefined datatype of the appropriate datatype class
(<code>H5Tcopy</code>), and then set the datatype properties appropriate
to the datatype class. The table below shows how to create a datatype
to describe a 1024-bit unsigned integer.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t new_type = H5Tcopy (H5T_NATIVE_INT);
H5Tset_precision(new_type, 1024);
H5Tset_sign(new_type, H5T_SGN_NONE);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 5. Create a new datatype</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>Composite datatypes are created with a specific API call for each datatype
class. The table below shows the creation method for each datatype class. A
newly created
datatype cannot be used until the datatype properties are set. For example,
a newly created compound datatype has no members and cannot be used.</p>
<table width="400" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 14. Functions to create each datatype class</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Datatype Class</b></td>
<td width="50%"><b>Function to Create</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>COMPOUND</td>
<td><code>H5Tcreate</code></td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>OPAQUE</td>
<td><code>H5Tcreate</code></td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>ENUM</td>
<td><code>H5Tenum_create</code></td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>ARRAY</td>
<td><code>H5Tarray_create</code></td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>VL</td>
<td><code>H5Tvlen_create</code></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<p>Once the datatype is created and the datatype properties set, the datatype
object can be used. </p>
<p>Predefined datatypes are defined by the library during initialization
using the same mechanisms as described here. Each predefined datatype is
locked (<code>H5Tlock</code>), so that it cannot be changed or destroyed.
User-defined datatypes may also be locked using <code>H5Tlock</code>. </p>
<!-- NEW PAGE -->
<h4><em>6.4.3.1. User-defined Atomic Datatypes</em></h4>
<p>Table 15 summarizes the API methods that set properties of atomic
types. Table 16 shows properties specific to numeric types, Table 17
shows properties specific to the string datatype class. Note that
offset, pad, etc. do not apply to strings. Table 18 shows the specific
property of the OPAQUE datatype class.</p>
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 15. API methods that set properties of atomic datatypes</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Functions</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_size (hid_t <i>type</i>,
<br />size_t <i>size</i>)</code></td>
<td>Set the total size of the element
in bytes. This includes padding which may appear on either side of the
actual value. If this property is reset to a smaller value which
would cause the significant part of the data to extend beyond the
edge of the datatype, then the offset property is decremented a
bit at a time. If the offset reaches zero and the significant
part of the data still extends beyond the edge of the datatype
then the precision property is decremented a bit at a time.
Decreasing the size of a datatype may fail if the
<code>H5T_FLOAT</code> bit fields would extend beyond the significant
part of the type. </td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_order
(hid_t <i>type</i>, H5T_order_t <i>order</i>)</code></td>
<td>Set the byte order to little-endian
(<code>H5T_ORDER_LE</code>) or big-endian (<code>H5T_ORDER_BE</code>).</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_precision
(hid_t <i>type</i>, size_t <i>precision</i>)</code></td>
<td>Set the number of significant bits
of a datatype. The <code>offset</code> property (defined below)
identifies its location. The size property defined above represents
the entire size (in bytes) of the datatype. If the precision is
decreased then padding bits are inserted on the MSB side of the
significant bits (this will fail for <code>H5T_FLOAT</code> types
if it results in the sign, mantissa, or exponent bit field extending
beyond the edge of the significant bit field). On the other hand,
if the precision is increased so that it “hangs over”
the edge of the total size then the offset property is decremented
a bit at a time. If the offset reaches zero and the significant
bits still hang over the edge, then the total size is increased
a byte at a time. </td>
</tr>
<!-- NEW PAGE -->
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_offset
(hid_t <i>type</i>, size_t <i>offset</i>)</code></td>
<td>Set the bit location of the least
significant bit of a bit field whose length is <code>precision</code>.
The bits of the entire data are numbered beginning at zero at the
least significant bit of the least significant byte (the byte at
the lowest memory address for a little-endian type or the byte
at the highest address for a big-endian type). The offset property
defines the bit location of the least significant bit of a bit field
whose length is precision. If the offset is increased so the
significant bits “hang over” the edge of the datum, then
the size property is automatically incremented.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_pad (hid_t
<i>type</i>, H5T_pad_t <i>lsb</i>, H5T_pad_t <i>msb</i>)</code></td>
<td>Set the padding to zeros
(<code>H5T_PAD_ZERO</code>) or ones (<code>H5T_PAD_ONE</code>). Padding
is the bits of a data element which are not significant as defined
by the <code>precision</code> and <code>offset</code> properties.
Padding in the low-numbered bits is <code><i>lsb</i></code>
padding and padding in the high-numbered bits is
<code><i>msb</i></code> padding. </td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 16. API methods that set properties of numeric datatypes</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Functions</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_sign
(hid_t <i>type</i>, H5T_sign_t <i>sign</i>)</code></td>
<td><b>(INTEGER)</b> Integer
data can be signed two’s complement (<code>H5T_SGN_2</code>)
or unsigned (<code>H5T_SGN_NONE</code>).</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_fields
(hid_t <i>type</i>, size_t <i>spos</i>, size_t <i>epos</i>,
size_t <i>esize</i>, size_t <i>mpos</i>, size_t <i>msize</i>)
</code></td>
<td><b>(FLOAT)</b> Set the
properties define the location (bit position of least significant
bit of the field) and size (in bits) of each field. The sign bit
is always of length one and none of the fields are allowed to overlap.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_ebias (hid_t <i>type</i>,
size_t <i>ebias</i>)</code></td>
<td><b>(FLOAT)</b> The exponent
is stored as a non-negative value which is <code>ebias</code> larger
than the true exponent.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_norm
(hid_t <i>type</i>, H5T_norm_t <i>norm</i>)</code></td>
<td><b>(FLOAT)</b> This
property describes the normalization method of the mantissa.
<ul>
<li><code>H5T_NORM_MSBSET</code>: the mantissa is shifted left
(if non-zero) until the first bit after the radix point is set and
the exponent is adjusted accordingly. All bits of the mantissa
after the radix point are stored. </li>
<li><code>H5T_NORM_IMPLIED</code>: the mantissa is shifted left
(if non-zero) until the first bit after the radix point is set and
the exponent is adjusted accordingly. The first bit after the
radix point is not stored since it is always set. </li>
<li><code>H5T_NORM_NONE</code>: the fractional part of the
mantissa is stored without normalizing it. </li></ul></td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_inpad
(hid_t <i>type</i>, H5T_pad_t <i>inpad</i>)</code></td>
<td><b>(FLOAT)</b> If any
internal bits (that is, bits between the sign bit, the mantissa field,
and the exponent field but within the precision field) are unused,
then they will be filled according to the value of this property.
The padding can be: <code>H5T_PAD_NONE</code>, <code>H5T_PAD_ZERO</code>
or <code>H5T_PAD_ONE</code>.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 17. API methods that set properties of string datatypes</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Functions</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_size (hid_t <i>type</i>,
<br />size_t <i>size</i>)</code></td>
<td>Set the length of the string, in bytes.
The precision is automatically set to 8*<code>size</code>.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_precision
(hid_t <i>type</i>, size_t <i>precision</i>)</code></td>
<td>The precision must be a multiple of 8.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_cset
(hid_t type_id, H5T_cset_t cset )</code></td>
<td>Two character sets are currently
supported: ASCII (<code>H5T_CSET_ASCII</code>) and UTF-8
(<code>H5T_CSET_UTF8</code>).</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_strpad
(hid_t type_id, H5T_str_t strpad )</code></td>
<td>The string datatype has a fixed
length, but the string may be shorter than the length. This property
defines the storage mechanism for the left over bytes. The method
used to store character strings differs with the programming language:
<ul>
<li>C usually null terminates strings </li>
<li>Fortran left-justifies and space-pads strings</li>
</ul>
<p>Valid string padding values, as passed in the parameter strpad,
are as follows: </p>
<dl>
<dt><code>H5T_STR_NULLTERM</code> (0)
<dd>Null terminate (as C does)
<dt><code>H5T_STR_NULLPAD</code> (1)
<dd>Pad with zeros
<dt><code>H5T_STR_SPACEPAD</code> (2)
<dd>Pad with spaces (as FORTRAN does).
</dl></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 18. API methods that set properties of opaque datatypes</b></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Functions</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tset_tag (hid_t type_id
<br />const char *tag )</code></td>
<td>Tags the opaque datatype type_id
with an ASCII identifier tag.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<!-- NEW PAGE -->
<h4>Examples</h4>
<p>The example below shows how to create a 128-bit little-endian signed
integer type. Increasing the precision of a type automatically increases
the total size. Note that the proper procedure is to begin from a type
of the intended datatype class which in this case is a
<code>NATIVE INT</code>.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t new_type = H5Tcopy (H5T_NATIVE_INT);
H5Tset_precision (new_type, 128);
H5Tset_order (new_type, H5T_ORDER_LE);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 6. Create a new 128-bit little-endian signed integer
datatype</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The figure below shows the storage layout as the type is defined. The
<code>H5Tcopy</code> creates a datatype that is the same as
<code>H5T_NATIVE_INT</code>. In this example, suppose this is a 32-bit
big-endian number (Figure a). The precision is set to 128 bits,
which automatically extends the size to 8 bytes (Figure b). Finally,
the byte order is set to little-endian (Figure c).</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table align="center" border="0" width="100%">
<tr><td>
<table border="1" align="left">
<tr>
<td valign="middle" align="center"><code>Byte 0</code></td>
<td valign="middle" align="center"><code>Byte 1</code></td>
<td valign="middle" align="center"><code>Byte 2</code></td>
<td valign="middle" align="center"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
<td valign="middle" align="center"><code>45678901</code></td>
</tr>
</table>
</td></tr>
<tr><td>
<table border="0" align="left">
<tr>
<td>a) The <code>H5T_NATIVE_INT</code> datatype<br /> </td></tr>
</table>
</td></tr>
<tr><td>
<table border="1" align="left">
<tr>
<td valign="middle" align="center"><code>Byte 0</code></td>
<td valign="middle" align="center"><code>Byte 1</code></td>
<td valign="middle" align="center"><code>Byte 2</code></td>
<td valign="middle" align="center"><code>Byte 3</code></td>
<td valign="middle" align="center"><code>Byte 4</code></td>
<td valign="middle" align="center"><code>Byte 5</code></td>
<td valign="middle" align="center"><code>Byte 6</code></td>
<td valign="middle" align="center"><code>Byte 7</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
<td valign="middle" align="center"><code>45678901</code></td>
<td valign="middle" align="center"><code>23456789</code></td>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
</tr>
</table>
</td></tr>
<tr><td>
<table border="0" align="left">
<tr>
<td>b) Precision is extended to 128-bits, and the size is
automatically adjusted.<br /> </td></tr>
</table>
</td></tr>
<tr><td>
<table border="1" align="left">
<tr>
<td valign="middle" align="center"><code>Byte 0</code></td>
<td valign="middle" align="center"><code>Byte 1</code></td>
<td valign="middle" align="center"><code>Byte 2</code></td>
<td valign="middle" align="center"><code>Byte 3</code></td>
<td valign="middle" align="center"><code>Byte 4</code></td>
<td valign="middle" align="center"><code>Byte 5</code></td>
<td valign="middle" align="center"><code>Byte 6</code></td>
<td valign="middle" align="center"><code>Byte 7</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
<td valign="middle" align="center"><code>45678901</code></td>
<td valign="middle" align="center"><code>23456789</code></td>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
</tr>
</table>
</td></tr>
<tr><td>
<table border="0" align="left">
<tr><td>c) The byte order is switched.</td></tr>
</table>
</td></tr>
</table>
</td></tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 6. The storage layout for a new 128-bit little-endian
signed integer datatype</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The significant bits of a data element can be offset from the beginning of
the memory for that element by an amount of padding. The <code>offset</code>
property specifies the number of bits of padding that appear to the
“right of” the value. The table and figure below show how
a 32-bit unsigned integer with 16-bits of precision having the value
<code>0x1122</code> will be laid out in memory.</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="5" align="left" valign="bottom">
<b>Table 19. Memory Layout for a 32-bit unsigned integer</b></td>
</tr>
<tr><td colspan="5"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td><b>Byte Position</b></td>
<td><b>Big-Endian <br />Offset=0</b></td>
<td><b>Big-Endian <br />Offset=16</b></td>
<td><b>Little-Endian <br />Offset=0</b></td>
<td><b>Little-Endian <br />Offset=16</b></td>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>0:</td>
<td>[pad]</td>
<td>[0x11]</td>
<td>[0x22]</td>
<td>[pad]</td>
</tr>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>1:</td>
<td>[pad]</td>
<td>[0x22]</td>
<td>[0x11]</td>
<td>[pad]</td>
</tr>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>2:</td>
<td>[0x11]</td>
<td>[pad]</td>
<td>[pad]</td>
<td>[0x22]</td>
</tr>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>3:</td>
<td>[0x22]</td>
<td>[pad]</td>
<td>[pad]</td>
<td>[0x11]</td>
</tr>
<tr><td colspan="5"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<table width="400" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table align="center" border="0" width="100%">
<tr>
<td valign="middle" align="center">Big-Endian: Offset = 0</td>
</tr>
<tr><td>
<table border="1" align="center">
<tr>
<td valign="middle" align="center"><code>Byte 0</code></td>
<td valign="middle" align="center"><code>Byte 1</code></td>
<td valign="middle" align="center"><code>Byte 2</code></td>
<td valign="middle" align="center"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
<td valign="middle" align="center"><code>45678901</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><em>PPPPPPPP</em></code></td>
<td valign="middle" align="center"><code><em>PPPPPPPP</em></code></td>
<td valign="middle" align="center"><code>00010001</code></td>
<td valign="middle" align="center"><code>00100010</code></td>
</tr>
</table>
</td></tr>
<tr>
<td valign="middle" align="center"> <br />Big-Endian: Offset = 16</td>
</tr>
<tr>
<td>
<table border="1" align="center">
<tr>
<td valign="middle" align="center"><code>Byte 0</code></td>
<td valign="middle" align="center"><code>Byte 1</code></td>
<td valign="middle" align="center"><code>Byte 2</code></td>
<td valign="middle" align="center"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
<td valign="middle" align="center"><code>45678901</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>00010001</code></td>
<td valign="middle" align="center"><code>00100010</code></td>
<td valign="middle" align="center"><code><em>PPPPPPPP</em></code></td>
<td valign="middle" align="center"><code><em>PPPPPPPP</em></code></td>
</tr>
</table>
</td></tr>
<tr>
<td valign="middle" align="center"> <br />Little-Endian:
Offset = 0</td>
</tr>
<tr>
<td>
<table border="1" align="center">
<tr>
<td valign="middle" align="center"><code>Byte 0</code></td>
<td valign="middle" align="center"><code>Byte 1</code></td>
<td valign="middle" align="center"><code>Byte 2</code></td>
<td valign="middle" align="center"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
<td valign="middle" align="center"><code>45678901</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>00010001</code></td>
<td valign="middle" align="center"><code>00100010</code></td>
<td valign="middle" align="center"><code><em>PPPPPPPP</em></code></td>
<td valign="middle" align="center"><code><em>PPPPPPPP</em></code></td>
</tr>
</table>
</td></tr>
<tr>
<td valign="middle" align="center"> <br />Little-Endian:
Offset = 16</td>
</tr>
<tr>
<td>
<table border="1" align="center">
<tr>
<td valign="middle" align="center"><code>Byte 0</code></td>
<td valign="middle" align="center"><code>Byte 1</code></td>
<td valign="middle" align="center"><code>Byte 2</code></td>
<td valign="middle" align="center"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
<td valign="middle" align="center"><code>45678901</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><em>PPPPPPPP</em></code></td>
<td valign="middle" align="center"><code><em>PPPPPPPP</em></code></td>
<td valign="middle" align="center"><code>00010001</code></td>
<td valign="middle" align="center"><code>00100010</code></td>
</tr>
</table>
</td></tr>
</table>
</td></tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 7. Memory Layout for a 32-bit unsigned integer</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>If the offset is incremented then the total size is incremented also
if necessary to prevent significant bits of the value from hanging over
the edge of the datatype. </p>
<p>The bits of the entire data are numbered beginning at zero at the
least significant bit of the least significant byte (the byte at the
lowest memory address for a little-endian type or the byte at the
highest address for a big-endian type). The <code>offset</code>
property defines the bit location of the least signficant bit of a
bit field whose length is <code>precision</code>. If the offset is
increased so the significant bits “hang over” the edge
of the datum, then the <code>size</code> property is automatically
incremented. </p>
<p>To illustrate the properties of the integer datatype class, the example
below shows how to create a user-defined datatype that describes a
24-bit signed integer that starts on the third bit of a 32-bit word.
The datatype is specialized from a 32-bit integer, the <em>precision</em>
is set to 24 bits, and the <em>offset</em> is set to 3.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t dt;
dt = H5Tcopy(H5T_SDT_I32LE);
H5Tset_precision(dt, 24);
H5Tset_offset(dt,3);
H5Tset_pad(dt, H5T_PAD_ZERO, H5T_PAD_ONE);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 7. A user-defined datatype with a 24-bit signed integer</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The figure below shows the storage layout for a data element. Note that
the unused bits in the offset will be set to zero and the unused bits at
the end will be
set to one, as specified in the <code>H5Tset_pad</code> call.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<br />
<table border="1" align="center" width="67%">
<tr>
<td valign="middle" align="center"><code>Byte 0</code></td>
<td valign="middle" align="center"><code>Byte 1</code></td>
<td valign="middle" align="center"><code>Byte 2</code></td>
<td valign="middle" align="center"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
<td valign="middle" align="center"><code>45678901</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong><em>ooo</em></strong>00000</code></td>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00s<strong><em>ppppp</em></strong></code></td>
</tr>
<tr>
<td valign="middle" align="center" colspan="4">
<img src="Images/Dtypes_fig14.JPG">
</td>
</tr>
</table>
<br />
<tr><td>
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 8. A user-defined integer datatype a range of -1,048,583
to 1,048,584</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>To illustrate a user-defined floating point number, the example below
shows how to create a 24-bit floating point number that starts 5 bits
into a 4 byte word. The floating point number is defined to have a
mantissa of 19 bits (bits 5-23), an exponent of 3 bits (25-27), and
the sign bit is bit 28. (Note that this is an illustration of what
can be done and is not necessarily a floating point format that a
user would require.)</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t dt;
dt = H5Tcopy(H5T_IEEE_F32LE);
H5Tset_precision(dt, 24);
H5Tset_fields (dt, 28, 25, 3, 5, 19);
H5Tset_pad(dt, H5T_PAD_ZERO, H5T_PAD_ONE);
H5Tset_inpad(dt, H5T_PAD_ZERO);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 8. A user-defined 24-bit floating point datatype</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="500" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table border="1" align="center" width="67%">
<tr>
<td valign="middle" align="center"><code>Byte 0</code></td>
<td valign="middle" align="center"><code>Byte 1</code></td>
<td valign="middle" align="center"><code>Byte 2</code></td>
<td valign="middle" align="center"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>01234567</code></td>
<td valign="middle" align="center"><code>89012345</code></td>
<td valign="middle" align="center"><code>67890123</code></td>
<td valign="middle" align="center"><code>45678901</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong><em>ooooo</em>
</strong>mmm</code></td>
<td valign="middle" align="center"><code>mmmmmmmm</code></td>
<td valign="middle" align="center"><code>mmmmmmmm</code></td>
<td valign="middle" align="center"><code><strong>i</strong>eees<strong>
<em>ppp</em></strong></code></td>
</tr>
<tr>
<td valign="middle" align="center" colspan="4">
<img src="Images/Dtypes_fig16.JPG">
</td>
</tr>
</table>
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 9. A user-defined floating point datatype</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The figure above shows the storage layout of a data element for this
datatype. Note that there is an unused bit (24) between the mantissa and
the exponent. This bit is filled with the <em>inpad</em> value which
in this case is 0. </p>
<p>The sign bit is always of length one and none of the fields are allowed
to overlap. When expanding a floating-point type one should set the
precision first; when decreasing the size one should set the field
positions and sizes first. </p>
<h4>6.4.3.2. Composite Datatypes</h4>
<p>All composite datatypes must be user-defined;
there are no predefined composite datatypes. </p>
<h4>6.4.3.2.1. Compound Datatypes</h4>
<p>The subsections below describe how to create a compound datatype
and how to write and read data of a compound datatype.
<h4>6.4.3.2.1.1. Defining Compound Datatypes</h4>
<p>Compound datatypes are conceptually similar to a C struct or
Fortran derived types. The compound datatype defines a contiguous
sequence of bytes, which are formatted using one up to 2^16 datatypes
(members). A compound datatype may have any number of members, in
any order, and the members may have any datatype, including compound.
Thus, complex nested compound datatypes can be created. The total
size of the compound datatype is greater than or equal to the sum
of the size of its members, up to a maximum of 2^32 bytes. HDF5 does
not support datatypes with distinguished records or the equivalent
of C unions or Fortran EQUIVALENCE statements.</p>
<p>Usually a C struct or Fortran derived type 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 HDF5 C library provides a macro
<code>HOFFSET (s,m)</code> to calculate the member’s offset. The HDF5
Fortran applications have to calculate offsets by using sizes of members
datatypes and by taking in consideration the order of members in the
Fortran derived type.</p>
<dl>
<dt><code>HOFFSET(s,m)</code>
<dd>This macro computes the offset of member <em>m</em> within a struct
<em>s</em></dd>
<dt><code>offsetof(s,m)</code>
<dd>This macro defined in <code>stddef.h</code> does exactly the same
thing as the <code>HOFFSET()</code> macro.</dd>
</dl>
<p><em>Note for Fortran users</em>: Offsets of Fortran structure members
correspond to the offsets within a packed datatype (see explanation below)
stored in an HDF5 file.</p>
<p>Each member of a compound datatype must have a descriptive name which
is the key used to uniquely identify the member within the compound
datatype. A member name in an HDF5 datatype does not necessarily have
to be the same as the name of the member in the C struct or Fortran
derived type, although this is often the case. Nor does one need to
define all members of the C struct or Fortran derived type in the HDF5
compound datatype (or vice versa).</p>
<p>Unlike atomic datatypes which are derived from other atomic datatypes,
compound datatypes are created from scratch. First, one creates an empty
compound datatype and specifies its total size. Then members are added to
the compound datatype in any order. Each member type is inserted at a
designated offset. Each member has a name which is the key used to uniquely
identify the member within the compound datatype.</p>
<p>The example below shows a way of creating an HDF5 C compound datatype to
describe a complex number. This is a structure with two components,
“real” and “imaginary”, and each component
is a double. An equivalent C struct whose type is defined by the
<code>complex_t</code> struct is shown.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct {
double re; /*real part*/
double im; /*imaginary part*/
} complex_t;
hid_t complex_id = H5Tcreate (H5T_COMPOUND, sizeof (complex_t));
H5Tinsert (complex_id, “real”, HOFFSET(complex_t,re),
H5T_NATIVE_DOUBLE);
H5Tinsert (complex_id, “imaginary”, HOFFSET(complex_t,im),
H5T_NATIVE_DOUBLE);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 9. A compound datatype for complex numbers in C</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The example below shows a way of creating an HDF5 Fortran compound
datatype to describe a complex number. This is a Fortran derived type
with two components, “real” and “imaginary”,
and each component is DOUBLE PRECISION. An equivalent Fortran TYPE
whose type is defined by the TYPE <code>complex_t</code> is shown.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
TYPE complex_t
DOUBLE PRECISION re ! real part
DOUBLE PRECISION im; ! imaginary part
END TYPE complex_t
CALL h5tget_size_f(H5T_NATIVE_DOUBLE, re_size, error)
CALL h5tget_size_f(H5T_NATIVE_DOUBLE, im_size, error)
complex_t_size = re_size + im_size
CALL h5tcreate_f(H5T_COMPOUND_F, complex_t_size, type_id)
offset = 0
CALL h5tinsert_f(type_id, “real”, offset, H5T_NATIVE_DOUBLE, error)
offset = offset + re_size
CALL h5tinsert_f(type_id, “imaginary”, offset, H5T_NATIVE_DOUBLE, error)</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 10. A compound datatype for complex numbers in Fortran</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p><em>Important Note</em>: The compound datatype is created with a size
sufficient to hold all its members. In the C example above, the size of
the C struct and the <code>HOFFSET</code> macro are used as a convenient
mechanism to determine the appropriate size and offset. Alternatively, the
size and offset could be manually determined: the size can be set to
16 with “real” at offset 0 and “imaginary” at
offset 8. However, different platforms and compilers have different
sizes for “double” and may have alignment restrictions
which require additional padding within the structure. It is much
more portable to use the <code>HOFFSET</code> macro which assures
that the values will be correct for any platform.</p>
<p>The figure below shows how the compound datatype would be laid out
assuming that <code>NATIVE_DOUBLE</code> are 64-bit numbers and that
there are no alignment requirements. The total size of the compound
datatype will be 16 bytes, the “real” component will
start at byte 0, and “imaginary” will start at byte 8.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table border="1" align="center" width="550">
<tr>
<td valign="top" align="right" rowspan="4" width="150">
<img src="Images/Dtypes_fig18_a.jpg">
</td>
<td valign="middle" align="center" width="100"><code>Byte 0</code></td>
<td valign="middle" align="center" width="100"><code>Byte 1</code></td>
<td valign="middle" align="center" width="100"><code>Byte 2</code></td>
<td valign="middle" align="center" width="100"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 4</code></td>
<td valign="middle" align="center"><code>Byte 5</code></td>
<td valign="middle" align="center"><code>Byte 6</code></td>
<td valign="middle" align="center"><code>Byte 7</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
</tr>
<tr>
<td valign="top" align="right" rowspan="4" width="150">
<img src="Images/Dtypes_fig18_b.jpg">
</td>
<td valign="middle" align="center"><code>Byte 8</code></td>
<td valign="middle" align="center"><code>Byte 9</code></td>
<td valign="middle" align="center"><code>Byte 10</code></td>
<td valign="middle" align="center"><code>Byte 11</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 12</code></td>
<td valign="middle" align="center"><code>Byte 13</code></td>
<td valign="middle" align="center"><code>Byte 14</code></td>
<td valign="middle" align="center"><code>Byte 15</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
</tr>
</table>
<table align="center" border="0" width="550">
<tr>
<td valign="top" align="right" width="150"> </td>
<td valign="top" align="left" colspan="4">Total size of
compound datatype is 16 bytes</td>
</tr>
</table>
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 10. Layout of a compound datatype</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The members of a compound datatype may be any HDF5 datatype
including the compound, array, and variable-length (VL) types. The
figure and example below show the memory layout and code
which creates a compound datatype composed of two complex
values, and each complex value is also a compound datatype as in the
figure above.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table border="1" align="center" width="550">
<tr>
<td valign="top" align="right" rowspan="4" width="150">
<img src="Images/Dtypes_fig19_a.jpg">
</td>
<td valign="middle" align="center" width="100"><code>Byte 0</code></td>
<td valign="middle" align="center" width="100"><code>Byte 1</code></td>
<td valign="middle" align="center" width="100"><code>Byte 2</code></td>
<td valign="middle" align="center" width="100"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 4</code></td>
<td valign="middle" align="center"><code>Byte 5</code></td>
<td valign="middle" align="center"><code>Byte 6</code></td>
<td valign="middle" align="center"><code>Byte 7</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
</tr>
<tr>
<td valign="top" align="right" rowspan="4">
<img src="Images/Dtypes_fig19_b.jpg" align="middle">
</td>
<td valign="middle" align="center"><code>Byte 8</code></td>
<td valign="middle" align="center"><code>Byte 9</code></td>
<td valign="middle" align="center"><code>Byte 10</code></td>
<td valign="middle" align="center"><code>Byte 11</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 12</code></td>
<td valign="middle" align="center"><code>Byte 13</code></td>
<td valign="middle" align="center"><code>Byte 14</code></td>
<td valign="middle" align="center"><code>Byte 15</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
</tr>
<tr>
<td valign="top" align="right" rowspan="4">
<img src="Images/Dtypes_fig19_c.jpg"></td>
<td valign="middle" align="center" width="100"><code>Byte 16</code></td>
<td valign="middle" align="center" width="100"><code>Byte 17</code></td>
<td valign="middle" align="center" width="100"><code>Byte 18</code></td>
<td valign="middle" align="center" width="100"><code>Byte 19</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 20</code></td>
<td valign="middle" align="center"><code>Byte 21</code></td>
<td valign="middle" align="center"><code>Byte 22</code></td>
<td valign="middle" align="center"><code>Byte 23</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
<td valign="middle" align="center"><code><strong>rrrrrrrr</strong></code></td>
</tr>
<tr>
<td valign="top" align="right" rowspan="4">
<img src="Images/Dtypes_fig19_d.jpg"></td>
<td valign="middle" align="center"><code>Byte 24</code></td>
<td valign="middle" align="center"><code>Byte 25</code></td>
<td valign="middle" align="center"><code>Byte 26</code></td>
<td valign="middle" align="center"><code>Byte 27</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 28</code></td>
<td valign="middle" align="center"><code>Byte 29</code></td>
<td valign="middle" align="center"><code>Byte 30</code></td>
<td valign="middle" align="center"><code>Byte 31</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
<td valign="middle" align="center"><code><strong>iiiiiiii</strong></code></td>
</tr>
</table>
<table align="center" width="550">
<tr>
<td width="150"> </td>
<td>Total size of compound datatype is 32 bytes.</td>
</tr>
</table>
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 11. Layout of a compound datatype nested within a compound
datatype</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct {
complex_t x;
complex_t y;
} surf_t;
hid_t complex_id, surf_id; /*hdf5 datatypes*/
complex_id = H5Tcreate (H5T_COMPOUND, sizeof(complex_t));
H5Tinsert (complex_id, “re”, HOFFSET(complex_t,re),
H5T_NATIVE_DOUBLE);
H5Tinsert (complex_id, “im”, HOFFSET(complex_t,im),
H5T_NATIVE_DOUBLE);
surf_id = H5Tcreate (H5T_COMPOUND, sizeof(surf_t));
H5Tinsert (surf_id, “x”, HOFFSET(surf_t,x), complex_id);
H5Tinsert (surf_id, “y”, HOFFSET(surf_t,y), complex_id);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 11. Code for a compound datatype nested within a compound
datatype</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>Note that a similar result could be accomplished by creating a
compound datatype and inserting four fields. See the figure below. This
results in the same layout as the figure above. The difference
would be how the fields are addressed. In the first case, the
real part of ‘y’ is called ‘y.re’; in the
second case it is ‘y-re’.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct {
complex_t x;
complex_t y;
} surf_t;
hid_t surf_id = H5Tcreate (H5T_COMPOUND, sizeof(surf_t));
H5Tinsert (surf_id, “x-re”, HOFFSET(surf_t,x.re),
H5T_NATIVE_DOUBLE);
H5Tinsert (surf_id, “x-im”, HOFFSET(surf_t,x.im),
H5T_NATIVE_DOUBLE);
H5Tinsert (surf_id, “y-re”, HOFFSET(surf_t,y.re),
H5T_NATIVE_DOUBLE);
H5Tinsert (surf_id, “y-im”, HOFFSET(surf_t,y.im),
H5T_NATIVE_DOUBLE); </pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 12. Another compound datatype nested within a
compound datatype </b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The members of a compound datatype do not always
fill all the bytes. The <code>HOFFSET</code> macro
assures that the members will be laid out according
to the requirements of the platform and language.
The example below shows an example of a C struct which requires
extra bytes of padding on many platforms. The second
element, ‘b’, is a 1-byte character followed by an 8
byte double, ‘c’. On many systems, the 8-byte value must
be stored on a 4- or 8-byte boundary. This requires the struct
to be larger than the sum of the size of its elements. </p>
<p>In the example below, <code>sizeof</code> and
<code>HOFFSET</code> are used to assure that the
members are inserted at the correct offset to match the
memory conventions of the platform. The figure below shows how
this data element would be stored in memory, assuming the
double must start on a 4-byte boundary. Notice the extra
bytes between ‘b’ and ‘c’.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct s1_t {
int a;
char b;
double c;
} s1_t;
s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
H5Tinsert(s1_tid, “a_name”, HOFFSET(s1_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, “b_name”, HOFFSET(s1_t, b), H5T_NATIVE_CHAR);
H5Tinsert(s1_tid, “c_name”, HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 13. A compound datatype that requires padding</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig23.JPG">
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 12. Memory layout of a compound datatype that requires
padding </b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>However, data stored on disk does not require
alignment, so unaligned versions of compound data
structures can be created to improve space efficiency
on disk. These unaligned compound datatypes can be
created by computing offsets by hand to eliminate
inter-member padding, or the members can be packed by
calling <code>H5Tpack</code> (which modifies a datatype
directly, so it is usually preceded by a call to
<code>H5Tcopy</code>). </p>
<p>The example below shows how to create a disk version of the
compound datatype from the figure above in order to store
data on disk in as compact a form as possible.
Packed compound datatypes should generally not be used to
describe memory as they may violate alignment constraints
for the architecture being used. Note also that using a
packed datatype for disk storage may involve a higher
data conversion cost.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t s2_tid = H5Tcopy (s1_tid);
H5Tpack (s2_tid);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 14. Create a packed compound datatype in C</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The example below shows the sequence of Fortran calls to
create a packed compound datatype. An HDF5 Fortran
compound datatype never describes a compound datatype
in memory and compound data is <em>ALWAYS</em> written
by fields as described in the next section. Therefore
packing is not needed unless the offset of each consecutive
member is not equal to the sum of the sizes of the
previous members.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
CALL h5tcopy_f(s1_id, s2_id, error)
CALL h5tpack_f(s2_id, error)</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 15. Create a packed compound datatype in Fortran</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<h4>6.4.3.2.1.2. Creating and Writing Datasets with Compound Datatypes</h4>
<p>Creating datasets with compound datatypes is similar
to creating datasets with any other HDF5 datatypes. But
writing and reading may be different since datasets that
have compound datatypes can be written or read by a field
(member) or subsets of fields (members). The compound datatype
is the only composite datatype that supports “sub-setting” by
the elements the datatype is built from.</p>
<p>The example below shows a C example of creating and writing a dataset
with a compound datatype.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct s1_t {
int a;
float b;
double c;
} s1_t;
s1_t data[LENGTH];
/* Initialize data */
for (i = 0; i < LENGTH; i++) {
data[i].a = i;
data[i].b = i*i;
data[i].c = 1./(i+1);
...
s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
H5Tinsert(s1_tid, “a_name”, HOFFSET(s1_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, “b_name”, HOFFSET(s1_t, b), H5T_NATIVE_FLOAT);
H5Tinsert(s1_tid, “c_name”, HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE);
...
dataset_id = H5Dcreate(file_id, “SDScompound.h5”, s1_t, space_id,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (dataset_id, s1_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 16. Create and write a dataset with a compound datatype in C</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<p>The example below shows the content of the file written on
a little-endian machine.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
HDF5 “SDScompound.h5” {
GROUP “/” {
DATASET “ArrayOfStructures” {
DATATYPE H5T_COMPOUND {
H5T_STD_I32LE “a_name”;
H5T_IEEE_F32LE “b_name”;
H5T_IEEE_F64LE “c_name”;
}
DATASPACE SIMPLE { ( 3 ) / ( 3 ) }
DATA {
(0): {
0,
0,
1
},
(1): {
1,
1,
0.5
},
(2): {
2,
4,
0.333333
}
}
}
}
}</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 17. Create and write a little-endian dataset with a compound
datatype in C</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<p>It is not necessary to write the whole data at once.
Datasets with compound datatypes can be written by
field or by subsets of fields. In order to do this one
has to remember to set the transfer property of the dataset
using the <code>H5Pset_preserve</code> call and to define the
memory datatype that corresponds to a field. The example below
shows how float and double fields are written to the
dataset.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct sb_t {
float b;
double c;
} sb_t;
typedef struct sc_t {
float b;
double c;
} sc_t;
sb_t data1[LENGTH];
sc_t data2[LENGTH];
/* Initialize data */
for (i = 0; i < LENGTH; i++) {
data1.b = i*i;
data2.c = 1./(i+1);
}
...
/* Create dataset as in example 15 */
...
/* Create memory datatypes corresponding to float and
double datatype fileds */
sb_tid = H5Tcreate (H5T_COMPOUND, sizeof(sb_t));
H5Tinsert(sb_tid, “b_name”, HOFFSET(sb_t, b), H5T_NATIVE_FLOAT);
sc_tid = H5Tcreate (H5T_COMPOUND, sizeof(sc_t));
H5Tinsert(sc_tid, “c_name”, HOFFSET(sc_t, c), H5T_NATIVE_DOUBLE);
...
/* Set transfer property */
xfer_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_preserve(xfer_id, 1);
H5Dwrite (dataset_id, sb_tid, H5S_ALL, H5S_ALL, xfer_id, data1);
H5Dwrite (dataset_id, sc_tid, H5S_ALL, H5S_ALL, xfer_id, data2);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 18. Writing floats and doubles to a dataset</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<p>The figure below shows the content of the file written on a
little-endian machine. Only float and double fields are
written. The default fill value is used to initialize the
unwritten integer field.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
HDF5 “SDScompound.h5” {
GROUP “/” {
DATASET “ArrayOfStructures” {
DATATYPE H5T_COMPOUND {
H5T_STD_I32LE “a_name”;
H5T_IEEE_F32LE “b_name”;
H5T_IEEE_F64LE “c_name”;
}
DATASPACE SIMPLE { ( 3 ) / ( 3 ) }
DATA {
(0): {
0,
0,
1
},
(1): {
0,
1,
0.5
},
(2): {
0,
4,
0.333333
}
}
}
}
}</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 19. Writing floats and doubles to a dataset on a little-endian
system</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<p>The example below contains a Fortran example that creates and writes
a dataset with a compound datatype. As this example illustrates,
writing and reading compound datatypes in Fortran is <em>always</em>
done by fields. The content of the written file is the same as
shown in the example above.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
! One cannot write an array of a derived datatype in Fortran.
TYPE s1_t
INTEGER a
REAL b
DOUBLE PRECISION c
END TYPE s1_t
TYPE(s1_t) d(LENGTH)
! Therefore, the following code initializes an array corresponding
! to each field in the derived datatype and writes those arrays
! to the dataset
INTEGER, DIMENSION(LENGTH) :: a
REAL, DIMENSION(LENGTH) :: b
DOUBLE PRECISION, DIMENSION(LENGTH) :: c
! Initialize data
do i = 1, LENGTH
a(i) = i-1
b(i) = (i-1) * (i-1)
c(i) = 1./i
enddo
...
! Set dataset transfer property to preserve partially initialized fields
! during write/read to/from dataset with compound datatype.
!
CALL h5pcreate_f(H5P_DATASET_XFER_F, plist_id, error)
CALL h5pset_preserve_f(plist_id, .TRUE., error)
...
!
! Create compound datatype.
!
! First calculate total size by calculating sizes of each member
!
CALL h5tget_size_f(H5T_NATIVE_INTEGER, type_sizei, error)
CALL h5tget_size_f(H5T_NATIVE_REAL, type_sizer, error)
CALL h5tget_size_f(H5T_NATIVE_DOUBLE, type_sized, error)
type_size = type_sizei + type_sizer + type_sized
CALL h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, error)
!
! Insert memebers
!
!
! INTEGER member
!
offset = 0
CALL h5tinsert_f(dtype_id, “a_name”, offset, H5T_NATIVE_INTEGER, error)
!
! REAL member
!
offset = offset + type_sizei
CALL h5tinsert_f(dtype_id, “b_name”, offset, H5T_NATIVE_REAL, error)
!
! DOUBLE PRECISION member
!
offset = offset + type_sizer
CALL h5tinsert_f(dtype_id, “c_name”, offset, H5T_NATIVE_DOUBLE, error)
!
! Create the dataset with compound datatype.
!
CALL h5dcreate_f(file_id, dsetname, dtype_id, dspace_id, &
dset_id, error, H5P_DEFAULT_F, H5P_DEFAULT_F, H5P_DEFAULT_F)
!
...
! Create memory types. We have to create a compound datatype
! for each member we want to write.
!
!
CALL h5tcreate_f(H5T_COMPOUND_F, type_sizei, dt1_id, error)
offset = 0
CALL h5tinsert_f(dt1_id, “a_name”, offset, H5T_NATIVE_INTEGER, error)
!
CALL h5tcreate_f(H5T_COMPOUND_F, type_sizer, dt2_id, error)
offset = 0
CALL h5tinsert_f(dt2_id, “b_name”, offset, H5T_NATIVE_REAL, error)
!
CALL h5tcreate_f(H5T_COMPOUND_F, type_sized, dt3_id, error)
offset = 0
CALL h5tinsert_f(dt3_id, “c_name”, offset, H5T_NATIVE_DOUBLE, error)
!
! Write data by fields in the datatype. Fields order is not important.
!
CALL h5dwrite_f(dset_id, dt3_id, c, data_dims, error, xfer_prp = plist_id)
CALL h5dwrite_f(dset_id, dt2_id, b, data_dims, error, xfer_prp = plist_id)
CALL h5dwrite_f(dset_id, dt1_id, a, data_dims, error, xfer_prp = plist_id)</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 20. Create and write a dataset with a compound datatype in
Fortran</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<h4>6.4.3.2.1.3. Reading Datasets with Compound Datatypes</h4>
<p>Reading datasets with compound datatypes may be a
challenge. For general applications there is no way to
know <em>a priori</em> the corresponding C structure.
Also, C structures cannot be allocated on the fly during discovery
of the dataset’s datatype. For general C , C++, Fortran
and Java application the following steps will be required
to read and to interpret data from the dataset with
compound datatype:</p>
<dl>
<dt>
<ol>
<li>Get the identifier of the compound datatype in the file
with the <code>H5Dget_type</code> call</li>
<li>Find the number of the compound datatype members
with the <code>H5Tget_nmembers</code> call</li>
<li>Iterate through compound datatype members</li>
</ol>
<dd>
<ul>
<li>Get member class with the
<code>H5Tget_member_class</code> call</li>
<li>Get member name with the
<code>H5Tget_member_name</code> call</li>
<li>Check class type against predefined classes</li>
<ul>
<li><code>H5T_INTEGER</code></li>
<li><code>H5T_FLOAT</code></li>
<li><code>H5T_STRING</code></li>
<li><code>H5T_BITFIELD</code></li>
<li><code>H5T_OPAQUE</code></li>
<li><code>H5T_COMPOUND</code></li>
<li><code>H5T_REFERENCE</code></li>
<li><code>H5T_ENUM</code></li>
<li><code>H5T_VLEN</code></li>
<li><code>H5T_ARRAY</code></li>
</ul>
<li>If class is <code>H5T_COMPOUND</code>,
then go to step 2 and repeat all steps under
step 3. If class is not <code>H5T_COMPOUND</code>,
then a member is of an atomic class and can be
read to a corresponding buffer after discovering
all necessary information specific to each atomic
type (e.g. size of the integer or floats, super
class for enumerated and array datatype,
and it sizes, etc.)</li>
</ul>
</dd>
</dl>
<p>The examples below show how to read a dataset with a known
compound datatype.</p>
<p>The first example below shows the steps needed to read data of a
known structure. First, build a memory datatype
the same way it was built when the dataset was created, and then
second use the datatype in a <code>H5Dread</code> call.</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct s1_t {
int a;
float b;
double c;
} s1_t;
s1_t *data;
...
s1_tid = H5Tcreate(H5T_COMPOUND, sizeof(s1_t));
H5Tinsert(s1_tid, “a_name”, HOFFSET(s1_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, “b_name”, HOFFSET(s1_t, b), H5T_NATIVE_FLOAT);
H5Tinsert(s1_tid, “c_name”, HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE);
...
dataset_id = H5Dopen(file_id, “SDScompound.h5”, H5P_DEFAULT);
...
data = (s1_t *) malloc (sizeof(s1_t)*LENGTH);
H5Dread(dataset_id, s1_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 21. Read a dataset using a memory datatype
<!-- used to be Figure 25f --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>Instead of building a memory datatype, the application could use the
<code>H5Tget_native_type</code> function. See the example below.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct s1_t {
int a;
float b;
double c;
} s1_t;
s1_t *data;
hid_t file_s1_t, mem_s1_t;
...
dataset_id = H5Dopen(file_id, “SDScompound.h5”, H5P_DEFAULT);
/* Discover datatype in the file */
file_s1_t = H5Dget_type(dataset_id);
/* Find corresponding memory datatype */
mem_s1_t = H5Tget_native_type(file_s1_t, H5T_DIR_DEFAULT);
...
data = (s1_t *) malloc (sizeof(s1_t)*LENGTH);
H5Dread (dataset_id, mem_s1_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 22. Read a dataset using <code>H5Tget_native_type</code>
<!-- used to be Figure 25g --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<p>The example below shows how to read just one float member of a
compound datatype.</p>
<!-- used to be Example 25h -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct s1_t {
float b;
} sf_t;
sf_t *data;
...
sf_tid = H5Tcreate(H5T_COMPOUND, sizeof(sf_t));
H5Tinsert(s1_tid, “b_name”, HOFFSET(sf_t, b), H5T_NATIVE_FLOAT);
...
dataset_id = H5Dopen(file_id, “SDScompound.h5”, H5P_DEFAULT);
...
data = (sf_t *) malloc (sizeof(sf_t)*LENGTH);
H5Dread(dataset_id, sf_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 23. Read one floating point member of a compound datatype
<!-- used to be Figure 25h --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The example below <!-- used to be Figure 25i --> shows how to read float
and
double members of a compound datatype into
a structure that has those fields in a different
order. Please notice that <code>H5Tinsert</code>
calls can be used in an order different from the
order of the structures members.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct s1_t {
double c;
float b;
} sdf_t;
sdf_t *data;
...
sdf_tid = H5Tcreate(H5T_COMPOUND, sizeof(sdf_t));
H5Tinsert(sdf_tid, “b_name”, HOFFSET(sdf_t, b), H5T_NATIVE_FLOAT);
H5Tinsert(sdf_tid, “c_name”, HOFFSET(sdf_t, c), H5T_NATIVE_DOUBLE);
...
dataset_id = H5Dopen(file_id, “SDScompound.h5”, H5P_DEFAULT);
...
data = (sdf_t *) malloc (sizeof(sdf_t)*LENGTH);
H5Dread(dataset_id, sdf_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 24. Read float and double members of a compound datatype
<!-- used to be Figure 25i --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<h4>6.4.3.2.2. Array</h4>
<p>Many scientific datasets have multiple measurements for each point
in a space. There are several natural ways to represent this data,
depending on the variables and how they are used in computation.
See the table and the figure below.</p>
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Table 20. Representing data with multiple measurements</b></td>
</tr>
<tr><td colspan="5"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="25%"><b>Storage Strategy</b></td>
<td width="2%"> </td>
<td width="25%"><b>Stored as</b></td>
<td width="2%"> </td>
<td width="46%"><b>Remarks</b></td>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Mulitple planes</td>
<td> </td>
<td>Several datasets with identical dataspaces</td>
<td> </td>
<td>This is optimal when variables are
accessed individually, or when often uses only selected variables.</td>
</tr>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Additional dimension</td>
<td> </td>
<td>One dataset, the last “dimension”
is a vector of variables</td>
<td> </td>
<td>This can give good performance, although
selecting only a few variables may be slow. This may not reflect the
science.</td>
</tr>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Record with multiple values</td>
<td> </td>
<td>One dataset with compound datatype</td>
<td> </td>
<td>This enables the variables to be read all
together or selected. Also handles “vectors” of
heterogenous data.</td>
</tr>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Vector or Tensor value</td>
<td> </td>
<td>One dataset, each data element is a small
array of values.</td>
<td> </td>
<td>This uses the same amount of space as
the previous two, and may represent the science model better.</td>
</tr>
<tr><td colspan="5"><hr color="green" size="3" /></td></tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="400" cellspacing="0" align="center">
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td align="left">
<img src="Images/Dtypes_fig26_pic1of4.JPG"></td>
<td> </td>
<td align="center">
<img src="Images/Dtypes_fig26_pic2of4.JPG"></td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<img src="Images/Dtypes_fig26_pic3of4.JPG"></td>
<td> </td>
<td align="center">
<img src="Images/Dtypes_fig26_pic4of4.JPG"></td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" colspan="3" >
<b>Figure 13. Representing data with multiple measurements</b>
</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<p>The HDF5 <code>H5T_ARRAY</code> datatype defines
the data element to be a homogeneous, multi-dimensional
array. See Figure 13d above. The elements of the array
can be any HDF5 datatype (including compound and array), and
the size of the datatype is the total size of the array.
A dataset of array datatype cannot be subdivided for I/O
within the data element: the entire array of the data element
must be transferred. If the data elements need to be accessed
separately, e.g., by plane, then the array datatype should not
be used. The table below <!-- formerly Table 22 -->
shows advantages and disadvantages of various
storage methods.</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="5" align="left" valign="bottom">
<b>Table 21. Storage method advantages and disadvantages</b></td>
</tr>
<tr><td colspan="5"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="20%"><b>Method</b></td>
<td width="2%"> </td>
<td width="38%"><b>Advantages</b></td>
<td width="2%"> </td>
<td width="38%"><b>Disadvantages</b></td>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>a) Multiple Datasets</td>
<td> </td>
<td>Easy to access each plane, can select any plane(s)</td>
<td> </td>
<td>Less efficient to access a ‘column’ through the
planes</td>
</tr>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>b) N+1 Dimension</td>
<td> </td>
<td>All access patterns supported</td>
<td> </td>
<td>Must be homogeneous datatype<br /><br />
The added dimension may not make sense in the scientific
model</td>
</tr>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>c) Compound Datatype</td>
<td> </td>
<td>Can be heterogenous datatype</td>
<td> </td>
<td>Planes must be named, selection is by plane<br /><br />
Not a natural representation for a matrix</td>
</tr>
<tr><td colspan="5"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>d) Array</td>
<td> </td>
<td>A natural representation for vector or tensor data</td>
<td> </td>
<td>Cannot access elements separately (no access by plane)</td>
</tr>
<tr><td colspan="5"><hr color="green" size="3" /></td></tr>
</table>
<br />
<p>An array datatype may be multi-dimensional with 1 to
<code>H5S_MAX_RANK</code> (the maximum rank of a dataset is currently
32) dimensions. The dimensions can be any size greater than 0, but
unlimited dimensions are not supported (although the datatype can be
a variable-length datatype).</p>
<p>An array datatype is created with the <code>H5Tarray_create</code>
call, which specifies the number of dimensions, the size of each
dimension, and the base type of the array. The array datatype can
then be used in any way that any datatype object is used. The example
below <!-- formerly Figure 27 --> shows the creation of a datatype
that is a two-dimensional array of native integers, and this is then
used to create a dataset. Note that the dataset can be a dataspace
that is any number and size of dimensions. The figure below
<!-- formerly Figure 28 --> shows the layout in memory assuming that
the native integers are 4 bytes. Each data element has 6 elements,
for a total of 24 bytes.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t file, dataset;
hid_t datatype, dataspace;
hsize_t adims[] = {3, 2};
datatype = H5Tarray_create(H5T_NATIVE_INT, 2, adims, NULL);
dataset = H5Dcreate(file, datasetname, datatype, dataspace,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 25. Create a two-dimensional array datatype
<!-- formerly Figure 27 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig28.JPG" width="550">
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 14. Memory layout of a two-dimensional array datatype
<!-- formerly Figure 28 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<h4>6.4.3.2.3. Variable-length Datatypes</h4>
<p>A variable-length (VL) datatype is a one-dimensional sequence of a
datatype which are not fixed in length from one dataset location to
another, i.e., each data element may have a different number of members.
Variable-length datatypes cannot be divided, the entire data element
must be transferred.</p>
<p>VL datatypes are useful to the scientific community in many different
ways, possibly including: </p>
<ul>
<li><em>Ragged arrays</em>: Multi-dimensional ragged arrays can be
implemented with the last (fastest changing) dimension being ragged by
using a VL datatype as the type of the element stored. </li>
<li><em>Fractal arrays</em>: A nested VL datatype can be used to implement
ragged arrays of ragged arrays, to whatever nesting depth is required
for the user. </li>
<li><em>Polygon lists</em>: A common storage requirement is to
efficiently store arrays of polygons with different numbers of
vertices. A VL datatypes can be used to efficiently and succinctly
describe an array of polygons with different numbers of vertices. </li>
<li><em>Character strings</em>: Perhaps the most common use of VL
datatypes will be to store C-like VL character strings in dataset
elements or as attributes of objects. </li>
<li><em>Indices, e.g. of objects within the file</em>: An array of
VL object references could be used as an index to all the objects
in a file which contain a particular sequence of dataset values. </li>
<li><em>Object Tracking</em>: An array of VL dataset region references
can be used as a method of tracking objects or features appearing
in a sequence of datasets. </li>
</ul>
<p>A VL datatype is created by calling <code>H5Tvlen_create</code> which
specifies the base datatype. The first example below <!-- formerly
Figure 29 --> shows an example of code that creates a VL datatype
of unsigned integers. Each data element is a one-dimensional array of
zero or more members and is stored in the <code>hvl_t</code> structure.
See the second example below. <!-- formerly Figure 30 --></p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
tid1 = H5Tvlen_create (H5T_NATIVE_UINT);
dataset=H5Dcreate(fid1, “Dataset1”, tid1, sid1, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 26. Create a variable-length datatype of unsigned integers
<!-- formerly Figure 29 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct {
size_t len; /* Length of VL data (in base type units) */
void *p; /* Pointer to VL data */
} hvl_t;</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 27. Data element storage for members of the VL datatype
<!-- formerly Figure 30 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<p>The first example below <!-- formerly Figure 31 --> shows how the VL
data is written. For each of the 10 data elements,
a length and data buffer must be allocated. Below the two examples is a
figure <!-- formerly Figure 33 --> that shows how the data is
laid out in memory. </p>
<p>An analogous procedure must be used to read the data. See the second
example below.
An appropriate array of <code>vl_t</code> must be allocated,
and the data read. It is then traversed one data element at a time.
The <code>H5Dvlen_reclaim</code> call frees the data buffer for the buffer.
With each element possibly being of different sequence lengths for a
dataset with a VL datatype, the memory for the VL datatype
must be dynamically allocated. Currently there are two methods of managing the
memory for VL datatypes: the standard C malloc/free memory allocation routines
or a method of calling user-defined memory management routines to allocate or
free memory (set with <code>H5Pset_vlen_mem_manager</code>). Since the memory
allocated when reading (or writing) may be complicated to release,
the <code>H5Dvlen_reclaim</code> function
is provided to traverse a memory buffer and free the VL datatype information
without leaking memory.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hvl_t wdata[10]; /* Information to write */
/* Allocate and initialize VL data to write */
for(i=0; i < 10; i++) {
wdata[i].p = malloc((i+1)*sizeof(unsigned int));
wdata[i].len = i+1;
for(j=0; j<(i+1); j++)
((unsigned int *)wdata[i].p)[j]=i*10+j;
}
ret=H5Dwrite(dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 28. Write VL data
<!-- formerly Figure 31 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hvl_t rdata[SPACE1_DIM1];
ret=H5Dread(dataset, tid1, H5S_ALL, H5S_ALL, xfer_pid, rdata);
for(i=0; i<SPACE1_DIM1; i++) {
printf(“%d: len %d ”,rdata[i].len);
for(j=0; j<rdata[i].len; j++) {
printf(“ value: %u\n”,((unsigned int *)rdata[i].p)[j]);
}
}
ret=H5Dvlen_reclaim(tid1, sid1, xfer_pid, rdata);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 29. Read VL data
<!-- formerly Figure 32 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig33.JPG" width="550">
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 15. Memory layout of a VL datatype
<!-- formerly Figure 33 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The user program must carefully manage these relatively complex data
structures.
The <code>H5Dvlen_reclaim</code> function performs a standard traversal,
freeing all the data. This function analyzes the datatype and dataspace
objects, and visits each VL data element, recursing through nested
types. By default, the system <code>free</code> is called for the
pointer in each <code>vl_t</code>. Obviously, this call assumes that
all of this memory was allocated with the system <code>malloc</code>.</p>
<p>The user program may specify custom memory manager routines, one for
allocating and one for freeing. These may be set with the
<code>H5Pvlen_mem_manager</code>, and must have the following prototypes: </p>
<ul>
<li><code>typedef void *(*H5MM_allocate_t)(size_t size, void *info);</code> </li>
<li><code>typedef void (*H5MM_free_t)(void *mem, void *free_info);</code> </li>
</ul>
<p>The utility function <code>H5Dget_vlen_buf_size</code> checks the
number of bytes required to store the VL data from the dataset. This
function analyzes the datatype and dataspace object to visit all the
VL data elements, to determine the number of bytes required to store
the data for the in the destination storage (memory). The
<code>size</code> value is adjusted for data conversion and alignment
in the destination.</p>
<SCRIPT language="JavaScript">
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document.writeln ("
<a name="NonNumDtypes">
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<a href="#TOP"><font size="-1">(Top)</font></a>
</div>
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<a name="NonNumDtypes">
<h3 class=pagebefore>6.5. Other Non-numeric Datatypes</h3>
</a>
<p>Several datatype classes define special types of objects.</p>
<h4>6.5.1. Strings</h4>
<p>Text data is represented by arrays of characters, called strings.
Many programming languages support different conventions for storing strings,
which may be fixed or variable-length, and may have different rules for
padding unused storage. HDF5 can represent strings in several ways.
See the figure below.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table align="center" width="100%">
<tr align="left">
<td width="5%"> </td>
<td width="25%" align="left" valign="top">The Strings to store are: </td>
<td width="70%" align="left">“Four score”,<br /> “lazy programmers.”</td>
</tr>
<tr>
<td colspan="3"> </td>
</tr>
</table>
<table width="100%">
<tr align="left">
<td width="5%"> </td>
<td valign="top" align="right">
<strong>a)</strong>
</td>
<td><code>H5T_NATIVE_CHAR</code> the dataset is a one-dimensional
array with 29 elements, each element is a single character.
</td>
</tr>
</table>
<table align="center" width="100%">
<tr>
<td width="5%"> </td>
<td colspan="2">
<table border="1" width="100%">
<tr>
<td align="center">0</td>
<td align="center">1</td>
<td align="center">2</td>
<td align="center">3</td>
<td align="center">4</td>
<td align="center">...</td>
<td align="center">25</td>
<td align="center">26</td>
<td align="center">27</td>
<td align="center">28</td>
</tr>
<tr>
<td align="center">‘F’</td>
<td align="center">‘o’</td>
<td align="center">‘u’</td>
<td align="center">‘r’</td>
<td align="center">‘ ’</td>
<td align="center">...</td>
<td align="center">‘r’</td>
<td align="center">‘s’</td>
<td align="center">‘.’</td>
<td align="center">‘\0’</td>
</tr>
</table>
</td>
</tr>
<tr><td colspan="3"> </td></tr>
</table>
<table width="100%">
<tr align="left">
<td width="5%"> </td>
<td align="right" valign="top"><strong>b)</strong></td>
<td>Fixed-length string<br />
The dataset is a one-dimensional array with 2 elements,
each element is 20 characters.
</td>
</tr>
</table>
<table align="center" width="100%">
<tr>
<td width="15%"> </td>
<td colspan="2">
<table border="1" width="50%">
<tr align="center">
<td> 0 </td>
<td><pre>“Four score\0 ”</pre></td>
</tr>
<tr align="center">
<td> 1 </td>
<td><pre>“lazy programmers.\0”</pre></td>
</tr>
</table>
</td>
</tr>
<tr><td colspan="3"> </td></tr>
</table>
<table width="100%">
<tr align="left">
<td width="5%"> </td>
<td align="right" valign="top"><strong>c)</strong></td>
<td>Variable-length string<br />
The dataset is a one-dimensional array with 2
elements, each element is a variable-length string.<br />
This is the same result when stored as fixed-length
string, except that first element of the array will
need only 11 bytes for storage instead of 20.
</td>
</tr>
</table>
<table align="center" width="100%">
<tr>
<td width="15%"> </td>
<td colspan="2">
<table border="1" width="50%">
<tr align="center">
<td> 0 </td>
<td><pre>“Four score\0”</pre></td>
</tr>
<tr align="center">
<td> 1 </td>
<td><pre>“lazy programmers.\0”</pre></td>
</tr>
</table>
</td>
</tr>
<tr><td colspan="3"> </td></tr>
</table>
<table align="center" width="100%">
<tr>
<td width="15%"> </td>
<td colspan="2">
<img src="Images/Dtypes_fig34.JPG">
</td>
</table>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 16. Ways to represent strings
<!-- formerly Figure 34 --></b><hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>First, a dataset may have a dataset with datatype
<code>H5T_NATIVE_CHAR</code>, with each character of the string as an
element of the dataset. This will store an unstructured block of text
data, but gives little indication of any structure in the text. See
item a in the figure above. </p>
<p>A second alternative is to store the data using the datatype class
<code>H5T_STRING</code>,
with each element a fixed length. See item b in the figure above. In this
approach, each element might be a word or a sentence, addressed by
the dataspace. The dataset reserves space for the specified number of
characters, although some strings may be shorter. This approach is
simple and usually is fast to access, but can waste storage space if
the length of the Strings varies.</p>
<p>A third alternative is to use a variable-length datatype. See item c in
the figure above. This can be done using the standard mechanisms
described above (e.g., using <code>H5T_NATIVE_CHAR</code>
instead of <code>H5T_NATIVE_INT</code> in Example 25 above). The
program would use <code>vl_t</code> structures to write and
read the data.</p>
<p>A fourth alternative is to use a special feature of the string datatype
class to set the size of the datatype to <code>H5T_VARIABLE</code>. See
item c in the figure above. The example below <!-- formerly Figure 35 -->
shows a declaration of a datatype of type <code>H5T_C_S1</code>
which is set to <code>H5T_VARIABLE</code>. The HDF5 Library automatically
translates between this and the <code>vl_t</code> structure. (Note: the
<code>H5T_VARIABLE</code> size can only be used with string datatypes.)</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
tid1 = H5Tcopy (H5T_C_S1);
ret = H5Tset_size (tid1, H5T_VARIABLE);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 30. Set the string datatype size to <code>H5T_VARIABLE</code>
<!-- formerly Figure 35 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>Variable-length strings can be read into C strings (i.e., pointers to zero
terminated arrays of <code>char</code>). See the figure below. </p>
<table width="650" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
char *rdata[SPACE1_DIM1];
ret=H5Dread(dataset, tid1, H5S_ALL, H5S_ALL, xfer_pid, rdata);
for(i=0; i<SPACE1_DIM1; i++) {
printf(“%d: len: %d, str is: %s\n”, i, strlen(rdata[i]),rdata[i]);
}
ret=H5Dvlen_reclaim(tid1, sid1, xfer_pid, rdata);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 31. Read variable-length strings into C strings
<!-- formerly Figure 36 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!--
3.23.2012. I commented out the "Strings in Mixed Environments" section below.
I have spent too many GMQS hours and have to stop charging GMQS for awhile. MEE.
<a name="stringsInMixedEnvironments">
<b>Strings in Mixed Environments</b></a>
<p>In the figures above, the strings are terminated with NULLs.
Suppose in another scenario that the strings were stored on disk and
were not terminated with NULLs, and suppose that the users of the data
would be using applications that expected strings to be terminated with
NULLs? What APIs might an application use to properly handle the strings?
</p>
<p>The figure below shows the strings “Four score” and
“seven years ago” stored as fixed-length dataset elements
without NULL terminators.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table align="center" width="100%">
<tr>
<td colspan="2">
<table align="center" border="1" width="70%">
<tr>
<td width="50%" align="center">0</td>
<td width="50%" align="center">1</td>
</tr>
<tr>
<td align="center">‘Four score
’</td>
<td align="center">‘seven years ago
’</td>
</tr>
</table>
</td>
</tr>
</table>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 17???. Strings stored as fixed-length dataset elements
and not terminated with NULLs
</b><hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>
<p>??????? rewrite for this new example
The figure below shows how these strings might be stored using
a <b>fixed-length</b> datatype. This one-dimensional array uses the
<code>H5T_STRING</code> datatype. The dataset reserves space for a
specified number of characters in each string although some strings may
be shorter. In the example below, the size is set to 20. This approach
is simple and usually fast to access, but this approach can waste storage
space if the lengths of the strings vary. The single quotation marks are
used to show the 20 characters included in each dataset element.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table align="center" width="100%">
<tr>
<td colspan="2">
<table align="center" border="1" width="70%">
<tr>
<td width="50%" align="center">0</td>
<td width="50%" align="center">1</td>
</tr>
<tr>
<td align="center">‘Four score\0
’</td>
<td align="center">‘seven years ago\0
’</td>
</tr>
</table>
</td>
</tr>
</table>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 17???. Strings stored as fixed-length dataset elements
</b><hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>Please note that a data element of size 1 might be useful in an
environment where a NULL is not needed to terminate a string. If a NULL
is needed to terminate a string, then a data element of size 1
would not be useful.</p>
<br /><br />
-->
<h4>6.5.2. Reference</h4>
<p>In HDF5, objects (i.e. groups, datasets, and committed datatypes)
are usually accessed by name. There is another way to access stored
objects - by reference. There are two reference datatypes: object
reference and region reference. Object reference objects are created
with <code>H5Rcreate</code> and other calls (cross reference). These
objects can be stored and retrieved in a dataset as elements with
reference datatype. The first example below <!-- formerly Figure 37 -->
shows an example of code that creates references to four objects,
and then writes the array of object references to a dataset. The
second example below <!-- formerly Figure 38 -->shows a dataset of datatype
reference being read and one of the reference objects being
dereferenced to obtain an object pointer.</p>
<p>In order to store references to regions of a dataset, the datatype
should be <code>H5T_REGION_OBJ</code>. Note that a data element must
be either an object reference or a region reference: these are different
types and cannot be mixed within a single array.</p>
<p>A reference datatype cannot be divided for I/O: an element is read or
written completely.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
dataset=H5Dcreate(fid1, “Dataset3”, H5T_STD_REF_OBJ, sid1,
H5P_DEFAULT, H5P_DEFAULT, 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 committed 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);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 32. Create object references and write to a dataset
<!-- formerly Figure 37 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
rbuf = malloc(sizeof(hobj_ref_t)*SPACE1_DIM1);
/* 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]);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 33. Read a dataset with a reference datatype
<!-- formerly Figure 38 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<h4>6.5.3. ENUM</h4>
<p>The enum datatype implements a set of (name, value) pairs, similar
to C/C++ enum. The values are currently limited to native integer datatypes.
Each name can be the name of only one value, and each value can have only
one name. </p>
<p>The data elements of the ENUMERATION are stored according to the datatype,
e.g., as an array of integers. The example below <!-- formerly Figure 39 -->
shows an example of how to create
an enumeration with five elements. The elements map symbolic names to
2-byte integers. See the table below.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t hdf_en_colors = H5Tcreate(H5T_ENUM, sizeof(short));
short val;
H5Tenum_insert(hdf_en_colors, “RED”, (val=0,&val));
H5Tenum_insert(hdf_en_colors, “GREEN”, (val=1,&val));
H5Tenum_insert(hdf_en_colors, “BLUE”, (val=2,&val));
H5Tenum_insert(hdf_en_colors, “WHITE”, (val=3,&val));
H5Tenum_insert(hdf_en_colors, “BLACK”, (val=4,&val));
H5Dcreate(fileid, datasetname, hdf_en_colors, spaceid, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 34. Create an enumeration with five elements
<!-- formerly Figure 39 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="200" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 22. An enumeration<br />with five elements</b>
<!-- formerly Table 23 --></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Name</b></td>
<td width="50%"><b>Value</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>RED</td>
<td>0</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>GREEN</td>
<td>1</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>BLUE</td>
<td>2</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>WHITE</td>
<td>3</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>BLACK</td>
<td>4</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<!-- NEW PAGE -->
<p>The figure below <!-- formerly Figure 40 -->shows how an array of eight
values might be stored. Conceptually,
the array is an array of symbolic names [BLACK, RED, WHITE, BLUE, ...]. See
item a in the figure below. <!-- formerly Figure 40a -->
These are stored as the values and are short integers. So, the first 2 bytes
are the value associated with “BLACK”, which is the number 4,
and so on. See item b in the figure below. <!-- formerly Figure 40b --></p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table align="center" width="100%">
<tr>
<td align="center">a) Logical data to be written -
eight elements</td>
</tr>
<tr>
<td align="center">
<table>
<tr>
<td width="50" align="center">Index</td>
<td width="135" align="center">Name</td>
</tr>
</table>
<table border="1">
<tr>
<td width="30" align="center">0</td>
<td width="130" align="left">:BLACK</td>
</tr>
<tr>
<td width="30" align="center">1</td>
<td width="130" align="left">RED</td>
</tr>
<tr>
<td width="30" align="center">2</td>
<td width="130" align="left">WHITE</td>
</tr>
<tr>
<td width="30" align="center">3</td>
<td width="130" align="left">BLUE</td>
</tr>
<tr>
<td width="30" align="center">4</td>
<td width="130" align="left">RED</td>
</tr>
<tr>
<td width="30" align="center">5</td>
<td width="130" align="left">WHITE</td>
</tr>
<tr>
<td width="30" align="center">6</td>
<td width="130" align="left">BLUE</td>
</tr>
<tr>
<td width="30" align="center">7</td>
<td width="130" align="left">GREEN</td>
</tr>
</table>
</td>
</tr>
<tr><td> </td></tr>
<tr>
<td align="center"><img src="Images/Dtypes_fig40.JPG"></td>
</tr>
<tr>
<td align="center">b) The storage layout. Total size of the
array is 16 bytes, 2 bytes per element.
</td>
</tr>
</table>
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 17. Storing an enum array
<!-- formerly Figure 40 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The order that members are inserted into an enumeration type is
unimportant; the important part is the associations between the symbol
names and the values. Thus, two enumeration datatypes will be considered
equal if and only if both types have the same symbol/value associations
and both have equal underlying integer datatypes. Type equality is
tested with the <code>H5Tequal</code> function.</p>
<p>If a particular architecture type is required, a little-endian or
big-endian datatype for example, use a native integer datatype as the
ENUM base datatype and use <code>H5Tconvert</code> on values as they
are read from or written to a dataset. </p>
<!-- NEW PAGE -->
<h4>6.5.4. Opaque</h4>
<p>In some cases, a user may have data objects that should be stored and
retrieved as blobs with no attempt to interpret them. For example,
an application might wish to store an array of encrypted certificates
which are 100 bytes long.</p>
<p>While an arbitrary block of data may always be stored as bytes,
characters, integers, or whatever, this might mislead programs about
the meaning of the data. The opaque datatype defines data elements which
are uninterpreted by HDF5. The opaque data may be labeled with
<code>H5Tset_tag</code> with a string that might be used by an
application. For example, the encrypted certificates might have
a tag to indicate the encryption and the certificate standard.</p>
<h4>6.5.5. Bitfield</h4>
<p>Some data is represented as bits, where the number of bits is not an
integral byte and the bits are not necessarily interpreted as a standard
type. Some examples might include readings from machine registers (e.g.,
switch positions), a cloud mask, or data structures with several small
integers that should be store in a single byte.</p>
<p>This data could be stored as integers, strings, or enumerations.
However, these storage methods would likely result in considerable wasted
space. For example, storing a cloud mask with one byte per value would
use up to eight times the space of a packed array of bits. </p>
<p>The HDF5 bitfield datatype class defines a data element that is a
contiguous sequence of bits, which are stored on disk in a packed array.
The programming model is the same as for unsigned integers: the datatype
object is created by copying a predefined datatype, and then the
precision, offset, and padding are set.</p>
<p>While the use of the bitfield datatype will reduce storage space
substantially, there will still be wasted space if the bitfield as a
whole does not match the 1-, 2-, 4-, or 8-byte unit in which it is
written. The remaining unused space can be removed by applying the
<a href="10_Datasets.html#N-Bit">N-bit filter</a> to the dataset
containing the bitfield data. </p>
<!--
<h4>5.6. Time</h4>
<p>The HDF5 time datatype defines storage layout for various date and
time standards. Currently, only Unix "time" and "timeval" structs are
supported. The H5T_UNIX_D32BE (LE) defines storage for 4 bytes
(sufficient for the time struct), H5T_UNIX_D64BE (LE) is sufficient
for timeval. The data is treated as a single opaque value.</p>
-->
<SCRIPT language="JavaScript">
<!--
document.writeln ("
<a name="Fvalues">
<div align=right>
<a href="#TOP"><font size="-1">(Top)</font></a>
</div>
</a>
");
-->
</SCRIPT>
<a name="Fvalues">
<h3 class=pagebefore>6.6. Fill Values</h3>
</a>
<p>The “fill value” for a dataset is the specification of
the default value assigned to data elements that have not yet been
written. In the case of a dataset with an atomic datatype, the fill
value is a single value of the appropriate datatype, such as
‘0’ or ‘-1.0’. In the case of a dataset with
a composite datatype, the fill value is a single data element of the
appropriate type. For example, for an array or compound datatype,
the fill value is a single data element with values for all the
component elements of the array or compound datatype.</p>
<p>The fill value is set (permanently) when the dataset is created.
The fill value is set in the dataset creation properties
<!-- editingComment
<span class="editingComment">[ [ [
(see chapter ??)
] ] ]</span>
-->
in the <code>H5Dcreate</code> call. Note that the <code>H5Dcreate</code>
call must also include the datatype of the dataset, and the value provided
for the fill value will be interpreted as a single element of this datatype.
The example below <!-- formerly Figure 41 -->shows code which creates a
dataset of integers with fill
value -1. Any unwritten data elements will be set to -1.</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t plist_id;
int filler;
filler = -1;
plist_id = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(plist_id, H5T_NATIVE_INT, &filler);
/* Create the dataset with fill value ‘-1’. */
dataset_id = H5Dcreate(file_id, “/dset”, H5T_STD_I32BE,
dataspace_id, H5P_DEFAULT, plist_id, H5P_DEFAULT);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 35. Create a dataset with a fill value of -1
<!-- formerly Figure 41 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct s1_t {
int a;
char b;
double c;
} s1_t;
s1_t filler;
s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
H5Tinsert(s1_tid, “a_name”, HOFFSET(s1_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, “b_name”, HOFFSET(s1_t, b), H5T_NATIVE_CHAR);
H5Tinsert(s1_tid, “c_name”, HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE);
filler.a = -1;
filler.b = ‘*’;
filler.c = -2.0;
plist_id = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_fill_value(plist_id, s1_tid, &filler);
/* Create the dataset with fill value (-1, ‘*’, -2.0). */
dataset = H5Dcreate(file, datasetname, s1_tid, space, H5P_DEFAULT,
plist_id, H5P_DEFAULT);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 36. Create a fill value for a compound datatype
<!-- formerly Figure 42 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The figure above <!-- formerly Figure 42 -->shows how to create a fill
value for a compound datatype. The procedure is the same as the previous
example except the filler must be a structure with the correct fields.
Each field is initialized to the desired fill value.</p>
<p>The fill value for a dataset can be retrieved by reading the dataset
creation properties of the dataset and then by reading the fill value with
<code>H5Pget_fill_value</code>. The data will be read into memory using
the storage layout specified by the datatype. This transfer will convert
data in the same way as <code>H5Dread</code>.
The figure below <!-- formerly Figure 43 --> shows how to get the fill
value from the dataset created in Example 33 above.</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t plist2;
int filler;
dataset_id = H5Dopen(file_id, “/dset”, H5P_DEFAULT);
plist2 = H5Dget_create_plist(dataset_id);
H5Pget_fill_value(plist2, H5T_NATIVE_INT, &filler);
/* filler has the fill value, ‘-1’ */</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 37. Retrieve a fill value
<!-- formerly Figure 43 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>A similar procedure is followed for any datatype. The example below
<!-- formerly Figure 45 -->shows how to
read the fill value for the compound datatype created in an example above
<!-- formerly Figure 42 -->. Note that the program must pass an
element large enough to hold a fill value of the datatype indicated by the
argument to <code>H5Pget_fill_value</code>. Also, the program must
understand the datatype in order to interpret its components. This may
be difficult to determine without knowledge of the application that
created the dataset.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
char * fillbuf;
int sz;
dataset = H5Dopen( file, DATASETNAME, H5P_DEFAULT);
s1_tid = H5Dget_type(dataset);
sz = H5Tget_size(s1_tid);
fillbuf = (char *)malloc(sz);
plist_id = H5Dget_create_plist(dataset);
H5Pget_fill_value(plist_id, s1_tid, fillbuf);
printf(“filler.a: %d\n”,((s1_t *) fillbuf)->a);
printf(“filler.b: %c\n”,((s1_t *) fillbuf)->b);
printf(“filler.c: %f\n”,((s1_t *) fillbuf)->c);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 38. Read the fill value for a compound datatype
<!-- formerly Figure 44 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<SCRIPT language="JavaScript">
<!--
document.writeln ("
<a name="CCDtypes">
<div align=right>
<a href="#TOP"><font size="-1">(Top)</font></a>
</div>
</a>
");
-->
</SCRIPT>
<!-- NEW PAGE -->
<a name="CCDtypes">
<h3 class=pagebefore>6.7. Complex Combinations of Datatypes</h3>
</a>
<p>Several composite datatype classes define collections of other datatypes,
including other composite datatypes. In general, a datatype can be nested
to any depth, with any combination of datatypes.</p>
<p>For example, a compound datatype can have members that are other compound
datatypes, arrays, VL datatypes. An array can be an array of array,
an array of compound, or an array of VL. And a VL datatype can be a
variable-length array of compound, array, or VL datatypes.</p>
<p>These complicated combinations of datatypes form a logical tree,
with a single root datatype, and leaves which must be atomic datatypes
(predefined or user-defined). The figure below <!-- formerly Figure 45 -->
shows an example of a logical
tree describing a compound datatype constructed from different datatypes.</p>
<p>Recall that the datatype is a description of the layout of storage.
The complicated compound datatype is constructed from component datatypes,
each of which describe the layout of part of the storage. Any datatype can
be used as a component of a compound datatype, with the following
restrictions:</p>
<ol>
<li>No byte can be part of more than one component datatype (i.e., the
fields cannot overlap within the compound datatype)</li><br />
<li>The total size of the components must be less than or equal to the
total size of the compound datatype</li>
</ol>
<p>These restrictions are essentially the rules for C structures and similar
record types familiar from programming languages. Multiple typing, such
as a C union, is not allowed in HDF5 datatypes.</p>
<table width="500" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig45.JPG">
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 18. A compound datatype built with
different datatypes<!-- formerly Figure 45 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<h4>6.7.1. Creating a Complicated Compound Datatype</h4>
<p>To construct a complicated compound datatype, each component is
constructed, and then added to the enclosing datatype description.
The example below <!-- formerly Figure 46 --> shows
how to create a compound datatype with four members:</p>
<ul>
<li>“T1”, a compound datatype with three members</li>
<li>“T2”, a compound datatype with two members</li>
<li>“T3”, a one-dimensional array of integers</li>
<li>“T4”, a string</li>
</ul>
<p>Below the example code is a figure that shows this datatype as a logical
tree. <!-- formerly Figure 47 --> The output of the
<em>h5dump</em> utility is shown in the example below the figure.
<!-- the example was formerly called Figure 48.--></p>
<p>Each datatype is created as a separate datatype object. Figure 20 below
<!-- formerly Figure 49 --> shows
the storage layout for the four individual datatypes. Then the datatypes are
inserted into the outer datatype at an appropriate offset. Figure 21 below
<!-- formerly Figure 50 -->shows
the resulting storage layout. The combined record is 89 bytes long.</p>
<p>The Dataset is created using the combined compound datatype. The dataset
is declared to be a 4 by 3 array of compound data. Each data element is an
instance of the 89-byte compound datatype. Figure 22 below
<!-- formerly Figure 51 -->shows the layout of
the dataset, and expands one of the elements to show the relative position
of the component data elements.</p>
<p>Each data element is a compound datatype, which can be written or read
as a record, or each field may be read or written individually. The first
field (“T1”) is itself a compound datatype with three fields
(“T1.a”, “T1.b”, and “T1.c”).
“T1” can be read or written as a record, or individual
fields can be accessed. Similarly, the second filed is a compound datatype
with two fields (“T2.f1”, “T2.f2”).</p>
<p>The third field (“T3”) is an array datatype. Thus,
“T3” should be accessed as an array of 40 integers. Array
data can only be read or written as a single element, so all 40
integers must be read or written to the third field. The fourth
field (“T4”) is a single string of length 25.</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct s1_t {
int a;
char b;
double c;
} s1_t;
typedef struct s2_t {
float f1;
float f2;
} s2_t;
hid_t s1_tid, s2_tid, s3_tid, s4_tid, s5_tid;
/* Create a datatype for s1 */
s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
H5Tinsert(s1_tid, “a_name”, HOFFSET(s1_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, “b_name”, HOFFSET(s1_t, b), H5T_NATIVE_CHAR);
H5Tinsert(s1_tid, “c_name”, HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE);
/* Create a datatype for s2. *.
s2_tid = H5Tcreate (H5T_COMPOUND, sizeof(s2_t));
H5Tinsert(s2_tid, “f1”, HOFFSET(s2_t, f1), H5T_NATIVE_FLOAT);
H5Tinsert(s2_tid, “f2”, HOFFSET(s2_t, f2), H5T_NATIVE_FLOAT);
/* Create a datatype for an Array of integers */
s3_tid = H5Tarray_create(H5T_NATIVE_INT, RANK, dim);
/* Create a datatype for a String of 25 characters */
s4_tid = H5Tcopy(H5T_C_S1);
H5Tset_size(s4_tid, 25);
/*
* Create a compound datatype composed of one of each of these
* types.
* The total size is the sum of the size of each.
*/
sz = H5Tget_size(s1_tid) + H5Tget_size(s2_tid) + H5Tget_size(s3_tid)
+ H5Tget_size(s4_tid);
s5_tid = H5Tcreate (H5T_COMPOUND, sz);
/* insert the component types at the appropriate offsets */
H5Tinsert(s5_tid, “T1”, 0, s1_tid);
H5Tinsert(s5_tid, “T2”, sizeof(s1_t), s2_tid);
H5Tinsert(s5_tid, “T3”, sizeof(s1_t)+sizeof(s2_t), s3_tid);
H5Tinsert(s5_tid, “T4”, (sizeof(s1_t) +sizeof(s2_t)+
H5Tget_size(s3_tid)), s4_tid);
/*
* Create the dataset with this datatype.
*/
dataset = H5Dcreate(file, DATASETNAME, s5_tid, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 39. Create a compound datatype with four members
<!-- formerly Figure 46 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig47.JPG">
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 19. Logical tree for the compound
datatype with four members<!-- formerly Figure 47 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
DATATYPE H5T_COMPOUND {
H5T_COMPOUND {
H5T_STD_I32LE “a_name”;
H5T_STD_I8LE “b_name”;
H5T_IEEE_F64LE “c_name”;
} “T1”;
H5T_COMPOUND {
H5T_IEEE_F32LE “f1”;
H5T_IEEE_F32LE “f2”;
} “T2”;
H5T_ARRAY { [10] H5T_STD_I32LE } “T3”;
H5T_STRING {
STRSIZE 25;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
} “T4”;
}</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 40. Output from h5dump for the compound datatype
<!-- formerly Figure 48 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table align="center" border="0" width="100%">
<tr>
<td valign="middle" align="left">a) Compound type ‘s1_t’, size 16 bytes.</td>
</tr>
<tr><td>
<table border="1" align="center" width="100%">
<tr>
<td valign="middle" align="center" width="25%"><code>Byte 0</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 1</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 2</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>aaaaaaaa</code></td>
<td valign="middle" align="center"><code>aaaaaaaa</code></td>
<td valign="middle" align="center"><code>aaaaaaaa</code></td>
<td valign="middle" align="center"><code>aaaaaaaa</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 4</code></td>
<td valign="middle" align="center"><code>Byte 5</code></td>
<td valign="middle" align="center"><code>Byte 6</code></td>
<td valign="middle" align="center"><code>Byte 7</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>bbbbbbbb</code></td>
<td valign="middle" align="center"><code> </code></td>
<td valign="middle" align="center"><code> </code></td>
<td valign="middle" align="center"><code> </code></td>
</tr>
</table>
<table border="1" align="center" width="100%">
<tr>
<td valign="middle" align="center" width="25%"><code>Byte 8</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 9</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 10</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 11</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>cccccccc</code></td>
<td valign="middle" align="center"><code>cccccccc</code></td>
<td valign="middle" align="center"><code>cccccccc</code></td>
<td valign="middle" align="center"><code>cccccccc</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 12</code></td>
<td valign="middle" align="center"><code>Byte 13</code></td>
<td valign="middle" align="center"><code>Byte 14</code></td>
<td valign="middle" align="center"><code>Byte 15</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>cccccccc</code></td>
<td valign="middle" align="center"><code>cccccccc</code></td>
<td valign="middle" align="center"><code>cccccccc</code></td>
<td valign="middle" align="center"><code>cccccccc</code></td>
</tr>
</table>
</td></tr>
<tr>
<td valign="middle" align="left"> <br />b) Compound type ‘s2_t’, size 8 bytes.</td>
</tr>
<tr><td>
<table border="1" align="center" width="100%">
<tr>
<td valign="middle" align="center" width="25%"><code>Byte 0</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 1</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 2</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>ffffffff</code></td>
<td valign="middle" align="center"><code>ffffffff</code></td>
<td valign="middle" align="center"><code>ffffffff</code></td>
<td valign="middle" align="center"><code>ffffffff</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 4</code></td>
<td valign="middle" align="center"><code>Byte 5</code></td>
<td valign="middle" align="center"><code>Byte 6</code></td>
<td valign="middle" align="center"><code>Byte 7</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>gggggggg</code></td>
<td valign="middle" align="center"><code>gggggggg</code></td>
<td valign="middle" align="center"><code>gggggggg</code></td>
<td valign="middle" align="center"><code>gggggggg</code></td>
</tr>
</table>
</td></tr>
<tr>
<td valign="middle" align="left"> <br />c) Array type ‘s3_tid’, 40 integers, total size 40 bytes.</td>
</tr>
<tr><td>
<table border="1" align="center" width="100%">
<tr>
<td valign="middle" align="center" width="25%"><code>Byte 0</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 1</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 2</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00000000</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 4</code></td>
<td valign="middle" align="center"><code>Byte 5</code></td>
<td valign="middle" align="center"><code>Byte 6</code></td>
<td valign="middle" align="center"><code>Byte 7</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00000001</code></td>
</tr>
</table>
<table align="center" width="100%">
<tr>
<td align="center" colspan="4"> ... <br /> </td>
</tr>
</table>
<table border="1" align="center" width="100%">
<tr>
<td valign="middle" align="center" width="25%"><code>Byte 36</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 37</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 38</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 39</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code>00001010</code></td>
</tr>
</table>
</td></tr>
<tr>
<td valign="middle" align="left"> <br />d) String type ‘s4_tid’, size 25 bytes.</td>
</tr>
<tr><td>
<table border="1" align="center" width="100%">
<tr>
<td valign="middle" align="center" width="25%"><code>Byte 0</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 1</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 2</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>‘a’</code></td>
<td valign="middle" align="center"><code>‘b’</code></td>
<td valign="middle" align="center"><code>‘c’</code></td>
<td valign="middle" align="center"><code>‘d’</code></td>
</tr>
</table>
<table align="center" width="100%">
<tr>
<td align="center" colspan="4"> ... <br /> </td>
</tr>
</table>
<table border="1" align="center" width="100%">
<tr>
<td valign="middle" align="center" width="25%"><code>Byte 24</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 25</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 26</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 27</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>00000000</code></td>
<td valign="middle" align="center"><code> </code></td>
<td valign="middle" align="center"><code> </code></td>
<td valign="middle" align="center"><code> </code></td>
</tr>
</table>
</td></tr>
</table>
</td></tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 20. The storage layout for the
four member datatypes<!-- formerly Figure 49 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig50.JPG" width="550">
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 21. The storage layout of the combined four members
<!-- formerly Figure 50 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/></td>
</tr>
<tr align="center">
<td align="center"><img src="Images/Dtypes_fig51.JPG"
width="550"></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 22. The layout of the dataset
<!-- formerly Figure 51 --></b>
<hr color="green" size="3"/></td>
</tr>
<!-- 9.1.10, the JPG above, Dtypes_fig51.jpg, spells Element incorrectly -->
<!-- 9.1.10, the section above has text and many examples and figures.
Should the text be interspersed with the examples and figures at some
point? -->
</table>
<br />
<!-- NEW PAGE -->
<h4>6.7.2. Analyzing and Navigating a Compound Datatype</h4>
<p>A complicated compound datatype can be analyzed piece by piece to
discover the exact storage layout. In the example above, the outer
datatype is analyzed to discover that it is a compound datatype with
four members. Each member is analyzed in turn to construct a complete
map of the storage layout.</p>
<p>The example below <!-- formerly Figure 52 -->shows an example of code
that partially analyzes a nested
compound datatype. The name and overall offset and size of the component
datatype is discovered, and then its type is analyzed depending on the
datatype class. Through this method, the complete storage layout can be
discovered.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
s1_tid = H5Dget_type(dataset);
if (H5Tget_class(s1_tid) == H5T_COMPOUND) {
printf(“COMPOUND DATATYPE {\n”);
sz = H5Tget_size(s1_tid);
nmemb = H5Tget_nmembers(s1_tid);
printf(“ %d bytes\n”,sz);
printf(“ %d members\n”,nmemb);
for (i =0; i < nmemb; i++) {
s2_tid = H5Tget_member_type(s1_tid, i);
if (H5Tget_class(s2_tid) == H5T_COMPOUND) {
/* recursively analyze the nested type. */
} else if (H5Tget_class(s2_tid) == H5T_ARRAY) {
sz2 = H5Tget_size(s2_tid);
printf(“ %s: NESTED ARRAY DATATYPE offset %d size %d {\n”,
H5Tget_member_name(s1_tid, i),
H5Tget_member_offset(s1_tid, i),
sz2);
H5Tget_array_dims(s2_tid, dim);
s3_tid = H5Tget_super(s2_tid);
/* Etc., analyze the base type of the array */
} else {
/* analyze a simple type */
printf(“ %s: type code %d offset %d size %d\n”,
H5Tget_member_name(s1_tid, i),
H5Tget_class(s2_tid),
H5Tget_member_offset(s1_tid, i),
H5Tget_size(s2_tid));
}
/* and so on. */</pre></td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 41. Analyzing a compound datatype and its members
<!-- formerly Figure 52--></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<SCRIPT language="JavaScript">
<!--
document.writeln ("
<a name="LCDtypeObj">
<div align=right>
<a href="#TOP"><font size="-1">(Top)</font></a>
</div>
</a>
");
-->
</SCRIPT>
<br />
<!-- NEW PAGE -->
<a name="LCDtypeObj">
<h3 class=pagebefore>6.8. Life Cycle of the Datatype Object</h3>
</a>
<p>Application programs access HDF5 datatypes through identifiers.
Identifiers are obtained by creating a new datatype or by copying
or opening an existing datatype. The identifier can be used until
it is closed or until the library shuts down. See items a and b in
the figure below. <!-- formerly Figure 53a,b --> By default, a
datatype is <em>transient</em>, and it disappears when it is closed. </p>
<p>When a dataset or attribute is created (<code>H5Dcreate</code> or
<code>H5Acreate</code>), its datatype is stored in the HDF5
file as part of the dataset or attribute object. See item c in
the figure below. Once an object created, its datatype cannot
be changed or deleted. The datatype can be accessed by calling
<code>H5Dget_type</code>, <code>H5Aget_type</code>,
<code>H5Tget_super</code>, or <code>H5Tget_member_type</code>.
See item d in the figure below. These calls return an identifier to a
<em>transient</em> copy of the datatype of the dataset or attribute
unless the datatype is a committed datatype. </p>
<p>Note that when an object is created, the stored datatype is a copy
of the transient datatype. If two objects are created with the same
datatype, the information is stored in each object with the same
effect as if two different datatypes were created and used. </p>
<p>A transient datatype can be stored using <code>H5Tcommit</code> in the
HDF5 file as an independent, named object, called a committed datatype.
Committed datatypes were formerly known as named datatypes.
See item e in the figure below. Subsequently, when a committed datatype
is opened with <code>H5Topen</code> (item f), or is obtained with
<code>H5Tget_type</code> or similar call (item k), the return
is an identifier to a transient copy of the stored datatype. The identifier
can be used in the same way as other datatype identifiers except that
the committed datatype cannot be modified. When a committed datatype is
copied with <code>H5Tcopy</code>, the return is a new, modifiable,
transient datatype object (item f). </p>
<p>When an object is created using a committed datatype (<code>H5Dcreate</code>,
<code>H5Acreate</code>), the stored datatype is used without copying
it to the object. See item j in the figure below. In this case, if
multiple objects are created using the same committed datatype, they
all share the exact same datatype object. This saves space and makes
clear that the datatype is shared. Note that a committed datatype can
be shared by objects within the same HDF5 file, but not by objects
in other files. For more information on copying committed datatypes to
other HDF5 files, see the
“Copying Committed Datatypes with H5Ocopy” topic in
the “<a href="17_Additional.html">Additional Resources</a>”
chapter.</p>
<p>A committed datatype can be deleted from the file by calling
<code>H5Ldelete</code> which replaces <code>H5Gunlink</code>.
See item i in the figure below. If one or more objects are still using the
datatype, the committed datatype cannot be accessed with <code>H5Topen</code>,
but will not be removed from the file until it is no longer used.
<code>H5Tget_type</code> and similar calls will return a transient
copy of the datatype.</p>
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig53.JPG">
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 23. Life cycle of a datatype
<!-- formerly Figure 53 --> </b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>Transient datatypes are initially modifiable. Note that
when a datatype is copied or when it is written to the file (when an
object is created) or the datatype is used to create a composite
datatype, a copy of the current state of the datatype is used. If
the datatype is then modified, the changes have no effect on
datasets, attributes, or datatypes that have already been created.
See the figure below.</p>
<p>A transient datatype can be made <em>read-only</em>
(<code>H5Tlock</code>). Note that the datatype is still transient,
and otherwise does not change. A datatype that is <em>immutable</em>
is <em>read-only</em> but cannot be closed except when the entire
library is closed. The predefined types such as
<code>H5T_NATIVE_INT</code> are <em>immutable transient</em> types.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig54.JPG">
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 24. Transient datatype states: modifiable, read-only, and
immutable <!-- formerly Figure 54 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>To create two or more datasets that share a common datatype,
first commit the datatype, and then use that datatype to create the
datasets. See the example below.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t t1 = ...some transient type...;
H5Tcommit (file, “shared_type”, t1, H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
hid_t dset1 = H5Dcreate (file, “dset1”, t1, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
hid_t dset2 = H5Dcreate (file, “dset2”, t1, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
hid_t dset1 = H5Dopen (file, “dset1”, H5P_DEFAULT);
hid_t t2 = H5Dget_type (dset1);
hid_t dset3 = H5Dcreate (file, “dset3”, t2, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
hid_t dset4 = H5Dcreate (file, “dset4”, t2, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 42. Create a shareable datatype
<!-- formerly Figure 55 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="2" align="left" valign="bottom">
<b>Table 23. Datatype APIs</b>
<!-- formerly Table 24 --></td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td width="50%"><b>Function</b></td>
<td width="50%"><b>Description</b></td>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>hid_t H5Topen (hid_t location, <br />const
char *name)</code></td>
<td>A committed datatype can be opened by
calling this function, which returns a datatype identifier. The
identifier should eventually be released by calling
<code>H5Tclose()</code> to release resources. The committed
datatype returned by this function is read-only or a negative
value is returned for failure. The location is either a file or
group identifier.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>herr_t H5Tcommit (hid_t location,
const char *name, hid_t type, H5P_DEFAULT, H5P_DEFAULT,
<br />H5P_DEFAULT)</code></td>
<td>A transient datatype (not immutable) can
be written to a file and turned into a committed datatype by calling this
function. The location is either a file or group identifier and when
combined with name refers to a new committed datatype.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td><code>htri_t H5Tcommitted
(hid_t type)</code></td>
<td>A type can be queried to determine
if it is a committed type or a transient type. If this function returns a
positive value then the type is committed. Datasets which return committed
datatypes with <code>H5Dget_type()</code> are able to share the
datatype with other datasets in the same file.</td>
</tr>
<tr><td colspan="2"><hr color="green" size="3" /></td></tr>
</table>
<br />
<SCRIPT language="JavaScript">
<!--
document.writeln ("
<a name="Dtransfer">
<div align=right>
<a href="#TOP"><font size="-1">(Top)</font></a>
</div>
</a>
");
-->
</SCRIPT>
<br />
<!-- NEW PAGE -->
<a name="Dtransfer">
<h3 class=pagebefore>6.9. Data Transfer: Datatype Conversion and Selection</h3>
</a>
<p>When data is transferred (write or read), the storage layout of the data
elements may be different. For example, an integer might be stored on disk
in big-endian byte order and read into memory with little-endian byte order.
In this case, each data element will be transformed by the HDF5 Library
during the data transfer.</p>
<p>The conversion of data elements is controlled by specifying the datatype
of
the source and specifying the intended datatype of the destination.
The storage format on disk is the datatype specified when the dataset
is created. The datatype of memory must be specified in the library call.</p>
<p>In order to be convertible, the datatype of the source and destination
must have the same datatype class (with the exception of enumeration
type). Thus, integers can be converted to other integers, and floats to
other floats, but integers cannot (yet) be converted to floats. For
each atomic datatype class, the possible conversions are defined. An
enumeration datatype can be converted to an integer or a
floating-point number datatype.</p>
<p>Basically, any datatype can be converted to another datatype of the same
datatype class. The HDF5 Library automatically converts all properties.
If the destination is too small to hold the source value then an overflow
or underflow exception occurs. If a handler is defined with the
<code>H5Pset_type_conv_cb</code> function,
<!-- editingComment
<span class="editingComment">[ [ [
(see Chapter??)
] ] ]</span>
-->
it will be called. Otherwise,
a default action will be performed. The table below <!-- formerly Table 25-->
summarizes the default actions.</p>
<table width="600" cellspacing="0" align="center" cellpadding="0">
<tr valign="bottom">
<td colspan="3" align="left" valign="bottom">
<b>Table 24. Default actions for datatype conversion exceptions</b>
<!-- formerly Table 25 --></td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
<tr valign="top">
<td><b>Datatype Class</b></td>
<td><b>Possible Exceptions</b></td>
<td><b>Default Action</b></td>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Integer</td>
<td>Size, offset, pad</td>
<td> </td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Float</td>
<td>Size, offset, pad, ebits</td>
<td> </td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>String</td>
<td>Size</td>
<td>Truncates, zero terminate if required.</td>
</tr>
<tr><td colspan="3"><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td>Enumeration</td>
<td>No field</td>
<td>All bits set</td>
</tr>
<tr><td colspan="3"><hr color="green" size="3" /></td></tr>
</table>
<br />
<p>For example, when reading data from a dataset, the source datatype is the
datatype set when the dataset was created, and the destination datatype is
the description of the storage layout in memory. The destination datatype
must be specified in
the <code>H5Dread</code> call. The example below <!-- formerly Figure 56 -->
shows an example of reading a dataset
of 32-bit integers. The figure <!-- formerly Figure 57 -->below the example
shows the data transformation
that is performed.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
/* Stored as H5T_STD_BE32 */
/* Use the native memory order in the destination */
mem_type_id = H5Tcopy(H5T_NATIVE_INT);
status = H5Dread(dataset_id, mem_type_id, mem_space_id,
file_space_id, xfer_plist_id, buf );</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 43. Specify the destination datatype
with <code>H5Dread</code><!-- formerly Figure 56 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table align="center" width="100%">
<tr><td>
<table align="left">
<tr>
<td align="left">Source Datatype: <code>H5T_STD_BE32</code></td>
</tr>
</table>
</td></tr>
<tr><td>
<table align="left" border="1" width="100%">
<tr>
<td valign="middle" align="center" width="25%"><code>Byte 0</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 1</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 2</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>aaaaaaaa</code></td>
<td valign="middle" align="center"><code>bbbbbbbb</code></td>
<td valign="middle" align="center"><code>cccccccc</code></td>
<td valign="middle" align="center"><code>dddddddd</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 4</code></td>
<td valign="middle" align="center"><code>Byte 5</code></td>
<td valign="middle" align="center"><code>Byte 6</code></td>
<td valign="middle" align="center"><code>Byte 7</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>wwwwwwww</code></td>
<td valign="middle" align="center"><code>xxxxxxxx</code></td>
<td valign="middle" align="center"><code>yyyyyyyy</code></td>
<td valign="middle" align="center"><code>zzzzzzzz</code></td>
</tr>
</table>
</td></tr>
<tr>
<td>. . . .</td>
</tr>
<tr><td>
<table align="center" width="100%">
<tr>
<td width="45%"> </td>
<td width="10%" align="center"><img src="Images/Dtypes_fig57_arrow.jpg"></td>
<td width="45%" align="left">Automatically byte swapped<br /> during the <code>H5Dread</code></td>
</tr>
</table>
</td></tr>
<tr><td>
<table align="left">
<tr>
<td align="left">Destination Datatype: <code>H5T_STD_LE32</code></td>
</tr>
</table>
</td></tr>
<tr><td>
<table align="left" border="1" width="100%">
<tr>
<td valign="middle" align="center" width="25%"><code>Byte 0</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 1</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 2</code></td>
<td valign="middle" align="center" width="25%"><code>Byte 3</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>bbbbbbbb</code></td>
<td valign="middle" align="center"><code>aaaaaaaa</code></td>
<td valign="middle" align="center"><code>dddddddd</code></td>
<td valign="middle" align="center"><code>cccccccc</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>Byte 4</code></td>
<td valign="middle" align="center"><code>Byte 5</code></td>
<td valign="middle" align="center"><code>Byte 6</code></td>
<td valign="middle" align="center"><code>Byte 7</code></td>
</tr>
<tr>
<td valign="middle" align="center"><code>xxxxxxxx</code></td>
<td valign="middle" align="center"><code>wwwwwwww</code></td>
<td valign="middle" align="center"><code>zzzzzzzz</code></td>
<td valign="middle" align="center"><code>yyyyyyyy</code></td>
</tr>
</table>
</td></tr>
<tr>
<td>. . . .</td>
</tr>
<tr><td>
</table>
</td></tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 25. Layout of a datatype conversion
<!-- formerly Figure 57 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>One thing to note in the example above <!-- formerly Figure 56 -->is the
use of the predefined native datatype <code>H5T_NATIVE_INT</code>.
Recall that in this example, the data was stored as a 4-bytes
in big-endian order. The application wants to read this data into an array
of integers in memory. Depending on the system, the storage layout of memory
might be either big or little-endian, so the data may need to be transformed
on some platforms and not on others. The <code>H5T_NATIVE_INT</code> type
is set by the HDF5 Library to be the correct type to describe the storage
layout of the memory on the system. Thus, the code in the example above
<!-- Figure 56 -->will work correctly on any platform, performing a
transformation when needed.</p>
<p>There are predefined native types for most atomic datatypes, and
these can be combined in composite datatypes. In general, the predefined
native datatypes should always be used for data stored in memory.</p>
<table align="center" width="300" >
<tr >
<td style="background-color:#E6F2E6">
<hr color="green" size="3"/>
<b>Storage Properties </b><br />
<p>Predefined native datatypes describe the storage properties
of memory.</p>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>For composite datatypes, the component atomic datatypes will be converted.
For a variable-length datatype, the source and destination must have
compatible base datatypes. For a fixed-size string datatype, the length
and padding of the strings will be converted. Variable-length strings
are converted as variable-length datatypes.</p>
<p>For an array datatype, the source and destination must have the same rank
and dimensions, and the base datatype must be compatible. For example an
array datatype of 4 x 3 32-bit big-endian integers can be transferred to an
array datatype of 4 x 3 little-endian integers, but not to a 3 x 4 array.</p>
<p>For an enumeration datatype, data elements are converted by matching the
symbol names of the source and destination datatype. The figure below
<!-- formerly Figure 58 -->shows an example
of how two enumerations with the same names and different values would be
converted. The value ‘2’ in the source dataset would be converted
to ‘0x0004’ in the destination.</p>
<p>If the source data stream contains values which are not in the domain of
the conversion map then an overflow exception is raised within the library.</p>
<table width="400" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<table border="0">
<tr>
<td width="%"> 0 </td>
<td width="%"> </td>
<td width="%">RED</td>
<td width="%"><img src="Images/Dtypes_fig58_arrow.jpg"></td>
<td align="right" width="%">RED</td>
<td width="%"> </td>
<td width="%"> 0x0001</td>
</tr>
<tr>
<td width="%"> 1 </td>
<td width="%"> </td>
<td width="%">GREEN </td>
<td width="%"><img src="Images/Dtypes_fig58_arrow.jpg"></td>
<td align="right" width="%"> GREEN</td>
<td width="%"> </td>
<td width="%"> 0x0002</td>
</tr>
<tr>
<td width="%"> 2 </td>
<td width="%"> </td>
<td width="%">BLUE</td>
<td width="%"><img src="Images/Dtypes_fig58_arrow.jpg"></td>
<td align="right" width="%">BLUE</td>
<td width="%"> </td>
<td width="%"> 0x0004</td>
</tr>
<tr>
<td width="%"> 3 </td>
<td width="%"> </td>
<td width="%">WHITE</td>
<td width="%"><img src="Images/Dtypes_fig58_arrow.jpg"></td>
<td align="right" width="%">WHITE</td>
<td width="%"> </td>
<td width="%"> 0x0008</td>
</tr>
<tr>
<td width="%"> 4 </td>
<td width="%"> </td>
<td width="%">BLACK </td>
<td width="%"><img src="Images/Dtypes_fig58_arrow.jpg"></td>
<td align="right" width="%"> BLACK</td>
<td width="%"> </td>
<td width="%"> 0x0010</td>
</tr>
</table>
</td></tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 26. An enum datatype conversion
<!-- formerly Figure 58 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The library also allows conversion from enumeration to a numeric
datatype. A numeric datatype is either an integer or a floating-point
number. This conversion can simplify the application program because
the base type for an enumeration datatype is an integer datatype. The
application program can read the data from a dataset of enumeration
datatype in file into a memory buffer of numeric datatype. And it can
write enumeration data from memory into a dataset of numeric datatype
in file, too. </p>
<p>For compound datatypes, each field of the source and destination
datatype is converted according to its type. The name of the fields
must be the same in the source and the destination in order for the
data to be converted. </p>
<p>The example below <!-- formerly Figure 59 -->shows the compound
datatypes shows sample code to create a
compound datatype with the fields aligned on word boundaries (s1_tid)
and with the fields packed (s2_tid). The former is suitable as a description
of the storage layout in memory, the latter would give a more compact store
on disk. These types can be used for transferring data, with
<code>s2_tid</code> used to create the dataset, and
<code>s1_tid</code> used as the memory datatype.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct s1_t {
int a;
char b;
double c;
} s1_t;
s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
H5Tinsert(s1_tid, “a_name”, HOFFSET(s1_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, “b_name”, HOFFSET(s1_t, b), H5T_NATIVE_CHAR);
H5Tinsert(s1_tid, “c_name”, HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE);
s2_tid = H5Tcopy(s1_tid);
H5Tpack(s2_tid);</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 44. Create an aligned and packed compound datatype
<!-- formerly Figure 59 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>When the data is transferred, the fields within each data element will be
aligned according to the datatype specification. The figure below
<!-- formerly Figure 60 -->shows how one data
element would be aligned in memory and on disk. Note that the size and byte
order of the elements might also be converted during the transfer.</p>
<p>It is also possible to transfer some of the fields of compound datatypes.
Based on the example above, <!-- formerly Figure 59 --> the example below
<!-- formerly Figure 61 -->shows a compound datatype
that selects the first and third fields of the <code>s1_tid</code>.
The second datatype can be used as the memory datatype, in which case data
is read from or written to these two fields, while skipping the middle field.
The second figure below <!-- formerly Figure 62 -->shows the layout for
two data elements.</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig60.JPG" width="550">
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 27. Alignment of a compound datatype
<!-- formerly Figure 60 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
typedef struct s1_t {
int a;
char b;
double c;
} s1_t;
typedef struct s2_t { /* two fields from s1_t */
int a;
double c;
} s2_t;
s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
H5Tinsert(s1_tid, “a_name”, HOFFSET(s1_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, “b_name”, HOFFSET(s1_t, b), H5T_NATIVE_CHAR);
H5Tinsert(s1_tid, “c_name”, HOFFSET(s1_t, c), H5T_NATIVE_DOUBLE);
s2_tid = H5Tcreate (H5T_COMPOUND, sizeof(s2_t));
H5Tinsert(s1_tid, “a_name”, HOFFSET(s2_t, a), H5T_NATIVE_INT);
H5Tinsert(s1_tid, “c_name”, HOFFSET(s2_t, c), H5T_NATIVE_DOUBLE);
</pre> </td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 45. Transfer some fields of a compound datatype
<!-- formerly Figure 61 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<br />
<!-- NEW PAGE -->
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="center">
<hr color="green" size="3"/>
<img src="Images/Dtypes_fig62.JPG" width="550">
</td>
</tr>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left" >
<b>Figure 28. Layout when an element is skipped
<!-- formerly Figure 62 --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<!-- NEW PAGE -->
<a name="TextDescriptions">
<h3 class=pagebefore>6.10. Text Descriptions of Datatypes: Conversion to
and from</h3></a>
<p>HDF5 provides a means for generating a portable and human-readable
text descripition of a datatype and
for generating a datatype from such a text description.
This capability is particularly useful
for creating complex datatypes in a single step,
for creating a text description of a datatype for debugging purposes,
and for creating a portable datatype definition that can then be used
to recreate the datatype on many platforms or in other applications.</p>
<p>These tasks are handled by two functions provided in the HDF5 high-level
library (<a href="../HL/RM_H5LT.html" target="ExtWin">H5HL</a>):</p>
<div align="left">
<table >
<tr valign="top" align="left">
<td><span class="codeText">H5LTtext_to_dtype</span> </td>
<td>Creates an HDF5 datatype in a single step.</td>
</tr><tr valign="top" align="left">
<td><span class="codeText">H5LTdtype_to_text</span></td>
<td>Translates an HDF5 datatype into a text description.</td>
</tr>
</table>
</div>
<p>Note that this functionality requires that the
HDF5 High-Level Library (H5LT) be installed.
<!-- editingComment
See
<span class="editingComment">< < Quick Start > ></span>.
-->
<p>While <span class="codeText">H5LTtext_to_dtype</span> can be used to
generate any sort of datatype, it is particularly useful for
complex datatypes. </p>
<p><span class="codeText">H5LTdtype_to_text</span> is most likely to be
used in two sorts of situations:
when a datatype must be closely examined for debugging purpose
or to create a portable text description of the datatype
that can then be used to recreate the datatype on other platforms
or in other applications.</p>
<p>These two functions work for all valid HDF5 datatypes
except time, bitfield, and reference datatypes.</p>
<p>The currently supported text format used by
<span class="codeText">H5LTtext_to_dtype</span> and
<span class="codeText">H5LTdtype_to_text</span> is the
data description language (DDL) and conforms to the
<a href="../ddl.html" target="ExtWin"><cite>HDF5 DDL</cite></a>.
The portion of the <cite>HDF5 DDL</cite> that defines HDF5 datatypes
appears below.
</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
<datatype> ::= <atomic_type> | <compound_type> | <array_type> |
<variable_length_type>
<atomic_type> ::= <integer> | <float> | <time> | <string> |
<bitfield> | <opaque> | <reference> | <enum>
<integer> ::= H5T_STD_I8BE | H5T_STD_I8LE |
H5T_STD_I16BE | H5T_STD_I16LE |
H5T_STD_I32BE | H5T_STD_I32LE |
H5T_STD_I64BE | H5T_STD_I64LE |
H5T_STD_U8BE | H5T_STD_U8LE |
H5T_STD_U16BE | H5T_STD_U16LE |
H5T_STD_U32BE | H5T_STD_U32LE |
H5T_STD_U64BE | H5T_STD_U64LE |
H5T_NATIVE_CHAR | H5T_NATIVE_UCHAR |
H5T_NATIVE_SHORT | H5T_NATIVE_USHORT |
H5T_NATIVE_INT | H5T_NATIVE_UINT |
H5T_NATIVE_LONG | H5T_NATIVE_ULONG |
H5T_NATIVE_LLONG | H5T_NATIVE_ULLONG
<float> ::= H5T_IEEE_F32BE | H5T_IEEE_F32LE |
H5T_IEEE_F64BE | H5T_IEEE_F64LE |
H5T_NATIVE_FLOAT | H5T_NATIVE_DOUBLE |
H5T_NATIVE_LDOUBLE
<time> ::= TBD
<string> ::= H5T_STRING { STRSIZE <strsize> ;
STRPAD <strpad> ;
CSET <cset> ;
CTYPE <ctype> ;}
<strsize> ::= <int_value> | H5T_VARIABLE
<strpad> ::= H5T_STR_NULLTERM | H5T_STR_NULLPAD | H5T_STR_SPACEPAD
<cset> ::= H5T_CSET_ASCII | H5T_CSET_UTF8
<ctype> ::= H5T_C_S1 | H5T_FORTRAN_S1
<bitfield> ::= TBD
<opaque> ::= H5T_OPAQUE { OPQ_SIZE <opq_size>;
OPQ_TAG <opq_tag>; }
opq_size ::= <int_value>
opq_tag ::= "<string>"
<reference> ::= Not supported
<compound_type> ::= H5T_COMPOUND { <member_type_def>+ }
<member_type_def> ::= <datatype> <field_name> <offset><font size=1.7>opt</font> ;
<field_name> ::= "<identifier>"
<offset> ::= : <int_value>
<variable_length_type> ::= H5T_VLEN { <datatype> }
<array_type> ::= H5T_ARRAY { <dim_sizes> <datatype> }
<dim_sizes> ::= [<dimsize>] | [<dimsize>] <dim_sizes>
<dimsize> ::= <int_value>
<enum> ::= H5T_ENUM { <enum_base_type>; <enum_def>+ }
<enum_base_type> ::= <integer>
// Currently enums can only hold integer type data, but they may be
//expanded in the future to hold any datatype
<enum_def> ::= <enum_symbol> <enum_val>;
<enum_symbol> ::= "<identifier>"
<enum_val> ::= <int_value>
</pre>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 46. The definition of HDF5 datatypes from the
<!-- formerly Figure 63: -->
<a href="../ddl.html" target="ExtWin"><cite>HDF5 DDL</cite></a></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The definitions of opaque and compound datatype above are
revised for HDF5 Release 1.8. In Release 1.6.5. and earlier,
they were were defined as follows:
</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
<opaque> ::= H5T_OPAQUE { <identifier> }
<compound_type> ::= H5T_COMPOUND { <member_type_def>+ }
<member_type_def> ::= <datatype> <field_name> ;
<field_name> ::= <identifier></pre>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 47.
<!-- formerly Figure 64: -->
Old definitions of the opaque and compound datatypes</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<h4><em>Examples</em></h4>
<p>The code sample below illustrates the use of
<span class="codeText">H5LTtext_to_dtype</span> to generate a
variable-length string datatype.
</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t dtype;
if((dtype = H5LTtext_to_dtype(“H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLPAD;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
}”, H5LT_DDL))<0)
goto out;</pre>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 48. Creating a variable-length string datatype from
a text description<!-- formerly Figure 65: --></b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
<p>The code sample below illustrates the use of
<span class="codeText">H5LTtext_to_dtype</span> to generate a
complex array datatype.
</p>
<table width="600" cellspacing="0" align="center">
<tr valign="top">
<td align="left">
<hr color="green" size="3"/>
<pre>
hid_t dtype;
if((dtype = H5LTtext_to_dtype(“H5T_ARRAY { [5][7][13] H5T_ARRAY
{ [17][19] H5T_COMPOUND
{
H5T_STD_I8BE
\“arr_compound_1\”;
H5T_STD_I32BE
\“arr_compound_2\”;
}
}
}”, H5LT_DDL))<0)
goto out;</pre>
<tr><td><hr color="green" size="1" /></td></tr>
<tr valign="top">
<td align="left">
<b>Example 49. <!-- formerly Figure 66: -->
Creating a complex array datatype from a text description</b>
<hr color="green" size="3"/></td>
</tr>
</table>
<br />
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