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Added html files with references to the fortran 90 files.
(under examples/)
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Barbara Jones
2001-03-19 09:26:47 -05:00
parent 380eb42bc5
commit f11cef2c56
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doc/html/Tutor/crtdat.html
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@@ -36,68 +36,132 @@ width=78 height=27 alt="NCSA"><P></A>
<P>
A dataset is a multidimensional array of data elements, together with
supporting metadata. To create a dataset, the application program must specify
the location to create the dataset, the dataset name, the data type and space
of the data array, and the dataset creation properties.
the location at which to create the dataset, the dataset name, the datatype
and dataspace of the data array, and the dataset creation property list.
<P>
<H3> Data Types</H3>
A data type is a collection of data type properties, all of which can
<H3> Datatypes</H3>
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 data type.
information for data conversion to or from that datatype.
<P>
There are two categories of data types in HDF5: atomic and compound data
types. An atomic type is a type which cannot be decomposed into smaller
units at the API level. A compound data type is a collection of one or more
atomic types or small arrays of such types.
There are two categories of datatypes in HDF5: atomic and compound
datatypes. An <i>atomic datatype</i> is a datatype which cannot be
decomposed into smaller datatype units at the API level.
These include the integer, float, date and time, string, bitfield, and
opaque datatypes.
A <i>compound datatype</i> is a collection of one or more
atomic datatypes and/or small arrays of such datatypes.
<P>
Atomic types include integer, float, date and time, string, bit field, and
opaque. Figure 5.1 shows the HDF5 data types. Some of the HDF5 predefined
atomic data types are listed in Figure 5.2. In this tutorial, we consider
only
HDF5 predefined integers. For information on data types, see the HDF5
User's Guide.
Figure 5.1 shows the HDF5 datatypes. Some of the HDF5 predefined
atomic datatypes are listed in Figures 5.2a and 5.2b.
In this tutorial, we consider only HDF5 predefined integers.
For further information on datatypes, see
<a href="../Datatypes.html">The Datatype Interface (H5T)</a> in the
<cite>HDF5 User's Guide</cite>.
<P>
<B>Fig 5.1</B> &nbsp; <I>HDF5 data types</I>
<B>Fig 5.1</B> &nbsp; <I>HDF5 datatypes</I>
<PRE>
+-- integer
+-- floating point
+---- atomic ----+-- date and time
| +-- character string
HDF5 datatypes --| +-- bit field
HDF5 datatypes --| +-- bitfield
| +-- opaque
|
+---- compound
</PRE>
<B>Fig. 5.2</B> &nbsp; <I>Examples of HDF5 predefined data types</I>
<table width="52%" border="1" cellpadding="4">
<table width="100%" border="0" cellpadding="4">
<tr><td valign=top>
<B>Fig. 5.2a</B> &nbsp; <I>Examples of HDF5 predefined datatypes</I>
<table width="95%" border="1" cellpadding="0">
<tr bgcolor="#ffcc99" bordercolor="#FFFFFF">
<td width="20%"><b>Data Type</b></td>
<td width="20%"><b>Datatype</b></td>
<td width="80%"><b>Description</b></td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%">H5T_STD_I32LE</td>
<td width="80%">Four-byte, little-endian, signed two's complement integer</td>
<td bgcolor="#99cccc" width="20%"><code>H5T_STD_I32LE</code></td>
<td width="80%">Four-byte, little-endian, signed, two's complement integer</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%">H5T_STD_U16BE</td>
<td bgcolor="#99cccc" width="20%"><code>H5T_STD_U16BE</code></td>
<td width="80%">Two-byte, big-endian, unsigned integer</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%">H5T_IEEE_F32BE</td>
<td bgcolor="#99cccc" width="20%"><code>H5T_IEEE_F32BE</code></td>
<td width="80%">Four-byte, big-endian, IEEE floating point</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%">H5T_IEEE_F64LE</td>
<td bgcolor="#99cccc" width="20%"><code>H5T_IEEE_F64LE</code></td>
<td width="80%">Eight-byte, little-endian, IEEE floating point</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%">H5T_C_S1</td>
<td bgcolor="#99cccc" width="20%"><code>H5T_C_S1</code></td>
<td width="80%">One-byte, null-terminated string of eight-bit characters</td>
</tr>
</table>
<H3>Dataspaces</H3>
</td><td valign=top>
<B>Fig. 5.2b</B> &nbsp; <I>Examples of HDF5 predefined native datatypes</I>
<table width="95%" border="1" cellpadding="4">
<tr bgcolor="#ffcc99" bordercolor="#FFFFFF">
<td width="20%"><b>Native Datatype</b></td>
<td width="80%"><b>Corresponding C or FORTRAN Type</b></td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><B>C:</B></td>
<td width="80%">&nbsp; </td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_INT</code></td>
<td width="80%">int</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_FLOAT</code></td>
<td width="80%">float</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_CHAR</code></td>
<td width="80%">char</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_DOUBLE</code></td>
<td width="80%">double</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_LDOUBLE</code></td>
<td width="80%">long double</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><B>FORTRAN:</B></td>
<td width="80%">&nbsp; </td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_INT</code></td>
<td width="80%">integer</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_REAL</code></td>
<td width="80%">real</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_DOUBLE</code></td>
<td width="80%">double precision</td>
</tr>
<tr bordercolor="#FFFFFF">
<td bgcolor="#99cccc" width="20%"><code>H5T_NATIVE_CHAR</code></td>
<td width="80%">character</td>
</tr>
</table>
</table>
<H3> Datasets and Dataspaces</H3>
A dataspace describes the dimensionality of the data array. A dataspace
is either a regular N-dimensional array of data points, called a simple
@@ -114,27 +178,29 @@ of the data array, and the dataset creation properties.
</PRE>
The dimensions of a dataset can be fixed (unchanging), or they may be
unlimited, which means that they are extendible. A dataspace can also
describe portions of a dataset, making it possible to do partial I/O
unlimited, which means that they are extensible. A dataspace can also
describe a portion of a dataset, making it possible to do partial I/O
operations on selections.
<h3>Dataset creation properties</H3>
<h3>Dataset Creation Property Lists</H3>
When creating a dataset, HDF5 allows users to specify how raw data is
organized on disk and how the raw data is compressed. This information is
When creating a dataset, HDF5 allows the user to specify how raw data is
organized and/or compressed on disk. This information is
stored in a dataset creation property list and passed to the dataset
interface. The raw data on disk can be stored contiguously (in the same
linear way that it is organized in memory), partitioned into chunks and
stored externally, etc. In this tutorial, we use the default creation
property list; that is, no compression and
contiguous storage layout is used. For more information about the creation
properties, see the HDF5 User's Guide.
linear way that it is organized in memory), partitioned into chunks,
stored externally, etc. In this tutorial, we use the
default dataset creation property list; that is, contiguous storage layout
and no compression are used. For more information about
dataset creation property lists,
see <a href="../Datasets.html">The Dataset Interface (H5D)</a>
in the <cite>HDF5 User's Guide</cite>.
<P>
In HDF5, data types and spaces are independent objects, which are created
separately from any dataset that they might be attached to. Because of this the
creation of a dataset requires definitions of data type and dataspace.
In this tutorial, we use HDF5 predefined data types (integer) and consider
In HDF5, datatypes and dataspaces are independent objects which are created
separately from any dataset that they might be attached to. Because of this,
the creation of a dataset requires definition of the datatype and dataspace.
In this tutorial, we use HDF5 predefined datatypes (integer) and consider
only simple dataspaces. Hence, only the creation of dataspace objects is
needed.
<P>
@@ -142,158 +208,250 @@ needed.
To create an empty dataset (no data written) the following steps need to be
taken:
<OL>
<LI> Obtain the location id where the dataset is to be created.
<LI> Define the dataset characteristics and creation properties.
<LI> Obtain the location identifier where the dataset is to be created.
<LI> Define the dataset characteristics and the dataset creation property list.
<UL>
<LI> define a data type
<LI> define a dataspace
<LI> specify dataset creation properties
<LI> Define a datatype.
<LI> Define a dataspace.
<LI> Specify the dataset creation property list.
</UL>
<LI> Create the dataset.
<LI> Close the data type, dataspace, and the property list if necessary.
<LI> Close the datatype, the dataspace, and the property list if necessary.
<LI> Close the dataset.
</OL>
To create a simple dataspace, the calling program must contain the following
calls:
To create a simple dataspace, the calling program must contain a
call to create and close the dataspace. For example:
<P>
<I>C</I>:
<PRE>
dataspace_id = H5Screate_simple(rank, dims, maxdims);
H5Sclose(dataspace_id );
space_id = H5Screate_simple (rank, dims, maxdims);
status = H5Sclose (space_id );
</PRE>
<I>FORTRAN</I>:
<PRE>
CALL h5screate_simple_f (rank, dims, space_id, hdferr, maxdims=max_dims)
<i>or</i>
CALL h5screate_simple_f (rank, dims, space_id, hdferr)
CALL h5sclose_f (space_id, hdferr)
</PRE>
To create a dataset, the calling program must contain the following calls:
To create a dataset, the calling program must contain calls to create
and close the dataset. For example:
<P>
<I>C</I>:
<PRE>
dataset_id = H5Dcreate(hid_t loc_id, const char *name, hid_t type_id,
hid_t space_id, hid_t create_plist_id);
H5Dclose (dataset_id);
dset_id = H5Dcreate (hid_t loc_id, const char *name, hid_t type_id,
hid_t space_id, hid_t creation_prp);
status = H5Dclose (dset_id);
</PRE>
<I>FORTRAN</I>:
<PRE>
CALL h5dcreate_f (loc_id, name, type_id, space_id, dset_id, &
hdferr, creation_prp=creat_plist_id)
<i>or</i>
CALL h5dcreate_f (loc_id, name, type_id, space_id, dset_id, hdferr)
CALL h5dclose_f (dset_id, hdferr)
</PRE>
If using the pre-defined datatypes in FORTRAN, then a call must
be made to initialize and terminate access to the pre-defined datatypes:
<PRE>
CALL h5init_types_f (hdferr)
CALL h5close_types_f (hdferr)
</PRE>
<code>h5init_types_f</code> must be called before any HDF5 library
subroutine calls are made;
<code>h5close_types_f</code> must be called after the final HDF5 library
subroutine call.
See the programming example below for an illustration of the use of
these calls.
<P>
<H2> Programming Example</H2>
<A NAME="desc">
<H3><U>Description</U></H3>
The following example shows how to create an empty dataset.
It creates a file called 'dset.h5', defines the dataset dataspace, creates a
It creates a file called <code>dset.h5</code> in the C version
(<code>dsetf.h5</code> in Fortran), defines the dataset dataspace, creates a
dataset which is a 4x6 integer array, and then closes the dataspace,
the dataset, and the file. <BR>
[ <A HREF="examples/h5_crtdat.c">Download h5_crtdat.c</A> ]
<PRE>
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<UL>
[ <A HREF="examples/h5_crtdat.c">C Example</A> ]
-- <code>h5_crtdat.c</code><BR>
[ <A HREF="examples/dsetexample.f90">Fortran Example</A> ]
-- <code>dsetexample.f90</code><BR>
[ <A HREF="examples/java/CreateDataset.java">Java Example</A> ]
-- <code>CreateDataset.java</code>
</UL>
#include &lt;hdf5.h&gt;
#define FILE "dset.h5"
main() {
hid_t file_id, dataset_id, dataspace_id; /* identifiers */
hsize_t dims[2];
herr_t status;
/* Create a new file using default properties. */
file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create the data
space for the dataset. */
dims[0] = 4;
dims[1] = 6;
dataspace_id = H5Screate_simple(2, dims, NULL);
/* Create the dataset. */
dataset_id = H5Dcreate(file_id, "/dset", H5T_STD_I32BE, dataspace_id,
H5P_DEFAULT);
/* End access to the dataset and release resources used by it. */
status = H5Dclose(dataset_id);
/* Terminate access to the data space. */
status = H5Sclose(dataspace_id);
/* Close the file. */
status = H5Fclose(file_id);
}
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
</PRE>
<B>NOTE:</B> To download a tar file of the examples, including a Makefile,
please go to the <A HREF="references.html">References</A> page of this tutorial.
<A NAME="rem">
<H3><U>Remarks</U></H3>
<UL>
<LI> H5Screate_simple creates a new simple data space and returns a data space
identifier.
<LI><code>H5Screate_simple</code>/<code>h5screate_simple_f</code>
creates a new simple dataspace and returns a dataspace identifier.
<PRE>
<I>C</I>:
hid_t H5Screate_simple (int rank, const hsize_t * dims,
const hsize_t * maxdims)
<I>FORTRAN</I>:
h5screate_simple_f (rank, dims, space_id, hdferr, maxdims)
rank INTEGER
dims(*) INTEGER(HSIZE_T)
space_id INTEGER(HID_T)
hdferr INTEGER
(Valid values: 0 on success and -1 on failure)
maxdims(*) INTEGER(HSIZE_T), OPTIONAL
</PRE>
<UL>
<LI> The first parameter specifies the rank of the dataset.
<LI> The <I>rank</I> parameter specifies the rank, i.e., the number of
dimensions, of the dataset.
<LI> The second parameter specifies the size of the dataset.
<LI> The <I>dims</I> parameter specifies the size of the dataset.
<LI> The third parameter is for the upper limit on the size of the dataset.
If it is NULL, the upper limit is the same as the dimension
sizes specified by the second parameter.
<LI>The <I>maxdims</I> parameter specifies the upper limit on the
size of the dataset.
If this parameter is NULL in C (or not specified in FORTRAN),
then the upper limit is the same as the dimension
sizes specified by the <I>dims</I> parameter.
<LI>The function returns the dataspace identifier in C if successful;
otherwise it returns a negative value.
In FORTRAN, the dataspace identifier
is returned in the <I>space_id</I> parameter. If the call is successul
then a 0 is returned in <I>hdferr</I>; otherwise a -1 is returned.
</UL>
<P>
<LI> H5Dcreate creates a dataset at the specified location and returns a
dataset identifier.
<LI><code>H5Dcreate</code>/<code>h5dcreate_f</code> creates a dataset
at the specified location and returns a dataset identifier.
<PRE>
<I>C</I>:
hid_t H5Dcreate (hid_t loc_id, const char *name, hid_t type_id,
hid_t space_id, hid_t create_plist_id)
hid_t space_id, hid_t creation_prp)
<I>FORTRAN</I>:
h5dcreate_f (loc_id, name, type_id, space_id, dset_id, &
hdferr, creation_prp)
loc_id INTEGER(HID_T)
name CHARACTER(LEN=*)
type_id INTEGER(HID_T)
space_id INTEGER(HID_T)
dset_id INTEGER(HID_T)
hdferr INTEGER
(Valid values: 0 on success and -1 on failure)
creation_prp INTEGER(HID_T), OPTIONAL
</PRE>
<UL>
<LI> The first parameter is the location identifier.
<LI> The <I>loc_id</I> parameter is the location identifier.
<P>
<LI> The <I>name</I> parameter is the name of the dataset to create.
<LI> The second parameter is the name of the dataset to create.
<P>
<LI> The <I>type_id</I> parameter specifies the datatype identifier.
<LI> The third parameter is the data type identifier. H5T_STD_I32BE, a
32-bit Big Endian integer, is an HDF atomic data type.
<P>
<LI> The <I>space_id</I> parameter is the dataspace identifier.
<LI> The fourth parameter is the data space identifier.
<P>
<LI> The <I>creation_prp</I> parameter specifies the
dataset creation property list.
<code>H5P_DEFAULT</code> in C and <code>H5P_DEFAULT_F</code> in FORTRAN
specify the default dataset creation property list.
This parameter is optional in FORTRAN; if it is omitted,
the default dataset creation property list will be used.
<P>
<LI> The C function returns the dataset identifier if successful and
a negative value otherwise. The FORTRAN call returns the
dataset identifier in <I>dset_id</I>. If it is successful, then 0 is
returned in <I>hdferr</I>; otherwise a -1 is returned.
<LI> The last parameter specifies the dataset creation property list.
H5P_DEFAULT specifies the default dataset creation property list.
</UL>
<P>
<LI>H5Dcreate creates an empty array and initializes the data to 0.
<LI><code>H5Dcreate</code>/<code>h5dcreate_f</code> creates an empty array
and initializes the data to 0.
<P>
<LI> When a dataset is no longer accessed by a program, H5Dclose must be
called to release the resource used by the dataset. This call is mandatory.
<LI> When a dataset is no longer accessed by a program,
<code>H5Dclose</code>/<code>h5dclose_f</code> must be called to release
the resource used by the dataset. This call is mandatory.
<PRE>
hid_t H5Dclose (hid_t dataset_id)
<I>C</I>:
hid_t H5Dclose (hid_t dset_id)
<I>FORTRAN</I>:
h5dclose_f (dset_id, hdferr)
dset_id INTEGER(HID_T)
hdferr INTEGER
(Valid values: 0 on success and -1 on failure)
</PRE>
</UL>
<A NAME="fc">
<H3><U>File Contents</U></H3>
The file contents of 'dset.h5' are shown is <B>Figure 5.4</B> and <B>Figure 5.5</B>.
<table width="73%" border="1" cellspacing="4" bordercolor="#FFFFFF">
The contents of the file <code>dset.h5</code> (<code>dsetf.h5</code>
for FORTRAN) are shown in <B>Figure 5.4</B> and <B>Figures 5.5a </B>
and <B>5.5b</B>.
<P>
<table border="0">
<tr align=left><td>
<B>Figure 5.4</B> &nbsp; <I>Contents of <code>dset.h5</code> ( <code>dsetf.h5</code>)</i>
</td></tr><tr align=center><td>
<IMG src="img002.gif"> </PRE>
</td></tr></table>
<table width="100%" border="1" cellspacing="4" bordercolor="#FFFFFF">
<tr bordercolor="#FFFFFF">
<td width="37%"><b>Figure 5.4</b> &nbsp; <i>The Contents of 'dset.h5'</i>
</td>
<td width="63%"><b>Figure 5.5</b> &nbsp; <i>'dset.h5' in DDL</i> </td>
<td width="50%"><b>Figure 5.5a</b> &nbsp; <i><code>dset.h5</code> in DDL</i> </td>
<td width="50%"><b>Figure 5.5b</b> &nbsp; <i><code>dsetf.h5</code> in DDL</i> </td>
</tr>
<tr bordercolor="#000000">
<!-- <td width="37%"><IMG src="dseth5.jpg" width="206" height="333"></td> -->
<td width="37%"><IMG src="img002.gif"></td>
<td width="63%">
<pre> HDF5 "dset.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 4, 6 ) / ( 4, 6 ) }
DATA {
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0
}
}
<td width="35%">
<PRE>
HDF5 "dset.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 4, 6 ) / ( 4, 6 ) }
DATA {
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0
}
}
}
}
</PRE>
</td>
<td width="35%">
<pre>
HDF5 "dsetf.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 6, 4 ) / ( 6, 4 ) }
DATA {
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0
}
}
}
}
</pre>
</td>
</tr>
</table>
<p>
Note in Figures 5.5a and 5.5b that
<code>H5T_STD_I32BE</code>, a 32-bit Big Endian integer,
is an HDF atomic datatype.
<A NAME="ddl">
@@ -302,12 +460,12 @@ The following is the simplified DDL dataset definition:
<P>
<B>Fig. 5.6</B> &nbsp; <I>HDF5 Dataset Definition</I>
<PRE>
&lt;dataset&gt ::= DATASET "&lt;dataset_name&gt;" { &lt;data type&gt
&lt;dataset&gt ::= DATASET "&lt;dataset_name&gt;" { &lt;datatype&gt
&lt;dataspace&gt
&lt;data&gt
&lt;dataset_attribute&gt;* }
&lt;data type&gt ::= DATATYPE { &lt;atomic_type&gt }
&lt;datatype&gt ::= DATATYPE { &lt;atomic_type&gt }
&lt;dataspace&gt ::= DATASPACE { SIMPLE &lt;current_dims&gt / &lt;max_dims&gt }
@@ -329,8 +487,10 @@ The following is the simplified DDL dataset definition:
<!-- <A HREF="helpdesk.mail.html"> -->
<A HREF="mailto:hdfhelp@@ncsa.uiuc.edu">
hdfhelp@@ncsa.uiuc.edu</A>
<BR> <H6>Last Modified: August 27, 1999</H6><BR>
<br>
<BR> <H6>Last Modified: March 9, 2001</H6><BR>
<!-- modified by Barbara Jones - bljones@@ncsa.uiuc.edu -->
<!-- modified by Frank Baker - fbaker@@ncsa.uiuc.edu -->
</FONT>
<BR>
<!-- <A HREF="mailto:hdfhelp@@ncsa.uiuc.edu"> -->