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<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
<html>
<head>
<title>Datatype Interface (H5T)</title>
</head>
<body bgcolor="#FFFFFF">
<hr>
<center>
<table border=0 width=98%>
<tr><td valign=top align=left>
<a href="H5.intro.html">Introduction to HDF5</a>&nbsp;<br>
<a href="RM_H5Front.html">HDF5 Reference Manual</a>&nbsp;<br>
<a href="index.html">Other HDF5 documents and links</a>&nbsp;<br>
<!--
<a href="Glossary.html">Glossary</a><br>
-->
</td>
<td valign=top align=right>
And in this document, the
<a href="H5.user.html"><strong>HDF5 User's Guide:</strong></a>&nbsp;&nbsp;&nbsp;&nbsp;
<br>
<a href="Files.html">Files</a>&nbsp;&nbsp;
<a href="Datasets.html">Datasets</a>&nbsp;&nbsp;
Datatypes&nbsp;&nbsp;
<a href="Dataspaces.html">Dataspaces</a>&nbsp;&nbsp;
<a href="Groups.html">Groups</a>&nbsp;&nbsp;
<br>
<a href="References.html">References</a>&nbsp;&nbsp;
<a href="Attributes.html">Attributes</a>&nbsp;&nbsp;
<a href="Properties.html">Property Lists</a>&nbsp;&nbsp;
<a href="Errors.html">Error Handling</a>&nbsp;&nbsp;
<br>
<a href="Filters.html">Filters</a>&nbsp;&nbsp;
<a href="Caching.html">Caching</a>&nbsp;&nbsp;
<a href="Chunking.html">Chunking</a>&nbsp;&nbsp;
<a href="MountingFiles.html">Mounting Files</a>&nbsp;&nbsp;
<br>
<a href="Performance.html">Performance</a>&nbsp;&nbsp;
<a href="Debugging.html">Debugging</a>&nbsp;&nbsp;
<a href="Environment.html">Environment</a>&nbsp;&nbsp;
<a href="ddl.html">DDL</a>&nbsp;&nbsp;
</td></tr>
</table>
</center>
<hr>
<h1>The Datatype Interface (H5T)</h1>
<h2>1. Introduction</h2>
<p>The datatype interface provides a mechanism to describe the
storage format of individual data points of a data set and is
hopefully designed in such a way as to allow new features to be
easily added without disrupting applications that use the
datatype interface. A dataset (the H5D interface) is composed of a
collection or raw data points of homogeneous type organized
according to the data space (the H5S interface).
<p>A datatype is a collection of datatype properties, all of
which can be stored on disk, and which when taken as a whole,
provide complete information for data conversion to or from that
datatype. The interface provides functions to set and query
properties of a datatype.
<p>A <em>data point</em> is an instance of a <em>datatype</em>,
which is an instance of a <em>type class</em>. We have defined
a set of type classes and properties which can be extended at a
later time. The atomic type classes are those which describe
types which cannot be decomposed at the datatype interface
level; all other classes are compound.
<h2>2. General Datatype Operations</h2>
<p>The functions defined in this section operate on datatypes as
a whole. 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> Datatypes come in two flavors: named datatypes and transient
datatypes. A named datatype is stored in a file while the
transient flavor is independent of any file. Named datatypes
are always read-only, but transient types come in three
varieties: modifiable, read-only, and immutable. The difference
between read-only and immutable types is that immutable types
cannot be closed except when the entire library is closed (the
predefined types like <code>H5T_NATIVE_INT</code> are immutable
transient types).
<dl>
<dt><code>hid_t H5Tcreate (H5T_class_t <em>class</em>, size_t
<em>size</em>)</code>
<dd> Datatypes can be created by calling this
function, where <em>class</em> is a datatype class
identifier. However, the only class currently allowed is
<code>H5T_COMPOUND</code> to create a new empty compound
datatype where <em>size</em> is the total size in bytes of an
instance of this datatype. Other datatypes are created with
<code>H5Tcopy()</code>. All functions that return datatype
identifiers return a negative value for failure.
<br><br>
<dt><code>hid_t H5Topen (hid_t <em>location</em>, const char
*<em>name</em>)</code>
<dd>A named 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 named datatype returned by this
function is read-only or a negative value is returned for
failure. The <em>location</em> is either a file or group
identifier.
<br><br>
<dt><code>herr_t H5Tcommit (hid_t <em>location</em>, const char
*<em>name</em>, hid_t <em>type</em>)</code>
<dd>A transient datatype (not immutable) can be committed to a
file and turned into a named datatype by calling this
function. The <em>location</em> is either a file or group
identifier and when combined with <em>name</em> refers to a new
named datatype.
<br><br>
<dt><code>htri_t H5Tcommitted (hid_t <em>type</em>)</code>
<dd>A type can be queried to determine if it is a named type or
a transient type. If this function returns a positive value
then the type is named (that is, it has been committed perhaps
by some other application). Datasets which return committed
datatypes with <code>H5Dget_type()</code> are able to share
the datatype with other datasets in the same file.
<br><br>
<dt><code>hid_t H5Tcopy (hid_t <em>type</em>)</code>
<dd>This function returns a modifiable transient datatype
which is a copy of <em>type</em> or a negative value for
failure. If <em>type</em> is a dataset identifier then the type
returned is a modifiable transient copy of the datatype of
the specified dataset.
<br><br>
<dt><code>herr_t H5Tclose (hid_t <em>type</em>)</code>
<dd>Releases resources associated with a datatype. The
datatype identifier should not be subsequently used since the
results would be unpredictable. It is illegal to close an
immutable transient datatype.
<br><br>
<dt><code>htri_t H5Tequal (hid_t <em>type1</em>, hid_t
<em>type2</em>)</code>
<dd>Determines if two types are equal. If <em>type1</em> and
<em>type2</em> are the same then this function returns
<code>TRUE</code>, otherwise it returns <code>FALSE</code> (an
error results in a negative return value).
<br><br>
<dt><code>herr_t H5Tlock (hid_t <em>type</em>)</code>
<dd>A transient datatype can be locked, making it immutable
(read-only and not closable). The library does this to all
predefined types to prevent the application from inadvertently
modifying or deleting (closing) them, but the application is
also allowed to do this for its own datatypes. Immutable
datatypes are closed when the library closes (either by
<code>H5close()</code> or by normal program termination).
</dl>
<h2>3. Properties of Atomic Types</h2>
<p>An atomic type is a type which cannot be decomposed into
smaller units at the API level. All atomic types have a common
set of properties which are augmented by properties specific to
a particular type class. Some of these properties also apply to
compound datatypes, but we discuss them only as they apply to
atomic datatypes here. The properties and the functions that
query and set their values are:
<dl>
<dt><code>H5T_class_t H5Tget_class (hid_t <em>type</em>)</code>
<dd>This property holds one of the class names:
<code>H5T_INTEGER, H5T_FLOAT, H5T_TIME, H5T_STRING, or
H5T_BITFIELD</code>. This property is read-only and is set
when the datatype is created or copied (see
<code>H5Tcreate()</code>, <code>H5Tcopy()</code>). If this
function fails it returns <code>H5T_NO_CLASS</code> which has
a negative value (all other class constants are non-negative).
<br><br>
<dt><code>size_t H5Tget_size (hid_t <em>type</em>)</code>
<dt><code>herr_t H5Tset_size (hid_t <em>type</em>, size_t
<em>size</em>)</code>
<dd>This property is total size of the datum in bytes, including
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 <code>offset</code> 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 <code>precision</code> 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. Adjusting the
size of an <code>H5T_STRING</code> automatically adjusts the
precision as well. On error, <code>H5Tget_size()</code>
returns zero which is never a valid size.
<br><br>
<dt><code>H5T_order_t H5Tget_order (hid_t <em>type</em>)</code>
<dt><code>herr_t H5Tset_order (hid_t <em>type</em>, H5T_order_t
<em>order</em>)</code>
<dd>All atomic datatypes have a byte order which describes how
the bytes of the datatype are layed out in memory. If the
lowest memory address contains the least significant byte of
the datum then it is said to be <em>little-endian</em> or
<code>H5T_ORDER_LE</code>. If the bytes are in the oposite
order then they are said to be <em>big-endian</em> or
<code>H5T_ORDER_BE</code>. Some datatypes have the same byte
order on all machines and are <code>H5T_ORDER_NONE</code>
(like character strings). If <code>H5Tget_order()</code>
fails then it returns <code>H5T_ORDER_ERROR</code> which is a
negative value (all successful return values are
non-negative).
<br><br>
<dt><code>size_t H5Tget_precision (hid_t <em>type</em>)</code>
<dt><code>herr_t H5Tset_precision (hid_t <em>type</em>, size_t
<em>precision</em>)</code>
<dd>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. 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. The
<code>size</code> 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 <code>offset</code> property is
decremented a bit at a time. If the <code>offset</code>
reaches zero and the significant bits still hang over the
edge, then the total size is increased a byte at a time. The
precision of an <code>H5T_STRING</code> is read-only and is
always eight times the value returned by
<code>H5Tget_size()</code>. <code>H5Tget_precision()</code>
returns zero on failure since zero is never a valid precision.
<br><br>
<dt><code>size_t H5Tget_offset (hid_t <em>type</em>)</code>
<dt><code>herr_t H5Tset_offset (hid_t <em>type</em>, size_t
<em>offset</em>)</code>
<dd>While the <code>precision</code> property defines the number
of significant bits, the <code>offset</code> property defines
the location of those bits within the entire datum. 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. The
offset is a read-only property of an <code>H5T_STRING</code>
and is always zero. <code>H5Tget_offset()</code> returns zero
on failure which is also a valid offset, but is guaranteed to
succeed if a call to <code>H5Tget_precision()</code> succeeds
with the same arguments.
<br><br>
<dt><code>herr_t H5Tget_pad (hid_t <em>type</em>, H5T_pad_t
*<em>lsb</em>, H5T_pad_t *<em>msb</em>)</code>
<dt><code>herr_t H5Tset_pad (hid_t <em>type</em>, H5T_pad_t
<em>lsb</em>, H5T_pad_t <em>msb</em>)</code>
<dd>The bits of a datum which are not significant as defined by
the <code>precision</code> and <code>offset</code> properties
are called <em>padding</em>. Padding falls into two
categories: padding in the low-numbered bits is <em>lsb</em>
padding and padding in the high-numbered bits is <em>msb</em>
padding (bits are numbered according to the description for
the <code>offset</code> property). Padding bits can always be
set to zero (<code>H5T_PAD_ZERO</code>) or always set to one
(<code>H5T_PAD_ONE</code>). The current pad types are returned
through arguments of <code>H5Tget_pad()</code> either of which
may be null pointers.
</dl>
<h3>3.1. Properties of Integer Atomic Types</h3>
<p>Integer atomic types (<code>class=H5T_INTEGER</code>)
describe integer number formats. Such types include the
following information which describes the type completely and
allows conversion between various integer atomic types.
<dl>
<dt><code>H5T_sign_t H5Tget_sign (hid_t <em>type</em>)</code>
<dt><code>herr_t H5Tset_sign (hid_t <em>type</em>, H5T_sign_t
<em>sign</em>)</code>
<dd>Integer data can be signed two's complement
(<code>H5T_SGN_2</code>) or unsigned
(<code>H5T_SGN_NONE</code>). Whether data is signed or not
becomes important when converting between two integer
datatypes of differing sizes as it determines how values are
truncated and sign extended.
</dl>
<h3>3.2. Properties of Floating-point Atomic Types</h3>
<p>The library supports floating-point atomic types
(<code>class=H5T_FLOAT</code>) as long as the bits of the
exponent are contiguous and stored as a biased positive number,
the bits of the mantissa are contiguous and stored as a positive
magnitude, and a sign bit exists which is set for negative
values. Properties specific to floating-point types are:
<dl>
<dt><code>herr_t H5Tget_fields (hid_t <em>type</em>, size_t
*<em>spos</em>, size_t *<em>epos</em>, size_t
*<em>esize</em>, size_t *<em>mpos</em>, size_t
*<em>msize</em>)</code>
<dt><code>herr_t H5Tset_fields (hid_t <em>type</em>, size_t
<em>spos</em>, size_t <em>epos</em>, size_t <em>esize</em>,
size_t <em>mpos</em>, size_t <em>msize</em>)</code>
<dd>A floating-point datum 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 bit
positions are numbered beginning at zero at the beginning of
the significant part of the datum (see the descriptions of the
<code>precision</code> and <code>offset</code>
properties). 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.
<br><br>
<dt><code>size_t H5Tget_ebias (hid_t <em>type</em>)</code>
<dt><code>herr_t H5Tset_ebias (hid_t <em>type</em>, size_t
<em>ebias</em>)</code>
<dd>The exponent is stored as a non-negative value which is
<code>ebias</code> larger than the true exponent.
<code>H5Tget_ebias()</code> returns zero on failure which is
also a valid exponent bias, but the function is guaranteed to
succeed if <code>H5Tget_precision()</code> succeeds when
called with the same arguments.
<br><br>
<dt><code>H5T_norm_t H5Tget_norm (hid_t <em>type</em>)</code>
<dt><code>herr_t H5Tset_norm (hid_t <em>type</em>, H5T_norm_t
<em>norm</em>)</code>
<dd>This property determines the normalization method of the
mantissa.
<ul>
<li>If the value is <code>H5T_NORM_MSBSET</code> then 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>If its value is <code>H5T_NORM_IMPLIED</code> then 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>If its value is <code>H5T_NORM_NONE</code> then the fractional
part of the mantissa is stored without normalizing it.
</ul>
<br><br>
<dt><code>H5T_pad_t H5Tget_inpad (hid_t <em>type</em>)</code>
<dt><code>herr_t H5Tset_inpad (hid_t <em>type</em>, H5T_pad_t
<em>inpad</em>)</code>
<dd>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 <em>inpad</em>
argument can be <code>H5T_PAD_ZERO</code> if the internal
padding should always be set to zero, or <code>H5T_PAD_ONE</code>
if it should always be set to one.
<code>H5Tget_inpad()</code> returns <code>H5T_PAD_ERROR</code>
on failure which is a negative value (successful return is
always non-negative).
</dl>
<h3>3.3. Properties of Date and Time Atomic Types</h3>
<p>Dates and times (<code>class=H5T_TIME</code>) are stored as
character strings in one of the ISO-8601 formats like
"<em>1997-12-05 16:25:30</em>"; as character strings using the
Unix asctime(3) format like "<em>Thu Dec 05 16:25:30 1997</em>";
as an integer value by juxtaposition of the year, month, and
day-of-month, hour, minute and second in decimal like
<em>19971205162530</em>; as an integer value in Unix time(2)
format; or other variations.
<h3>3.4. Properties of Character String Atomic Types</h3>
<p>Fixed-length character string types are used to store textual
information. The <code>offset</code> property of a string is
always zero and the <code>precision</code> property is eight
times as large as the value returned by
<code>H5Tget_size()</code> (since precision is measured in bits
while size is measured in bytes). Both properties are
read-only.
<dl>
<dt><code>H5T_cset_t H5Tget_cset (hid_t <em>type</em>)</code>
<dt><code>herr_t H5Tset_cset (hid_t <em>type</em>, H5T_cset_t
<em>cset</em>)</code>
<dd>HDF5 is able to distinguish between character sets of
different nationalities and to convert between them to the
extent possible. The only character set currently supported
is <code>H5T_CSET_ASCII</code>.
<br><br>
<dt><code>H5T_str_t H5Tget_strpad (hid_t <em>type</em>)</code>
<dt><code>herr_t H5Tset_strpad (hid_t <em>type</em>, H5T_str_t
<em>strpad</em>)</code>
<dd>The method used to store character strings differs with the
programming language: C usually null terminates strings while
Fortran left-justifies and space-pads strings. This property
defines the storage mechanism and can be
<p>
<dl>
<dt><code>H5T_STR_NULLTERM</code>
<dd>A C-style string which is guaranteed to be null
terminated. When converting from a longer string the
value will be truncated and then a null character
appended.
<br><br>
<dt><code>H5T_STR_NULLPAD</code>
<dd>A C-style string which is padded with null characters
but not necessarily null terminated. Conversion from a
long string to a shorter <code>H5T_STR_NULLPAD</code>
string will truncate but not null terminate. Conversion
from a short value to a longer value will append null
characters as with <code>H5T_STR_NULLTERM</code>.
<br><br>
<dt><code>H5T_STR_SPACEPAD</code>
<dd>A Fortran-style string which is padded with space
characters. This is the same as
<code>H5T_STR_NULLPAD</code> except the padding character
is a space instead of a null.
</dl>
<p><code>H5Tget_strpad()</code> returns
<code>H5T_STR_ERROR</code> on failure, a negative value (all
successful return values are non-negative).
</dl>
<h3>3.5. Properties of Bit Field Atomic Types</h3>
<p>Converting a bit field (<code>class=H5T_BITFIELD</code>) from
one type to another simply copies the significant bits. If the
destination is smaller than the source then bits are truncated.
Otherwise new bits are filled according to the <code>msb</code>
padding type.
<h3>3.6. Character and String Datatype Issues</h3>
The <code>H5T_NATIVE_CHAR</code> and <code>H5T_NATIVE_UCHAR</code>
datatypes are actually numeric data (1-byte integers). If the
application wishes to store character data, then an HDF5
<em>string</em> datatype should be derived from
<code>H5T_C_S1</code> instead.
<h4>Motivation</h4>
HDF5 defines at least three classes of datatypes:
integer data, floating point data, and character data.
However, the C language defines only integer and
floating point datatypes; character data in C is
overloaded on the 8- or 16-bit integer types and
character strings are overloaded on arrays of those
integer types which, by convention, are terminated with
a zero element.
In C, the variable <code>unsigned char s[256]</code> is
either an array of numeric data, a single character string
with at most 255 characters, or an array of 256 characters,
depending entirely on usage. For uniformity with the
other <code>H5T_NATIVE_</code> types, HDF5 uses the
numeric interpretation of <code>H5T_NATIVE_CHAR</code>
and <code>H5T_NATIVE_UCHAR</code>.
<h4>Usage</h4>
To store <code>unsigned char s[256]</code> data as an
array of integer values, use the HDF5 datatype
<code>H5T_NATIVE_UCHAR</code> and a data space that
describes the 256-element array. Some other application
that reads the data will then be able to read, say, a
256-element array of 2-byte integers and HDF5 will
perform the numeric translation.
To store <code>unsigned char s[256]</code> data as a
character string, derive a fixed length string datatype
from <code>H5T_C_S1</code> by increasing its size to
256 characters. Some other application that reads the
data will be able to read, say, a space padded string
of 16-bit characters and HDF5 will perform the character
and padding translations.
<pre>
hid_t s256 = H5Tcopy(H5T_C_S1);
H5Tset_size(s256, 256);
</pre>
To store <code>unsigned char s[256]</code> data as
an array of 256 ASCII characters, use an
HDF5 data space to describe the array and derive a
one-character string type from <code>H5T_C_S1</code>.
Some other application will be able to read a subset
of the array as 16-bit characters and HDF5 will
perform the character translations.
The <code>H5T_STR_NULLPAD</code> is necessary because
if <code>H5T_STR_NULLTERM</code> were used
(the default) then the single character of storage
would be for the null terminator and no useful data
would actually be stored (unless the length were
incremented to more than one character).
<pre>
hid_t s1 = H5Tcopy(H5T_C_S1);
H5Tset_strpad(s1, H5T_STR_NULLPAD);
</pre>
<h4>Summary</h4>
The C language uses the term <code>char</code> to
represent one-byte numeric data and does not make
character strings a first-class datatype.
HDF5 makes a distinction between integer and
character data and maps the C <code>signed char</code>
(<code>H5T_NATIVE_CHAR</code>) and
<code>unsigned char</code> (<code>H5T_NATIVE_UCHAR</code>)
datatypes to the HDF5 integer type class.
<h2>4. Properties of Opaque Types</h2>
<p>Opaque types (<code>class=H5T_OPAQUE</code>) provide the
application with a mechanism for describing data which cannot be
otherwise described by HDF5. The only properties associated with
opaque types are a size in bytes and an ASCII tag which is
manipulated with <code>H5Tset_tag()</code> and
<code>H5Tget_tag()</code> functions. The library contains no
predefined conversion functions but the application is free to
register conversions between any two opaque types or between an
opaque type and some other type.
<h2>5. Properties of Compound Types</h2>
<p>A compound datatype is similar to a <code>struct</code> in C
or a common block in Fortran: it is a collection of one or more
atomic types or small arrays of such types. Each
<em>member</em> of a compound type has a name which is unique
within that type, and a byte offset that determines the first
byte (smallest byte address) of that member in a compound datum.
A compound datatype has the following properties:
<dl>
<dt><code>H5T_class_t H5Tget_class (hid_t <em>type</em>)</code>
<dd>All compound datatypes belong to the type class
<code>H5T_COMPOUND</code>. This property is read-only and is
defined when a datatype is created or copied (see
<code>H5Tcreate()</code> or <code>H5Tcopy()</code>).
<br><br>
<dt><code>size_t H5Tget_size (hid_t <em>type</em>)</code>
<dd>Compound datatypes have a total size in bytes which is
returned by this function. All members of a compound
datatype must exist within this size. A value of zero is returned
for failure; all successful return values are positive.
<br><br>
<dt><code>int H5Tget_nmembers (hid_t <em>type</em>)</code>
<dd>A compound datatype consists of zero or more members
(defined in any order) with unique names and which occupy
non-overlapping regions within the datum. In the functions
that follow, individual members are referenced by an index
number between zero and <em>N</em>-1, inclusive, where
<em>N</em> is the value returned by this function.
<code>H5Tget_nmembers()</code> returns -1 on failure.
<br><br>
<dt><code>char *H5Tget_member_name (hid_t <em>type</em>, int
<em>membno</em>)</code>
<dd>Each member has a name which is unique among its siblings in
a compound datatype. This function returns a pointer to a
null-terminated copy of the name allocated with
<code>malloc()</code> or the null pointer on failure. The
caller is responsible for freeing the memory returned by this
function.
<br><br>
<dt><code>size_t H5Tget_member_offset (hid_t <em>type</em>, int
<em>membno</em>)</code>
<dd>The byte offset of member number <em>membno</em> with
respect to the beginning of the containing compound datum is
returned by this function. A zero is returned on failure
which is also a valid offset, but this function is guaranteed
to succeed if a call to <code>H5Tget_member_class()</code>
succeeds when called with the same <em>type</em> and
<em>membno</em> arguments.
<br><br>
<dt><code>hid_t H5Tget_member_type (hid_t <em>type</em>, int
<em>membno</em>)</code>
<dd>Each member has its own datatype, a copy of which is
returned by this function. The returned datatype identifier
should be released by eventually calling
<code>H5Tclose()</code> on that type.
</dl>
<p>Properties of members of a compound datatype are
defined when the member is added to the compound type (see
<code>H5Tinsert()</code>) and cannot be subsequently modified.
This makes it imposible to define recursive data structures.
<a name="DTypes-PredefinedAtomic">
<h2>6. Predefined Atomic Datatypes</h2>
</a>
<p>The library predefines a modest number of datatypes having
names like <code>H5T_<em>arch</em>_<em>base</em></code> where
<em>arch</em> is an architecture name and <em>base</em> is a
programming type name. New types can be derived from the
predifined types by copying the predefined type (see
<code>H5Tcopy()</code>) and then modifying the result.
<p>
<center>
<table align=center width="80%">
<tr>
<th align=left width="20%">Architecture Name</th>
<th align=left width="80%">Description</th>
</tr>
<tr valign=top>
<td><code>IEEE</code></td>
<td>This architecture defines standard floating point
types in various byte orders.</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 valign=top>
<td><code>UNIX</code></td>
<td>Types which are specific to Unix operating systems are
defined in this architecture. The only type currently
defined is the Unix date and time types
(<code>time_t</code>).</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_STRING</code>
defines a base string type with null termination which
can be used to derive string types of other
lengths.</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 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 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 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 valign=top>
<td><code>ALPHA</code></td>
<td>All DEC Alpha CPU's, little-endian systems with IEEE
floating-point.</td>
</tr>
</table>
</center>
<p>The base name of most types consists of a letter, a precision
in bits, and an indication of the byte order. The letters are:
<p>
<center>
<table border align=center width="40%">
<tr>
<td align=center width="30%">B</td>
<td width="70%">Bitfield</td>
</tr>
<tr>
<td align=center>D</td>
<td>Date and time</td>
</tr>
<tr>
<td align=center>F</td>
<td>Floating point</td>
</tr>
<tr>
<td align=center>I</td>
<td>Signed integer</td>
</tr>
<tr>
<td align=center>R</td>
<td>References</td>
</tr>
<tr>
<td align=center>S</td>
<td>Character string</td>
</tr>
<tr>
<td align=center>U</td>
<td>Unsigned integer</td>
</tr>
</table>
</center>
<p>The byte order is a two-letter sequence:
<p>
<center>
<table border align=center width="40%">
<tr>
<td align=center width="30%">BE</td>
<td width="70%">Big endian</td>
</tr>
<tr>
<td align=center>LE</td>
<td>Little endian</td>
</tr>
<tr>
<td align=center>VX</td>
<td>Vax order</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th align=left><br><br>Example</th>
<th align=left><br><br>Description</th>
</tr>
<tr valign=top>
<td><code>H5T_IEEE_F64LE</code></td>
<td>Eight-byte, little-endian, IEEE floating-point</td>
</tr>
<tr valign=top>
<td><code>H5T_IEEE_F32BE</code></td>
<td>Four-byte, big-endian, IEEE floating point</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 valign=top>
<td><code>H5T_STD_U16BE</code></td>
<td>Two-byte, big-endian, unsigned integer</td>
</tr>
<tr valign=top>
<td><code>H5T_UNIX_D32LE</code></td>
<td>Four-byte, little-endian, time_t</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 valign=top>
<td><code>H5T_INTEL_B64</code></td>
<td>Eight-byte bit field on an Intel CPU</td>
</tr>
<tr valign=top>
<td><code>H5T_CRAY_F64</code></td>
<td>Eight-byte Cray floating point</td>
</tr>
<tr valign=top>
<td><code>H5T_STD_ROBJ</code></td>
<td>Reference to an entire object in a file</td>
</tr>
</table>
</center>
<p>The <code>NATIVE</code> architecture has base names which don't
follow the same rules as the others. Instead, native type names
are similar to the C type names. Here are some examples:
<p>
<center>
<table align=center width="80%">
<tr>
<th align=left><br><br>Example</th>
<th align=left><br><br>Corresponding C Type</th>
</tr>
<tr>
<td><code>H5T_NATIVE_CHAR</code></td>
<td><code>char</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_SCHAR</code></td>
<td><code>signed char</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_UCHAR</code></td>
<td><code>unsigned char</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_SHORT</code></td>
<td><code>short</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_USHORT</code></td>
<td><code>unsigned short</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_INT</code></td>
<td><code>int</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_UINT</code></td>
<td><code>unsigned</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_LONG</code></td>
<td><code>long</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_ULONG</code></td>
<td><code>unsigned long</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_LLONG</code></td>
<td><code>long long</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_ULLONG</code></td>
<td><code>unsigned long long</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_FLOAT</code></td>
<td><code>float</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_DOUBLE</code></td>
<td><code>double</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_LDOUBLE</code></td>
<td><code>long double</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_HSIZE</code></td>
<td><code>hsize_t</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_HSSIZE</code></td>
<td><code>hssize_t</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_HERR</code></td>
<td><code>herr_t</code></td>
</tr>
<tr>
<td><code>H5T_NATIVE_HBOOL</code></td>
<td><code>hbool_t</code></td>
</tr>
</table>
</center>
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: A 128-bit
integer</h4></caption>
<tr>
<td>
<p>To create a 128-bit, little-endian signed integer
type one could use the following (increasing the
precision of a type automatically increases the total
size):
<p><code><pre>
hid_t new_type = H5Tcopy (H5T_NATIVE_INT);
H5Tset_precision (new_type, 128);
H5Tset_order (new_type, H5T_ORDER_LE);
</pre></code>
</td>
</tr>
</table>
</center>
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: An 80-character
string</h4></caption>
<tr>
<td>
<p>To create an 80-byte null terminated string type one
might do this (the offset of a character string is
always zero and the precision is adjusted
automatically to match the size):
<p><code><pre>
hid_t str80 = H5Tcopy (H5T_C_S1);
H5Tset_size (str80, 80);
</pre></code>
</td>
</tr>
</table>
</center>
<p>A complete list of the datatypes predefined in HDF5 can be found in
<a href="PredefDTypes.html"><cite>HDF5 Predefined Datatypes</cite></a>
in the <a href="RM_H5Front.html"><cite>HDF5 Reference Manual</cite></a>.
<h2>7. Defining Compound Datatypes</h2>
<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 it's total
size. Then members are added to the compound datatype in any
order.
<p>Usually a C struct will be defined to hold a data point in
memory, and the offsets of the members in memory will be the
offsets of the struct members from the beginning of an instance
of the struct.
<dl>
<dt><code>HOFFSET(s,m)</code>
<dd>This macro computes the offset of member <em>m</em> within
a struct <em>s</em>.
<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.
</dl>
<p>Each member 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, although this is often the case. Nor does one need to
define all members of the C struct in the HDF5 compound
datatype (or vice versa).
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: A simple struct</h4></caption>
<tr>
<td>
<p>An HDF5 datatype is created to describe complex
numbers whose type is defined by the
<code>complex_t</code> struct.
<p><code><pre>
typedef struct {
double re; /*real part*/
double im; /*imaginary part*/
} complex_t;
hid_t complex_id = H5Tcreate (H5T_COMPOUND, sizeof tmp);
H5Tinsert (complex_id, "real", HOFFSET(complex_t,re),
H5T_NATIVE_DOUBLE);
H5Tinsert (complex_id, "imaginary", HOFFSET(complex_t,im),
H5T_NATIVE_DOUBLE);
</pre></code>
</td>
</tr>
</table>
</center>
<p>Member alignment is handled by the <code>HOFFSET</code>
macro. 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>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: A packed struct</h4></caption>
<tr>
<td>
<p>This example shows how to create a disk version of a
compound datatype 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><code><pre>
hid_t complex_disk_id = H5Tcopy (complex_id);
H5Tpack (complex_disk_id);
</pre></code>
</td>
</tr>
</table>
</center>
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: A flattened struct</h4></caption>
<tr>
<td>
<p>Compound datatypes that have a compound datatype
member can be handled two ways. This example shows
that the compound datatype can be flattened,
resulting in a compound type with only atomic
members.
<p><code><pre>
typedef struct {
complex_t x;
complex_t y;
} surf_t;
hid_t surf_id = H5Tcreate (H5T_COMPOUND, sizeof tmp);
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);
</code></pre>
</td>
</tr>
</table>
</center>
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: A nested struct</h4></caption>
<tr>
<td>
<p>However, when the <code>complex_t</code> is used
often it becomes inconvenient to list its members over
and over again. So the alternative approach to
flattening is to define a compound datatype and then
use it as the type of the compound members, as is done
here (the typedefs are defined in the previous
examples).
<p><code><pre>
hid_t complex_id, surf_id; /*hdf5 datatypes*/
complex_id = H5Tcreate (H5T_COMPOUND, sizeof c);
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 s);
H5Tinsert (surf_id, "x", HOFFSET(surf_t,x), complex_id);
H5Tinsert (surf_id, "y", HOFFSET(surf_t,y), complex_id);
</code></pre>
</td>
</tr>
</table>
</center>
<a name="Datatypes_Enum">&nbsp;</a>
<h2>8. Enumeration Datatypes</h2>
<h3>8.1. Introduction</h3>
<p>An HDF enumeration datatype is a 1:1 mapping between a set of
symbols and a set of integer values, and an order is imposed on
the symbols by their integer values. The symbols are passed
between the application and library as character strings and all
the values for a particular enumeration type are of the same
integer type, which is not necessarily a native type.
<h3>8.2. Creation</h3>
<p>Creation of an enumeration datatype resembles creation of a
compound datatype: first an empty enumeration type is created,
then members are added to the type, then the type is optionally
locked.
<dl>
<dt><code>hid_t H5Tcreate(H5T_class_t <em>type_class</em>,
size_t <em>size</em>)</code>
<dd>This function creates a new empty enumeration datatype based
on a native signed integer type. The first argument is the
constant <code>H5T_ENUM</code> and the second argument is the
size in bytes of the native integer on which the enumeration
type is based. If the architecture does not support a native
signed integer of the specified size then an error is
returned.
<pre>
/* Based on a native signed short */
hid_t hdf_en_colors = H5Tcreate(H5T_ENUM, sizeof(short));</pre>
<dt><code>hid_t H5Tenum_create(hid_t <em>base</em>)</code>
<dd>This function creates a new empty enumeration datatype based
on some integer datatype <em>base</em> and is a
generalization of the <code>H5Tcreate()</code> function. This
function is useful when creating an enumeration type based on
some non-native integer datatype, but it can be used for
native types as well.
<pre>
/* Based on a native unsigned short */
hid_t hdf_en_colors_1 = H5Tenum_create(H5T_NATIVE_USHORT);
/* Based on a MIPS 16-bit unsigned integer */
hid_t hdf_en_colors_2 = H5Tenum_create(H5T_MIPS_UINT16);
/* Based on a big-endian 16-bit unsigned integer */
hid_t hdf_en_colors_3 = H5Tenum_create(H5T_STD_U16BE);</pre>
<dt><code>herr_t H5Tenum_insert(hid_t <em>etype</em>, const char
*<em>symbol</em>, void *<em>value</em>)</code>
<dd>Members are inserted into the enumeration datatype
<em>etype</em> with this function. Each member has a symbolic
name <em>symbol</em> and some integer representation
<em>value</em>. The <em>value</em> argument must point to a value
of the same datatype as specified when the enumeration type
was created. The order of member insertion is not important
but all symbol names and values must be unique within a
particular enumeration type.
<pre>
short val;
H5Tenum_insert(hdf_en_colors, "RED", (val=0,&amp;val));
H5Tenum_insert(hdf_en_colors, "GREEN", (val=1,&amp;val));
H5Tenum_insert(hdf_en_colors, "BLUE", (val=2,&amp;val));
H5Tenum_insert(hdf_en_colors, "WHITE", (val=3,&amp;val));
H5Tenum_insert(hdf_en_colors, "BLACK", (val=4,&amp;val));</pre>
<dt><code>herr_t H5Tlock(hid_t <em>etype</em>)</code>
<dd>This function locks a datatype so it cannot be modified or
freed unless the entire HDF5 library is closed. Its use is
completely optional but using it on an application datatype
makes that datatype act like a predefined datatype.
<pre>
H5Tlock(hdf_en_colors);</pre>
</dl>
<h3>8.3. Integer Operations</h3>
<p>Because an enumeration datatype is derived from an integer
datatype, any operation which can be performed on integer
datatypes can also be performed on enumeration datatypes. This
includes:
<p>
<center>
<table>
<tr>
<td><code>H5Topen()</code></td>
<td><code>H5Tcreate()</code></td>
<td><code>H5Tcopy()</code></td>
<td><code>H5Tclose()</code></td>
</tr><tr>
<td><code>H5Tequal()</code></td>
<td><code>H5Tlock()</code></td>
<td><code>H5Tcommit()</code></td>
<td><code>H5Tcommitted()</code></td>
</tr><tr>
<td><code>H5Tget_class()</code></td>
<td><code>H5Tget_size()</code></td>
<td><code>H5Tget_order()</code></td>
<td><code>H5Tget_pad()</code></td>
</tr><tr>
<td><code>H5Tget_precision()</code></td>
<td><code>H5Tget_offset()</code></td>
<td><code>H5Tget_sign()</code></td>
<td><code>H5Tset_size()</code></td>
</tr><tr>
<td><code>H5Tset_order()</code></td>
<td><code>H5Tset_precision()</code></td>
<td><code>H5Tset_offset()</code></td>
<td><code>H5Tset_pad()</code></td>
</tr><tr>
<td><code>H5Tset_sign()</code></td>
</tr>
</table>
</center>
<p>In addition, the new function <code>H5Tget_super()</code> will
be defined for all datatypes that are derived from existing
types (currently just enumeration types).
<dl>
<dt><code>hid_t H5Tget_super(hid_t <em>type</em>)</code>
<dd>Return the datatype from which <em>type</em> is
derived. When <em>type</em> is an enumeration datatype then
the returned value will be an integer datatype but not
necessarily a native type. One use of this function would be
to create a new enumeration type based on the same underlying
integer type and values but with possibly different symbols.
<pre>
hid_t itype = H5Tget_super(hdf_en_colors);
hid_t hdf_fr_colors = H5Tenum_create(itype);
H5Tclose(itype);
short val;
H5Tenum_insert(hdf_fr_colors, "ouge", (val=0,&amp;val));
H5Tenum_insert(hdf_fr_colors, "vert", (val=1,&amp;val));
H5Tenum_insert(hdf_fr_colors, "bleu", (val=2,&amp;val));
H5Tenum_insert(hdf_fr_colors, "blanc", (val=3,&amp;val));
H5Tenum_insert(hdf_fr_colors, "noir", (val=4,&amp;val));
H5Tlock(hdf_fr_colors);</pre>
</dl>
<h3>8.4. Type Functions</h3>
<p>A small set of functions is available for querying properties
of an enumeration type. These functions are likely to be used
by browsers to display datatype information.
<dl>
<dt><code>int H5Tget_nmembers(hid_t <em>etype</em>)</code>
<dd>When given an enumeration datatype <em>etype</em> this
function returns the number of members defined for that
type. This function is already implemented for compound
datatypes.
<br><br>
<dt><code>char *H5Tget_member_name(hid_t <em>etype</em>, int
<em>membno</em>)</code>
<dd>Given an enumeration datatype <em>etype</em> this function
returns the symbol name for the member indexed by
<em>membno</em>. Members are numbered from zero to
<em>N</em>-1 where <em>N</em> is the return value from
<code>H5Tget_nmembers()</code>. The members are stored in no
particular order. This function is already implemented for
compound datatypes. If an error occurs then the null pointer
is returned. The return value should be freed by calling
<code>free()</code>.
<br><br>
<dt><code>herr_t H5Tget_member_value(hid_t <em>etype</em>, int
<em>membno</em>, void *<em>value</em>/*out*/)</code>
<dd>Given an enumeration datatype <em>etype</em> this function
returns the value associated with the member indexed by
<em>membno</em> (as described for
<code>H5Tget_member_name()</code>). The value returned
is in the domain of the underlying integer
datatype which is often a native integer type. The
application should ensure that the memory pointed to by
<em>value</em> is large enough to contain the result (the size
can be obtained by calling <code>H5Tget_size()</code> on
either the enumeration type or the underlying integer type
when the type is not known by the C compiler.
<pre>
int i, n = H5Tget_nmembers(hdf_en_colors);
for (i=0; i&lt;n; i++) {
char *symbol = H5Tget_member_name(hdf_en_colors, i);
short val;
H5Tget_member_value(hdf_en_colors, i, &amp;val);
printf("#%d %20s = %d\n", i, symbol, val);
free(symbol);
}</pre>
<p>
Output:
<pre>
#0 BLACK = 4
#1 BLUE = 2
#2 GREEN = 1
#3 RED = 0
#4 WHITE = 3</pre>
</dl>
<h3>8.5. Data Functions</h3>
<p>In addition to querying about the enumeration type properties,
an application may want to make queries about enumerated
data. These functions perform efficient mappings between symbol
names and values.
<dl>
<dt><code>herr_t H5Tenum_valueof(hid_t <em>etype</em>, const char
*<em>symbol</em>, void *<em>value</em>/*out*/)</code>
<dd>Given an enumeration datatype <em>etype</em> this function
returns through <em>value</em> the bit pattern associated with
the symbol name <em>symbol</em>. The <em>value</em> argument
should point to memory which is large enough to hold the result,
which is returned as the underlying integer datatype specified
when the enumeration type was created, often a native integer
type.
<br><br>
<dt><code>herr_t H5Tenum_nameof(hid_t <em>etype</em>, void
*<em>value</em>, char *<em>symbol</em>, size_t
<em>size</em>)</code>
<dd>This function translates a bit pattern pointed to by
<em>value</em> to a symbol name according to the mapping
defined in the enumeration datatype <em>etype</em> and stores
at most <em>size</em> characters of that name (counting the
null terminator) to the <em>symbol</em> buffer. If the name is
longer than the result buffer then the result is not null
terminated and the function returns failure. If <em>value</em>
points to a bit pattern which is not in the domain of the
enumeration type then the first byte of the <em>symbol</em>
buffer is set to zero and the function fails.
<pre>
short data[1000] = {4, 2, 0, 0, 5, 1, ...};
int i;
char symbol[32];
for (i=0; i&lt;1000; i++) {
if (H5Tenum_nameof(hdf_en_colors, data+i, symbol,
sizeof symbol))&lt;0) {
if (symbol[0]) {
strcpy(symbol+sizeof(symbol)-4, "...");
} else {
strcpy(symbol, "UNKNOWN");
}
}
printf("%d %s\n", data[i], symbol);
}
printf("}\n");</pre>
<p>
Output:
<pre>
4 BLACK
2 BLUE
0 RED
0 RED
5 UNKNOWN
1 GREEN
...</pre>
</dl>
<h3>8.6. Conversion</h3>
<p>Enumerated data can be converted from one type to another
provided the destination enumeration type contains all the
symbols of the source enumeration type. The conversion operates
by matching up the symbol names of the source and destination
enumeration types to build a mapping from source value to
destination value. For instance, if we are translating from an
enumeration type that defines a sequence of integers as the
values for the colors to a type that defines a different bit for
each color then the mapping might look like this:
<p><img src="EnumMap.gif" alt="Enumeration Mapping">
<p>That is, a source value of <code>2</code> which corresponds to
<code>BLUE</code> would be mapped to <code>0x0004</code>. The
following code snippet builds the second datatype, then
converts a raw data array from one datatype to another, and
then prints the result.
<pre>
/* Create a new enumeration type */
short val;
hid_t bits = H5Tcreate(H5T_ENUM, sizeof val);
H5Tenum_insert(bits, "RED", (val=0x0001,&amp;val));
H5Tenum_insert(bits, "GREEN", (val=0x0002,&amp;val));
H5Tenum_insert(bits, "BLUE", (val=0x0004,&amp;val));
H5Tenum_insert(bits, "WHITE", (val=0x0008,&amp;val));
H5Tenum_insert(bits, "BLACK", (val=0x0010,&amp;val));
/* The data */
short data[6] = {1, 4, 2, 0, 3, 5};
/* Convert the data from one type to another */
H5Tconvert(hdf_en_colors, bits, 5, data, NULL, plist_id);
/* Print the data */
for (i=0; i&lt;6; i++) {
printf("0x%04x\n", (unsigned)(data[i]));
}</pre>
<p>
Output:
<pre>
0x0002
0x0010
0x0004
0x0001
0x0008
0xffff</pre>
<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, causing the application defined
overflow handler to be invoked (see
<code>H5Tset_overflow()</code>). If no overflow handler is
defined then all bits of the destination value will be set.
<p>The HDF library will not provide conversions between enumerated
data and integers although the application is free to do so
(this is a policy we apply to all classes of HDF datatypes).
However, since enumeration types are derived from
integer types it is permissible to treat enumerated data as
integers and perform integer conversions in that context.
<h3>8.7. Symbol Order</h3>
<p>Symbol order is determined by the integer values associated
with each symbol. When the integer datatype is a native type,
testing the relative order of two symbols is an easy process:
simply compare the values of the symbols. If only the symbol
names are available then the values must first be determined by
calling <code>H5Tenum_valueof()</code>.
<pre>
short val1, val2;
H5Tenum_valueof(hdf_en_colors, "WHITE", &amp;val1);
H5Tenum_valueof(hdf_en_colors, "BLACK", &amp;val2);
if (val1 &lt; val2) ...</pre>
<p>When the underlying integer datatype is not a native type then
the easiest way to compare symbols is to first create a similar
enumeration type that contains all the same symbols but has a
native integer type (HDF type conversion features can be used to
convert the non-native values to native values). Once we have a
native type we can compare symbol order as just described. If
<code>foreign</code> is some non-native enumeration type then a
native type can be created as follows:
<pre>
int n = H5Tget_nmembers(foreign);
hid_t itype = H5Tget_super(foreign);
void *val = malloc(n * MAX(H5Tget_size(itype), sizeof(int)));
char *name = malloc(n * sizeof(char*));
int i;
/* Get foreign type information */
for (i=0; i&lt;n; i++) {
name[i] = H5Tget_member_name(foreign, i);
H5Tget_member_value(foreign, i,
(char*)val+i*H5Tget_size(foreign));
}
/* Convert integer values to new type */
H5Tconvert(itype, H5T_NATIVE_INT, n, val, NULL, plist_id);
/* Build a native type */
hid_t native = H5Tenum_create(H5T_NATIVE_INT);
for (i=0; i&lt;n; i++) {
H5Tenum_insert(native, name[i], ((int*)val)[i]);
free(name[i]);
}
free(name);
free(val);</pre>
<p>It is also possible to convert enumerated data to a new type
that has a different order defined for the symbols. For
instance, we can define a new type, <code>reverse</code> that
defines the same five colors but in the reverse order.
<pre>
short val;
int i;
char sym[8];
short data[5] = {0, 1, 2, 3, 4};
hid_t reverse = H5Tenum_create(H5T_NATIVE_SHORT);
H5Tenum_insert(reverse, "BLACK", (val=0,&amp;val));
H5Tenum_insert(reverse, "WHITE", (val=1,&amp;val));
H5Tenum_insert(reverse, "BLUE", (val=2,&amp;val));
H5Tenum_insert(reverse, "GREEN", (val=3,&amp;val));
H5Tenum_insert(reverse, "RED", (val=4,&amp;val));
/* Print data */
for (i=0; i&lt;5; i++) {
H5Tenum_nameof(hdf_en_colors, data+i, sym, sizeof sym);
printf ("%d %s\n", data[i], sym);
}
puts("Converting...");
H5Tconvert(hdf_en_colors, reverse, 5, data, NULL, plist_id);
/* Print data */
for (i=0; i&lt;5; i++) {
H5Tenum_nameof(reverse, data+i, sym, sizeof sym);
printf ("%d %s\n", data[i], sym);
}</pre>
<p>
Output:
<pre>
0 RED
1 GREEN
2 BLUE
3 WHITE
4 BLACK
Converting...
4 RED
3 GREEN
2 BLUE
1 WHITE
0 BLACK</pre>
<h3>8.8. Equality</h3>
<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.
<h3>8.9. Interacting with C's <code>enum</code> Type</h3>
<p>Although HDF enumeration datatypes are similar to C
<code>enum</code> datatypes, there are some important
differences:
<p>
<center>
<table border width="80%">
<tr>
<th>Difference</th>
<th>Motivation/Implications</th>
</tr>
<tr>
<td valign=top>Symbols are unquoted in C but quoted in
HDF.</td>
<td valign=top>This allows the application to manipulate
symbol names in ways that are not possible with C.</td>
</tr>
<tr>
<td valign=top>The C compiler automatically replaces all
symbols with their integer values but HDF requires
explicit calls to do the same.</td>
<td valign=top>C resolves symbols at compile time while
HDF resolves symbols at run time.</td>
</tr>
<tr>
<td valign=top>The mapping from symbols to integers is
<em>N</em>:1 in C but 1:1 in HDF.</td>
<td valign=top>HDF can translate from value to name
uniquely and large <code>switch</code> statements are
not necessary to print values in human-readable
format.</td>
</tr>
<tr>
<td valign=top>A symbol must appear in only one C
<code>enum</code> type but may appear in multiple HDF
enumeration types.</td>
<td valign=top>The translation from symbol to value in HDF
requires the datatype to be specified while in C the
datatype is not necessary because it can be inferred
from the symbol.</td>
</tr>
<tr>
<td valign=top>The underlying integer value is always a
native integer in C but can be a foreign integer type in
HDF.</td>
<td valign=top>This allows HDF to describe data that might
reside on a foreign architecture, such as data stored in
a file.</td>
</tr>
<tr>
<td valign=top>The sign and size of the underlying integer
datatype is chosen automatically by the C compiler but
must be fully specified with HDF.</td>
<td valign=top>Since HDF doesn't require finalization of a
datatype, complete specification of the type must be
supplied before the type is used. Requiring that
information at the time of type creation was a design
decision to simplify the library.</td>
</tr>
</table>
</center>
<p>The examples below use the following C datatypes:
<p>
<table width="90%" bgcolor="white">
<tr>
<td>
<code><pre>
/* English color names */
typedef enum {
RED,
GREEN,
BLUE,
WHITE,
BLACK
} c_en_colors;
/* Spanish color names, reverse order */
typedef enum {
NEGRO
BLANCO,
AZUL,
VERDE,
ROJO,
} c_sp_colors;
/* No enum definition for French names */
</pre></code>
</td>
</tr>
</table>
<h4>Creating HDF Types from C Types</h4>
<p>An HDF enumeration datatype can be created from a C
<code>enum</code> type simply by passing pointers to the C
<code>enum</code> values to <code>H5Tenum_insert()</code>. For
instance, to create HDF types for the <code>c_en_colors</code>
type shown above:
<p>
<table width="90%" bgcolor="white">
<tr>
<td>
<code><pre>
c_en_colors val;
hid_t hdf_en_colors = H5Tcreate(H5T_ENUM, sizeof(c_en_colors));
H5Tenum_insert(hdf_en_colors, "RED", (val=RED, &amp;val));
H5Tenum_insert(hdf_en_colors, "GREEN", (val=GREEN,&amp;val));
H5Tenum_insert(hdf_en_colors, "BLUE", (val=BLUE, &amp;val));
H5Tenum_insert(hdf_en_colors, "WHITE", (val=WHITE,&amp;val));
H5Tenum_insert(hdf_en_colors, "BLACK", (val=BLACK,&amp;val));</pre></code>
</td>
</tr>
</table>
<h4>Name Changes between Applications</h4>
<p>Occassionally two applicatons wish to exchange data but they
use different names for the constants they exchange. For
instance, an English and a Spanish program may want to
communicate color names although they use different symbols in
the C <code>enum</code> definitions. The communication is still
possible although the applications must agree on common terms
for the colors. The following example shows the Spanish code to
read the values assuming that the applications have agreed that
the color information will be exchanged using Enlish color
names:
<p>
<table width="90%" bgcolor="white">
<tr>
<td>
<code><pre>
c_sp_colors val, data[1000];
hid_t hdf_sp_colors = H5Tcreate(H5T_ENUM, sizeof(c_sp_colors));
H5Tenum_insert(hdf_sp_colors, "RED", (val=ROJO, &amp;val));
H5Tenum_insert(hdf_sp_colors, "GREEN", (val=VERDE, &amp;val));
H5Tenum_insert(hdf_sp_colors, "BLUE", (val=AZUL, &amp;val));
H5Tenum_insert(hdf_sp_colors, "WHITE", (val=BLANCO, &amp;val));
H5Tenum_insert(hdf_sp_colors, "BLACK", (val=NEGRO, &amp;val));
H5Dread(dataset, hdf_sp_colors, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);</pre></code>
</td>
</tr>
</table>
<h4>Symbol Ordering across Applications</h4>
<p>Since symbol ordering is completely determined by the integer values
assigned to each symbol in the <code>enum</code> definition,
ordering of <code>enum</code> symbols cannot be preserved across
files like with HDF enumeration types. HDF can convert from one
application's integer values to the other's so a symbol in one
application's C <code>enum</code> gets mapped to the same symbol
in the other application's C <code>enum</code>, but the relative
order of the symbols is not preserved.
<p>For example, an application may be defined to use the
definition of <code>c_en_colors</code> defined above where
<code>WHITE</code> is less than <code>BLACK</code>, but some
other application might define the colors in some other
order. If each application defines an HDF enumeration type based
on that application's C <code>enum</code> type then HDF will
modify the integer values as data is communicated from one
application to the other so that a <code>RED</code> value
in the first application is also a <code>RED</code> value in the
other application.
<p>A case of this reordering of symbol names was also shown in the
previous code snippet (as well as a change of language), where
HDF changed the integer values so 0 (<code>RED</code>) in the
input file became 4 (<code>ROJO</code>) in the <code>data</code>
array. In the input file, <code>WHITE</code> was less than
<code>BLACK</code>; in the application the opposite is true.
<p>In fact, the ability to change the order of symbols is often
convenient when the enumeration type is used only to group
related symbols that don't have any well defined order
relationship.
<h4>Internationalization</h4>
<p>The HDF enumeration type conversion features can also be used
to provide internationalization of debugging output. A program
written with the <code>c_en_colors</code> datatype could define
a separate HDF datatype for languages such as English, Spanish,
and French and cast the enumerated value to one of these HDF
types to print the result.
<p>
<table width="90%" bgcolor="white">
<tr>
<td>
<code><pre>
c_en_colors val, *data=...;
hid_t hdf_sp_colors = H5Tcreate(H5T_ENUM, sizeof val);
H5Tenum_insert(hdf_sp_colors, "ROJO", (val=RED, &amp;val));
H5Tenum_insert(hdf_sp_colors, "VERDE", (val=GREEN, &amp;val));
H5Tenum_insert(hdf_sp_colors, "AZUL", (val=BLUE, &amp;val));
H5Tenum_insert(hdf_sp_colors, "BLANCO", (val=WHITE, &amp;val));
H5Tenum_insert(hdf_sp_colors, "NEGRO", (val=BLACK, &amp;val));
hid_t hdf_fr_colors = H5Tcreate(H5T_ENUM, sizeof val);
H5Tenum_insert(hdf_fr_colors, "OUGE", (val=RED, &amp;val));
H5Tenum_insert(hdf_fr_colors, "VERT", (val=GREEN, &amp;val));
H5Tenum_insert(hdf_fr_colors, "BLEU", (val=BLUE, &amp;val));
H5Tenum_insert(hdf_fr_colors, "BLANC", (val=WHITE, &amp;val));
H5Tenum_insert(hdf_fr_colors, "NOIR", (val=BLACK, &amp;val));
void
nameof(lang_t language, c_en_colors val, char *name, size_t size)
{
switch (language) {
case ENGLISH:
H5Tenum_nameof(hdf_en_colors, &amp;val, name, size);
break;
case SPANISH:
H5Tenum_nameof(hdf_sp_colors, &amp;val, name, size);
break;
case FRENCH:
H5Tenum_nameof(hdf_fr_colors, &amp;val, name, size);
break;
}
}</pre></code>
</td>
</tr>
</table>
<h3>8.10. Goals That Have Been Met</h3>
<p>The main goal of enumeration types is to provide communication
of enumerated data using symbolic equivalence. That is, a
symbol written to a dataset by one application should be read as
the same symbol by some other application.
<p>
<table width="90%">
<tr>
<td valign=top><b>Architecture Independence</b></td>
<td valign=top>Two applications shall be able to exchange
enumerated data even when the underlying integer values
have different storage formats. HDF accomplishes this for
enumeration types by building them upon integer types.</td>
</tr>
<tr>
<td valign=top><b>Preservation of Order Relationship</b></td>
<td valign=top>The relative order of symbols shall be
preserved between two applications that use equivalent
enumeration datatypes. Unlike numeric values that have
an implicit ordering, enumerated data has an explicit
order defined by the enumeration datatype and HDF
records this order in the file.</td>
</tr>
<tr>
<td valign=top><b>Order Independence</b></td>
<td valign=top>An application shall be able to change the
relative ordering of the symbols in an enumeration
datatype. This is accomplished by defining a new type with
different integer values and converting data from one type
to the other.</td>
</tr>
<tr>
<td valign=top><b>Subsets</b></td>
<td valign=top>An application shall be able to read
enumerated data from an archived dataset even after the
application has defined additional members for the
enumeration type. An application shall be able to write
to a dataset when the dataset contains a superset of the
members defined by the application. Similar rules apply
for in-core conversions between enumerated datatypes.</td>
</tr>
<tr>
<td valign=top><b>Targetable</b></td>
<td valign=top>An application shall be able to target a
particular architecture or application when storing
enumerated data. This is accomplished by allowing
non-native underlying integer types and converting the
native data to non-native data.</td>
</tr>
<tr>
<td valign=top><b>Efficient Data Transfer</b></td>
<td valign=top>An application that defines a file dataset
that corresponds to some native C enumerated data array
shall be able to read and write to that dataset directly
using only Posix read and write functions. HDF already
optimizes this case for integers, so the same optimization
will apply to enumerated data.
</tr>
<tr>
<td valign=top><b>Efficient Storage</b></td>
<td valign=top>Enumerated data shall be stored in a manner
which is space efficient. HDF stores the enumerated data
as integers and allows the application to chose the size
and format of those integers.</td>
</tr>
</table>
<h2>9. Variable-length Datatypes</h2>
<h3>9.1. Overview And Justification</h3>
Variable-length (VL) datatypes are sequences of an existing datatype
(atomic, VL, or compound) which are not fixed in length from one dataset location
to another. In essence, they are similar to C character strings -- a sequence of
a type which is pointed to by a particular type of <em>pointer</em> -- although
they are implemented more closely to FORTRAN strings by including an explicit
length in the pointer instead of using a particular value to terminate the
sequence.
<p>
VL datatypes are useful to the scientific community in many different ways,
some of which are listed below:
<ul>
<li>Ragged arrays: 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. (Or as a field in a
compound datatype.)
<li>Fractal arrays: If a compound datatype has a VL field of another compound
type with VL fields (a <em>nested</em> VL datatype), this can be used to
implement ragged arrays of ragged arrays, to whatever nesting depth is
required for the user.
<li>Polygon lists: A common storage requirement is to efficiently store arrays
of polygons with different numbers of vertices. VL datatypes can be
used to efficiently and succinctly describe an array of polygons with
different numbers of vertices.
<li>Character strings: 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>Indices: 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. Perhaps an array something like the following:
<pre>
Value1: Object1, Object3, Object9
Value2: Object0, Object12, Object14, Object21, Object22
Value3: Object2
Value4: &lt;none&gt;
Value5: Object1, Object10, Object12
.
.
</pre>
<li>Object Tracking: An array of VL dataset region references can be used as
a method of tracking objects or features appearing in a sequence of
datasets. Perhaps an array of them would look like:
<pre>
Feature1: Dataset1:Region, Dataset3:Region, Dataset9:Region
Feature2: Dataset0:Region, Dataset12:Region, Dataset14:Region,
Dataset21:Region, Dataset22:Region
Feature3: Dataset2:Region
Feature4: &lt;none&gt;
Feature5: Dataset1:Region, Dataset10:Region, Dataset12:Region
.
.
</pre>
</ul>
<h3>9.2. Variable-length Datatype Memory Management</h3>
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.
Since the memory allocated when reading (or writing) may be complicated to
release, an HDF5 routine is provided to traverse a memory buffer and free the
VL datatype information without leaking memory.
<h4>Variable-length datatypes cannot be divided</h4>
VL datatypes are designed so that they cannot be subdivided by the library
with selections, etc. This design was chosen due to the complexities in
specifying selections on each VL element of a dataset through a selection API
that is easy to understand. Also, the selection APIs work on dataspaces, not
on datatypes. At some point in time, we may want to create a way for
dataspaces to have VL components to them and we would need to allow selections
of those VL regions, but that is beyond the scope of this document.
<h4>What happens if the library runs out of memory while reading?</h4>
It is possible for a call to <code>H5Dread</code> to fail while reading in
VL datatype information if the memory required exceeds that which is available.
In this case, the <code>H5Dread</code> call will fail gracefully and any
VL data which has been allocated prior to the memory shortage will be returned
to the system via the memory management routines detailed below.
It may be possible to design a <em>partial read</em> API function at a
later date, if demand for such a function warrants.
<h4>Strings as variable-length datatypes</h4>
Since character strings are a special case of VL data that is implemented
in many different ways on different machines and in different programming
languages, they are handled somewhat differently from other VL datatypes in HDF5.
<p>
HDF5 has native VL strings for each language API, which are stored the
same way on disk, but are exported through each language API in a natural way
for that language. When retrieving VL strings from a dataset, users may choose
to have them stored in memory as a native VL string or in HDF5's <code>hvl_t</code>
struct for VL datatypes.
<p>
VL strings may be created in one of two ways: by creating a VL datatype with
a base type of <code>H5T_NATIVE_ASCII</code>, <code>H5T_NATIVE_UNICODE</code>,
etc., or by creating a string datatype and setting its length to
<code>H5T_VARIABLE</code>. The second method is used to access
native VL strings in memory. The library will convert between the two types,
but they are stored on disk using different datatypes and have different
memory representations.
<p>
Multi-byte character representations, such as UNICODE or <em>wide</em>
characters in C/C++, will need the appropriate character and string datatypes
created so that they can be described properly through the datatype API.
Additional conversions between these types and the current ASCII characters
will also be required.
<p>
Variable-width character strings (which might be compressed data or some
other encoding) are not currently handled by this design. We will evaluate
how to implement them based on user feedback.
<h3>9.3. Variable-length Datatype API</h3>
<h4>Creation</h4>
VL datatypes are created with the <code>H5Tvlen_create()</code> function
as follows:
<dl>
<dd><em>type_id</em> = <code>H5Tvlen_create</code>(<em>hid_t</em> <code>base_type_id</code>);
</dl>
<p>
The base datatype will be the datatype that the sequence is composed of,
characters for character strings, vertex coordinates for polygon lists, etc.
The base datatype specified for the VL datatype can be of any HDF5 datatype,
including another VL datatype, a compound datatype, or an atomic datatype.
<h4>Query base datatype of VL datatype</h4>
It may be necessary to know the base datatype of a VL datatype before
memory is allocated, etc. The base datatype is queried with the
<code>H5Tget_super()</code> function, described in the H5T documentation.
<h4>Query minimum memory required for VL information</h4>
It order to predict the memory usage that <code>H5Dread</code> may need
to allocate to store VL data while reading the data, the
<code>H5Dget_vlen_size()</code> function is provided:
<dl>
<dd><em>herr_t</em>
<code>H5Dget_vlen_buf_size</code>(<em>hid_t</em> <code>dataset_id</code>,
<em>hid_t</em> <code>type_id</code>,
<em>hid_t</em> <code>space_id</code>,
<em>hsize_t</em> *<code>size</code>)
</dl>
(This function is not implemented in Release 1.2.)
<p>
This routine checks the number of bytes required to store the VL data from
the dataset, using the <code>space_id</code> for the selection in the dataset
on disk and the <code>type_id</code> for the memory representation of the
VL data in memory. The *<code>size</code> value is modified according to
how many bytes are required to store the VL data in memory.
<h4>Specifying how to manage memory for the VL datatype</h4>
The memory management method is determined by dataset transfer properties
passed into the <code>H5Dread</code> and <code>H5Dwrite</code> functions
with the dataset transfer property list.
<p>
Default memory management is set by using <code>H5P_DEFAULT</code>
for the dataset transfer property list identifier.
If <code>H5P_DEFAULT</code> is used with <code>H5Dread</code>,
the system <code>malloc</code> and <code>free</code> calls
will be used for allocating and freeing memory.
In such a case, <code>H5P_DEFAULT</code> should also be passed
as the property list identifier to <code>H5Dvlen_reclaim</code>.
<p>
The rest of this subsection is relevant only to those who choose
<i>not</i> to use default memory management.
<p>
The user can choose whether to use the
system <code>malloc</code> and <code>free</code> calls or
user-defined, or custom, memory management functions.
If user-defined memory management functions are to be used,
the memory allocation and free routines must be defined via
<code>H5Pset_vlen_mem_manager()</code>, as follows:
<dl>
<dd><em>herr_t</em>
<code>H5Pset_vlen_mem_manager</code>(<em>hid_t</em> <code>plist_id</code>,
<em>H5MM_allocate_t</em> <code>alloc</code>,
<em>void</em> *<code>alloc_info</code>,
<em>H5MM_free_t</em> <code>free</code>,
<em>void</em> *<code>free_info</code>)
</dl>
<p>
The <code>alloc</code> and <code>free</code> parameters
identify the memory management routines to be used.
If the user has defined custom memory management routines,
<code>alloc</code> and/or <code>free</code> should be set to make
those routine calls (i.e., the name of the routine is used as
the value of the parameter);
if the user prefers to use the system's <code> malloc</code>
and/or <code>free</code>, the <code>alloc</code> and
<code>free</code> parameters, respectively, should be set to
<code> NULL</code>
<p>
The prototypes for the user-defined functions would appear as follows:
<dl>
<dd><code>typedef</code> <em>void</em>
*(*<code>H5MM_allocate_t</code>)(<em>size_t</em> <code>size</code>,
<em>void</em> *<code>info</code>) ;
<dd><code>typedef</code> <em>void</em>
(*<code>H5MM_free_t</code>)(<em>void</em> *<code>mem</code>,
<em>void</em> *<code>free_info</code>) ;
</dl>
<p>
The <code>alloc_info</code> and <code>free_info</code> parameters can be
used to pass along any required information to the user's memory management
routines.
<p>
In summary, if the user has defined custom memory management
routines, the name(s) of the routines are passed in the
<code>alloc</code> and <code>free</code> parameters and the
custom routines' parameters are passed in the
<code>alloc_info</code> and <code>free_info</code> parameters.
If the user wishes to use the system <code> malloc</code> and
<code>free</code> functions, the <code>alloc</code> and/or
<code>free</code> parameters are set to <code> NULL</code>
and the <code>alloc_info</code> and <code>free_info</code>
parameters are ignored.
<h4>Recovering memory from VL buffers read in</h4>
The complex memory buffers created for a VL datatype may be reclaimed with
the <code>H5Dvlen_reclaim()</code> function call, as follows:
<dl>
<dd><em>herr_t</em>
<code>H5Dvlen_reclaim</code>(<em>hid_t</em> <code>type_id</code>,
<em>hid_t</em> <code>space_id</code>,
<em>hid_t</em> <code>plist_id</code>,
<em>void</em> *<code>buf</code>);
</dl>
<p>
The <code>type_id</code> must be the datatype stored in the buffer,
<code>space_id</code> describes the selection for the memory buffer
to free the VL datatypes within,
<code>plist_id</code> is the dataset transfer property list which
was used for the I/O transfer to create the buffer, and
<code>buf</code> is the pointer to the buffer to free the VL memory within.
The VL structures (<code>hvl_t</code>) in the user's buffer are
modified to zero out the VL information after it has been freed.
<p>
If nested VL datatypes were used to create the buffer,
this routine frees them from the bottom up,
releasing all the memory without creating memory leaks.
<h3>9.4. Code Examples</h3>
The following example creates the following one-dimensional array
of size 4 of variable-length datatype.
<pre>
0 10 20 30
11 21 31
22 32
33
</pre>
Each element of the VL datatype is of H5T_NATIVE_UINT type.
<p>
The array is stored in the dataset and then read back into memory.
Default memory management routines are used for writing the VL data.
Custom memory management routines are used for reading the VL data and
reclaiming memory space.
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: Variable-length Datatypes</h4></caption>
<tr>
<td>
<pre>
#include &lt;hdf5.h&gt;
#define FILE "vltypes.h5"
#define MAX(X,Y) ((X)&gt;(Y)?(X):(Y))
/* 1-D dataset with fixed dimensions */
#define SPACE_NAME "Space"
#define SPACE_RANK 1
#define SPACE_DIM 4
void *vltypes_alloc_custom(size_t size, void *info);
void vltypes_free_custom(void *mem, void *info);
/****************************************************************
**
** vltypes_alloc_custom(): VL datatype custom memory
** allocation routine. This routine just uses malloc to
** allocate the memory and increments the amount of memory
** allocated.
**
****************************************************************/
void *vltypes_alloc_custom(size_t size, void *info)
{
void *ret_value=NULL; /* Pointer to return */
int *mem_used=(int *)info; /* Get the pointer to the memory used */
size_t extra; /* Extra space needed */
/*
* This weird contortion is required on the DEC Alpha to keep the
* alignment correct.
*/
extra=MAX(sizeof(void *),sizeof(int));
if((ret_value=(void *)malloc(extra+size))!=NULL) {
*(int *)ret_value=size;
*mem_used+=size;
} /* end if */
ret_value=((unsigned char *)ret_value)+extra;
return(ret_value);
}
/******************************************************************
** vltypes_free_custom(): VL datatype custom memory
** allocation routine. This routine just uses free to
** release the memory and decrements the amount of memory
** allocated.
** ****************************************************************/
void vltypes_free_custom(void *_mem, void *info)
{
unsigned char *mem;
int *mem_used=(int *)info; /* Get the pointer to the memory used */
size_t extra; /* Extra space needed */
/*
* This weird contortion is required on the DEC Alpha to keep the
* alignment correct.
*/
extra=MAX(sizeof(void *),sizeof(int));
if(_mem!=NULL) {
mem=((unsigned char *)_mem)-extra;
*mem_used-=*(int *)mem;
free(mem);
} /* end if */
}
int main(void)
{
hvl_t wdata[SPACE_DIM]; /* Information to write */
hvl_t rdata[SPACE_DIM]; /* Information read in */
hid_t fid; /* HDF5 File IDs */
hid_t dataset; /* Dataset ID */
hid_t sid; /* Dataspace ID */
hid_t tid; /* Datatype ID */
hid_t xfer_pid; /* Dataset transfer property list ID */
hsize_t dims[] = {SPACE_DIM};
uint i,j; /* counting variables */
int mem_used=0; /* Memory used during allocation */
herr_t ret; /* Generic return value */
/*
* Allocate and initialize VL data to write
*/
for(i=0; i&lt;SPACE_DIM; i++) {
wdata[i].p= (unsigned int *)malloc((i+1)*sizeof(unsigned int));
wdata[i].len=i+1;
for(j=0; j&lt;(i+1); j++)
((unsigned int *)wdata[i].p)[j]=i*10+j;
} /* end for */
/*
* Create file.
*/
fid = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create dataspace for datasets.
*/
sid = H5Screate_simple(SPACE_RANK, dims, NULL);
/*
* Create a datatype to refer to.
*/
tid = H5Tvlen_create (H5T_NATIVE_UINT);
/*
* Create a dataset.
*/
dataset=H5Dcreate(fid, "Dataset", tid, sid, H5P_DEFAULT);
/*
* Write dataset to disk.
*/
ret=H5Dwrite(dataset, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
/*
* Change to the custom memory allocation routines for reading
* VL data
*/
xfer_pid=H5Pcreate(H5P_DATASET_XFER);
ret=H5Pset_vlen_mem_manager(xfer_pid, vltypes_alloc_custom,
&mem_used, vltypes_free_custom,
&mem_used);
/*
* Read dataset from disk. vltypes_alloc_custom and
* will be used to manage memory.
*/
ret=H5Dread(dataset, tid, H5S_ALL, H5S_ALL, xfer_pid, rdata);
/*
* Display data read in
*/
for(i=0; i&lt;SPACE_DIM; i++) {
printf("%d-th element length is %d \n", i,
(unsigned) rdata[i].len);
for(j=0; j&lt;rdata[i].len; j++) {
printf(" %d ",((unsigned int *)rdata[i].p)[j] );
}
printf("\n");
} /* end for */
/*
* Reclaim the read VL data. vltypes_free_custom will be used
* to reclaim the space.
*/
ret=H5Dvlen_reclaim(tid, sid, xfer_pid, rdata);
/*
* Reclaim the write VL data. C language free function will be
* used to reclaim space.
*/
ret=H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, wdata);
/*
* Close Dataset
*/
ret = H5Dclose(dataset);
/*
* Close datatype
*/
ret = H5Tclose(tid);
/*
* Close disk dataspace
*/
ret = H5Sclose(sid);
/*
* Close dataset transfer property list
*/
ret = H5Pclose(xfer_pid);
/*
* Close file
*/
ret = H5Fclose(fid);
}
</pre>
</td>
</tr>
</table>
</center>
And the output from this sample code would be as follows:
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: Variable-length Datatypes, Sample Output</h4></caption>
<tr>
<td>
<pre>
0-th element length is 1
0
1-th element length is 2
10 11
2-th element length is 3
20 21 22
3-th element length is 4
30 31 32 33
</pre>
</td>
</tr>
</table>
</center>
<p>
For further samples of VL datatype code, see the tests in <code>test/tvltypes.c</code>
in the HDF5 distribution.
<h2>10. Array Datatypes</h2>
The array class of datatypes, <code>H5T_ARRAY</code>, allows the
construction of true, homogeneous, multi-dimensional arrays.
Since these are homogeneous arrays, each element of the array will be
of the same datatype, designated at the time the array is created.
<p>
Arrays can be nested.
Not only is an array datatype used as an element of an HDF5 dataset,
but the elements of an array datatype may be of any datatype,
including another array datatype.
<p>
Array datatypes cannot be subdivided for I/O; the entire array must
be transferred from one dataset to another.
<p>
Within the limitations outlined in the next paragraph, array datatypes
may be <em>N</em>-dimensional and of any dimension size.
Unlimited dimensions, however, are not supported.
Functionality similar to unlimited dimension arrays is available through
the use of variable-length datatypes.
<p>
The maximum number of dimensions, i.e., the maximum rank, of an array
datatype is specified by the HDF5 library constant <code>H5S_MAX_RANK</code>.
The minimum rank is 1 (one).
All dimension sizes must be greater than 0 (zero).
<p>
One array dataype may only be converted to another array datatype
if the number of dimensions and the sizes of the dimensions are equal
and the datatype of the first array's elements can be converted
to the datatype of the second array's elements.
<h3>10.1 Array Datatype APIs</h2>
The functions for creating and manipulating array datadypes are
as follows:
<dir>
<table>
<tr>
<td><code><b>H5Tarray_create</b></code>
</td><td>&nbsp;&nbsp;
</td><td>Creates an array datatype.
</td></tr><tr><td colspan=3><dir>
<em>hid_t</em> <code>H5Tarray_create</code>(
<em>hid_t</em> <code>base</code>,
<em>int</em> <code>rank</code>,
<em>const hsize_t</em> <code>dims[/*rank*/]</code>,
<em>const int</em> <code>perm[/*rank*/]</code>
)
</dir>
</td></tr><tr>
<td><code><b>H5Tget_array_ndims</b></code>
</td><td>&nbsp;&nbsp;
</td><td>Retrieves the rank of the array datatype.
</td></tr><tr><td colspan=3><dir>
<em>int</em> <code>H5Tget_array_ndims</code>(
<em>hid_t</em> <code>adtype_id</code>
)
</dir>
</td></tr><tr>
<td><code><b>H5Tget_array_dims</b></code>
</td><td>&nbsp;&nbsp;
</td><td>Retrieves the dimension sizes of the array datatype.
</td></tr><tr><td colspan=3><dir>
<em>int</em> <code>H5Tget_array_dims</code>(
<em>hid_t</em> <code>adtype_id</code>,
<em>hsize_t *</em><code>dims[]</code>,
<em>int *</em><code>perm[]</code>
)
</dir>
</td></tr>
</table>
</dir>
<h3>10.2 Transition Issues in Adapting Existing Software<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
(Transition to HDF5 Release 1.4 Only)</h3>
The array datatype class is new with Release 1.4;
prior releases included an array element for compound datatypes.
<p>
The use of the array datatype class will not interfere with the
use of existing compound datatypes. Applications may continue to
read and write the older field arrays, but they will no longer be
able to create array fields in newly-defined compound datatypes.
<p>
Existing array fields will be transparently mapped to array datatypes
when they are read in.
<h3>10.3 Code Example</h3>
The following example creates an array datatype and a dataset
containing elements of the array datatype in an HDF5 file.
It then writes the dataset to the file.
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: Array Datatype</h4></caption>
<tr>
<td>
<pre>
#include &lt;hdf5.h&gt;
#define FILE "SDS_array_type.h5"
#define DATASETNAME "IntArray"
#define ARRAY_DIM1 5 /* array dimensions and rank */
#define ARRAY_DIM2 4
#define ARRAY_RANK 2
#define SPACE_DIM 10 /* dataset dimensions and rank */
#define RANK 1
int
main (void)
{
hid_t file, dataset; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t sdims[] = {SPACE_DIM}; /* dataset dimensions */
hsize_t adims[] = {ARRAY_DIM1, ARRAY_DIM2}; /* array dimensions */
hsize_t adims_out[2];
herr_t status;
int data[SPACE_DIM][ARRAY_DIM1][ARRAY_DIM2]; /* data to write */
int k, i, j;
int array_rank_out;
/*
* Data and output buffer initialization.
*/
for (k = 0; k &lt; SPACE_DIM; k++) {
for (j = 0; j &lt; ARRAY_DIM1; j++) {
for (i = 0; i &lt; ARRAY_DIM2; i++)
data[k][j][i] = k;
}
}
/*
* Create a new file using H5F_ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
*/
file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dataspace = H5Screate_simple(RANK, sdims, NULL);
/*
* Define array datatype for the data in the file.
*/
datatype = H5Tarray_create(H5T_NATIVE_INT, ARRAY_RANK, adims, NULL);
/*
* Create a new dataset within the file using defined dataspace and
* datatype and default dataset creation properties.
*/
dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace,
H5P_DEFAULT);
/*
* Write the data to the dataset using default transfer properties.
*/
status = H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Dclose(dataset);
/*
* Reopen dataset, and return information about its datatype.
*/
dataset = H5Dopen(file, DATASETNAME);
datatype = H5Dget_type(dataset);
array_rank_out = H5Tget_array_ndims(datatype);
status = H5Tget_array_dims(datatype, adims_out, NULL);
printf(" Array datatype rank is %d \n", array_rank_out);
printf(" Array dimensions are %d x %d \n", (int)adims_out[0],
(int)adims_out[1]);
H5Tclose(datatype);
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
</pre>
</td>
</tr>
</table>
</center>
<h2>11. Sharing Datatypes among Datasets</h2>
<p>If a file has lots of datasets which have a common datatype,
then the file could be made smaller by having all the datasets
share a single datatype. Instead of storing a copy of the
datatype in each dataset object header, a single datatype is stored
and the object headers point to it. The space savings is
probably only significant for datasets with a compound datatype,
since the atomic datatypes can be described with just a few
bytes anyway.
<p>To create a bunch of datasets that share a single datatype
just create the datasets with a committed (named) datatype.
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: Shared Datatypes</h4></caption>
<tr>
<td>
<p>To create two datasets that share a common datatype
one just commits the datatype, giving it a name, and
then uses that datatype to create the datasets.
<p><code><pre>
hid_t t1 = ...some transient type...;
H5Tcommit (file, "shared_type", t1);
hid_t dset1 = H5Dcreate (file, "dset1", t1, space, H5P_DEFAULT);
hid_t dset2 = H5Dcreate (file, "dset2", t1, space, H5P_DEFAULT);
</code></pre>
<p>And to create two additional datasets later which
share the same type as the first two datasets:
<p><code><pre>
hid_t dset1 = H5Dopen (file, "dset1");
hid_t t2 = H5Dget_type (dset1);
hid_t dset3 = H5Dcreate (file, "dset3", t2, space, H5P_DEFAULT);
hid_t dset4 = H5Dcreate (file, "dset4", t2, space, H5P_DEFAULT);
</code></pre>
</td>
</tr>
</table>
</center>
<a name="Datatypes-DataConversion">
<h2>12. Data Conversion</h2>
</a>
<p>The library is capable of converting data from one type to
another and does so automatically when reading or writing the
raw data of a dataset, attribute data, or fill values. The
application can also change the type of data stored in an array.
<p>In order to insure that data conversion exceeds disk I/O rates,
common data conversion paths can be hand-tuned and optimized for
performance. The library contains very efficient code for
conversions between most native datatypes and a few non-native
datatypes, but if a hand-tuned conversion function is not
available, then the library falls back to a slower but more
general conversion function. The application programmer can
define additional conversion functions when the libraries
repertoire is insufficient. In fact, if an application does
define a conversion function which would be of general interest,
we request that the function be submitted to the HDF5
development team for inclusion in the library.
<p><b>Note:</b> The HDF5 library contains a deliberately limited
set of conversion routines. It can convert from one integer
format to another, from one floating point format to another,
and from one struct to another. It can also perform byte
swapping when the source and destination types are otherwise the
same. The library does not contain any functions for converting
data between integer and floating point formats. It is
anticipated that some users will find it necessary to develop
float to integer or integer to float conversion functions at the
application level; users are invited to submit those functions
to be considered for inclusion in future versions of the
library.
<p>A conversion path contains a source and destination datatype
and each path contains a <em>hard</em> conversion function
and/or a <em>soft</em> conversion function. The only difference
between hard and soft functions is the way in which the library
chooses which function applies: A hard function applies to a
specific conversion path while a soft function may apply to
multiple paths. When both hard and soft functions apply to a
conversion path, then the hard function is favored and when
multiple soft functions apply, the one defined last is favored.
<p>A data conversion function is of type <code>H5T_conv_t</code>,
which is defined as follows:
<dir><pre><em>typedef</em> herr_t (<em>*H5T_conv_t</em>) (hid_t <em>src_id</em>,
hid_t <em>dst_id</em>,
H5T_cdata_t *<em>cdata</em>,
hsize_t <em>nelmts</em>,
size_t <em>buf_stride</em>,
size_t <em>bkg_stride</em>,
void *<em>buffer</em>,
void *<em>bkg_buffer</em>,
hid_t <em>dset_xfer_plist</em>);</pre></dir>
<p>The conversion function is called with
the source and destination datatypes (<em>src_id</em> and
<em>dst_id</em>),
the path-constant data struct (<em>cdata</em>),
the number of instances of the datatype to convert (<em>nelmts</em>),
a conversion buffer (<em>buffer</em>) which initially contains
an array of data having the source type and on return will
contain an array of data having the destination type,
a temporary or background buffer (<em>bkg_buffer</em>,
see description of <code>H5T_BKG_YES</code> below),
conversion and background buffer strides (<em>buf_stride</em> and
<em>bkg_stride</em>) that indicate what data is to be converted, and
a dataset transfer properties list (<em>dset_xfer_plist</em>).
<p><em>buf_stride</em> and <em>bkg_stride</em> are in bytes and
are related to the size of the datatype.
If every data element is to be converted, the parameter's value
is equal to the size of the datatype;
if every other data element is to be converted, the parameter's value
is equal to twice the size of the datatype; etc.
<p><em>dset_xfer_plist</em> may contain properties that are passed
to the read and write calls.
This parameter is currently used only with variable-length data.
<p><em>bkg_buffer</em> and <em>bkg_stride</em> are used only with
compound datatypes.
<p>The path-constant data struct, <code>H5T_cdata_t</code>,
is declared as follows:
<dir><pre><em>typedef</em> struct <em>*H5T_cdata_t</em> (H5T_cmd_t <em>command</em>,
H5T_bkg_t <em>need_bkg</em>,
hbool_t *<em>recalc</em>,
void *<em>priv</em>)</pre></dir>
<p>The <code>command</code> field of the <em>cdata</em> argument
determines what happens within the conversion function. It's
values can be:
<dl>
<dt><code>H5T_CONV_INIT</code>
<dd>This command is to hard conversion functions when they're
registered or soft conversion functions when the library is
determining if a conversion can be used for a particular path.
The <em>src_type</em> and <em>dst_type</em> are the end-points
of the path being queried and <em>cdata</em> is all zero. The
library should examine the source and destination types and
return zero if the conversion is possible and negative
otherwise (hard conversions need not do this since they've
presumably been registered only on paths they support). If
the conversion is possible the library may allocate and
initialize private data and assign the pointer to the
<code>priv</code> field of <em>cdata</em> (or private data can
be initialized later). It should also initialize the
<code>need_bkg</code> field described below. The <em>buf</em>
and <em>background</em> pointers will be null pointers.
<br><br>
<dt><code>H5T_CONV_CONV</code>
<dd>This command indicates that data points should be converted.
The conversion function should initialize the
<code>priv</code> field of <em>cdata</em> if it wasn't
initialize during the <code>H5T_CONV_INIT</code> command and
then convert <em>nelmts</em> instances of the
<em>src_type</em> to the <em>dst_type</em>. The
<em>buffer</em> serves as both input and output. The
<em>background</em> buffer is supplied according to the value
of the <code>need_bkg</code> field of <em>cdata</em> (the
values are described below).
<br><br>
<dt><code>H5T_CONV_FREE</code>
<dd>The conversion function is about to be removed from some
path and the private data (the
<code><em>cdata</em>->priv</code> pointer) should be freed and
set to null. All other pointer arguments are null, the
<em>src_type</em> and <em>dst_type</em> are invalid
(negative), and the <em>nelmts</em> argument is zero.
<br><br>
<dt><em>Others...</em>
<dd>Other commands might be implemented later and conversion
functions that don't support those commands should return a
negative value.
</dl>
<p>Whether a background buffer is supplied to a conversion
function, and whether the background buffer is initialized
depends on the value of <code><em>cdata</em>->need_bkg</code>
which the conversion function should have initialized during the
H5T_CONV_INIT command. It can have one of these values:
<dl>
<dt><code>H5T_BKG_NONE</code>
<dd>No background buffer will be supplied to the conversion
function. This is the default.
<br><br>
<dt><code>H5T_BKG_TEMP</code>
<dd>A background buffer will be supplied but it will not be
initialized. This is useful for those functions requiring some
extra buffer space as the buffer can probably be allocated
more efficiently by the library (the application can supply
the buffer as part of the dataset transfer property list).
<br><br>
<dt><code>H5T_BKG_YES</code>
<dd>An initialized background buffer is passed to the conversion
function. The buffer is initialized with the current values
of the destination for the data which is passed in through the
<em>buffer</em> argument. It can be used to "fill in between
the cracks". For instance, if the destination type is a
compound datatype and we are initializing only part of the
compound datatype from the source type then the background
buffer can be used to initialize the other part of the
destination.
</dl>
<p>The <code>recalc</code> field of <em>cdata</em> is set when the
conversion path table changes. It can be used by conversion
function that cache other conversion paths so they know when
their cache needs to be recomputed.
<p>Once a conversion function is written it can be registered and
unregistered with these functions:
<dl>
<dt><code>herr_t H5Tregister(H5T_pers_t <em>pers</em>, const
char *<em>name</em>, hid_t <em>src_type</em>, hid_t
<em>dest_type</em>, H5T_conv_t <em>func</em>)</code>
<dd>Once a conversion function is written, the library must be
notified so it can be used. The function can be registered as
a hard (<code>H5T_PERS_HARD</code>) or soft
(<code>H5T_PERS_SOFT</code>) conversion depending on the value
of <em>pers</em>, displacing any previous conversions for all
applicable paths. The <em>name</em> is used only for
debugging but must be supplied. If <em>pers</em> is
<code>H5T_PERS_SOFT</code> then only the type classes of the
<em>src_type</em> and <em>dst_type</em> are used. For
instance, to register a general soft conversion function that
can be applied to any integer to integer conversion one could
say: <code>H5Tregister(H5T_PERS_SOFT, "i2i", H5T_NATIVE_INT,
H5T_NATIVE_INT, convert_i2i)</code>. One special conversion
path called the "no-op" conversion path is always defined by
the library and used as the conversion function when no data
transformation is necessary. The application can redefine this
path by specifying a new hard conversion function with a
negative value for both the source and destination datatypes,
but the library might not call the function under certain
circumstances.
<br><br>
<dt><code>herr_t H5Tunregister (H5T_pers_t <em>pers</em>, const
char *<em>name</em>, hid_t <em>src_type</em>, hid_t
<em>dest_type</em>, H5T_conv_t <em>func</em>)</code>
<dd>Any conversion path or function that matches the critera
specified by a call to this function is removed from the type
conversion table. All fields have the same interpretation as
for <code>H5Tregister()</code> with the added feature that any
(or all) may be wild cards. The
<code>H5T_PERS_DONTCARE</code> constant should be used to
indicate a wild card for the <em>pers</em> argument. The wild
card <em>name</em> is the null pointer or empty string, the
wild card for the <em>src_type</em> and <em>dest_type</em>
arguments is any negative value, and the wild card for the
<em>func</em> argument is the null pointer. The special no-op
conversion path is never removed by this function.
</dl>
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: A conversion
function</h4></caption>
<tr>
<td>
<p>Here's an example application-level function that
converts Cray <code>unsigned short</code> to any other
16-bit unsigned big-endian integer. A cray
<code>short</code> is a big-endian value which has 32
bits of precision in the high-order bits of a 64-bit
word.
<p><code><pre>
1 typedef struct {
2 size_t dst_size;
3 int direction;
4 } cray_ushort2be_t;
5
6 herr_t
7 cray_ushort2be (hid_t src, hid_t dst,
8 H5T_cdata_t *cdata, hsize_t nelmts,
9 size_t buf_str, size_t bkg_str, void *buf,
10 const void *background, hid_t plist)
11 {
12 unsigned char *src = (unsigned char *)buf;
13 unsigned char *dst = src;
14 cray_ushort2be_t *priv = NULL;
15
16 switch (cdata-&gt;command) {
17 case H5T_CONV_INIT:
18 /*
19 * We are being queried to see if we handle this
20 * conversion. We can handle conversion from
21 * Cray unsigned short to any other big-endian
22 * unsigned integer that doesn't have padding.
23 */
24 if (!H5Tequal (src, H5T_CRAY_USHORT) ||
25 H5T_ORDER_BE != H5Tget_order (dst) ||
26 H5T_SGN_NONE != H5Tget_signed (dst) ||
27 8*H5Tget_size (dst) != H5Tget_precision (dst)) {
28 return -1;
29 }
30
31 /*
32 * Initialize private data. If the destination size
33 * is larger than the source size, then we must
34 * process the elements from right to left.
35 */
36 cdata-&gt;priv = priv = malloc (sizeof(cray_ushort2be_t));
37 priv-&gt;dst_size = H5Tget_size (dst);
38 if (priv-&gt;dst_size&gt;8) {
39 priv-&gt;direction = -1;
40 } else {
41 priv-&gt;direction = 1;
42 }
43 break;
44
45 case H5T_CONV_FREE:
46 /*
47 * Free private data.
48 */
49 free (cdata-&gt;priv);
50 cdata-&gt;priv = NULL;
51 break;
52
53 case H5T_CONV_CONV:
54 /*
55 * Convert each element, watch out for overlap src
56 * with dst on the left-most element of the buffer.
57 */
58 priv = (cray_ushort2be_t *)(cdata-&gt;priv);
59 if (priv-&gt;direction&lt;0) {
60 src += (nelmts - 1) * 8;
61 dst += (nelmts - 1) * dst_size;
62 }
63 for (i=0; i&lt;n; i++) {
64 if (src==dst && dst_size&lt;4) {
65 for (j=0; j&lt;dst_size; j++) {
66 dst[j] = src[j+4-dst_size];
67 }
68 } else {
69 for (j=0; j&lt;4 && j&lt;dst_size; j++) {
70 dst[dst_size-(j+1)] = src[3-j];
71 }
72 for (j=4; j&lt;dst_size; j++) {
73 dst[dst_size-(j+1)] = 0;
74 }
75 }
76 src += 8 * direction;
77 dst += dst_size * direction;
78 }
79 break;
80
81 default:
82 /*
83 * Unknown command.
84 */
85 return -1;
86 }
87 return 0;
88 }
</pre></code>
<p>The <em>background</em> argument is ignored since
it's generally not applicable to atomic datatypes.
</td>
</tr>
</table>
</center>
<p>
<center>
<table border align=center width="100%">
<caption align=bottom><h4>Example: Soft
Registration</h4></caption>
<tr>
<td>
<p>The convesion function described in the previous
example applies to more than one conversion path.
Instead of enumerating all possible paths, we register
it as a soft function and allow it to decide which
paths it can handle.
<p><code><pre>
H5Tregister(H5T_PERS_SOFT, "cus2be",
H5T_NATIVE_INT, H5T_NATIVE_INT,
cray_ushort2be);
</pre></code>
<p>This causes it to be consulted for any conversion
from an integer type to another integer type. The
first argument is just a short identifier which will
be printed with the datatype conversion statistics.
</td>
</tr>
</table>
</center>
<p><b>NOTE:</b> The idea of a master soft list and being able to
query conversion functions for their abilities tries to overcome
problems we saw with AIO. Namely, that there was a dichotomy
between generic conversions and specific conversions that made
it very difficult to write a conversion function that operated
on, say, integers of any size and order as long as they don't
have zero padding. The AIO mechanism required such a function
to be explicitly registered (like
<code>H5Tregister_hard()</code>) for each an every possible
conversion path whether that conversion path was actually used
or not.
<hr>
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</address>
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<br>
Describes HDF5 Release 1.4.2, July 2001
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