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<HTML><HEAD>
<TITLE>HDF5 Tutorial - References to Dataset Regions
</TITLE>
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<H1><BIG><BIG><BIG><FONT COLOR="#c101cd"> References to Dataset Regions</FONT>
</BIG></BIG></BIG></H1>
<hr noshade size=1>
<BODY>
<H2>Contents:</H2>
<UL>
<LI> <A HREF="#def">References to Dataset Regions</A>
<LI> <A HREF="#def1">Creating and Storing References to Dataset Regions</A>
<LI> <A HREF="#def2">Reading References to Dataset Regions</A>
<LI> Programming Example
<UL>
<LI> <A HREF="#desc">Description</A>
<LI> <A HREF="#rem">Remarks</A>
<LI> <A HREF="#fc">File Contents</A>
</UL>
</UL>
<HR>
<A NAME="def">
<H2>References to Dataset Regions</H2>
Previously you learned about creating, reading, and writing
dataset selections. Here you will learn how to store dataset
selections in a file, and how to read them back using references
to dataset regions.
<P>
A dataset region reference points to the dataset selection by storing the
relative file address of the dataset header and the global heap offset of
the referenced selection. The selection referenced is located by retrieving
the coordinates of the areas in the selection from the global heap. This
internal mechanism of storing and retrieving dataset selections is transparent
to the user. A reference to a dataset selection (a region) is constant for
the life of the dataset.
<A NAME="def1">
<H2>Creating and Storing References to Dataset Regions</H2>
The following steps are involved in creating and storing references to
dataset regions:
<OL>
<LI> Create a dataset in which to store the dataset regions (the selections).
<P>
<LI> Create selections in the dataset(s).
The dataset(s) should already exist in the file.
<P>
<LI> Create references to the selections and store them in a buffer.
<P>
<LI> Write the dataset region references to the file.
<P>
<LI> Close all objects.
</OL>
<A NAME="def2">
<H2>Reading References to Dataset Regions</H2>
The following steps are involved in reading references to dataset
regions and referenced dataset regions (selections).
<OL>
<LI> Open and read the dataset containing references to the dataset regions.
The datatype <CODE>H5T_STD_REF_DSETREG</CODE> must be used during
the read operation.
<P>
<LI>Use <CODE>H5Rdereference</CODE> / <CODE>h5rdeference_f</CODE> to
obtain the dataset identifier from the read
dataset region reference.
<dir><dir><dir>
<B><font size=-1>OR</font></B>
</dir></dir></dir>
Use <CODE>H5Rget_region</CODE> / <CODE>h5rget_region_f</CODE> to obtain
the dataspace identifier for the dataset
containing the selection from the read dataset region reference.
<P>
<LI> Obtain information about the selection or read selected data from
the dataset.
<P>
<LI> Close all objects when they are no longer needed.
</OL>
<H2> Programming Example</H2>
<A NAME="desc">
<H3><U>Description</U></H3>
The example below first creates a dataset in the file. Then it creates a
dataset to store references to the dataset regions (selections).
The first selection is a 6 x 6 hyperslab. The second selection is a point
selection in the same dataset.
References to both selections are created and stored in the buffer and then
written to the dataset in the file.
<P>
After creating the dataset and references, the program reads the dataset
containing the dataset region references.
It reads data from the dereferenced dataset and displays the number of
elements and raw data. Then it reads two selections, a hyperslab selection
and a point selection. The program queries a number of points in the
hyperslab and their coordinates and displays them. Then it queries a number of
selected points and their coordinates and displays the information.<BR>
<P>
To obtain the example, download:
<UL>
[<A HREF="examples/h5_ref2reg.c">C example</A> ]
- <code>h5_ref2reg.c</code><BR>
[<A HREF="examples/refregexample.f90">FORTRAN example</A> ]
- <code>refregexample.f90</code>
</UL>
<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.
<P>
Following is the output from the examples:
<P>
<I><U>Output of C Example</U></I>
<PRE>
Selected hyperslab:
0 0 0 3 3 4 0 0 0
0 0 0 3 4 4 0 0 0
Selected points:
1 0 0 0 0 0 0 0 6
0 0 0 0 0 0 5 0 0
</PRE>
<I><U>Output of FORTRAN Example</U></I>
<PRE>
Hyperslab selection
3*0, 2*3, 4, 3*0
3*0, 3, 2*4, 3*0
Point selection
1, 7*0, 6
6*0, 5, 2*0
</PRE>
<A NAME="rem">
<H3><U>Remarks</U></H3>
<UL>
<LI> The following code creates a dataset to store references to the
dataset(s) regions (selections). Notice that the
<CODE>H5T_STD_REF_DSETREG</CODE> datatype is used.
<P>
<I><B>C:</I></B>
<pre>
dset1 = H5Dcreate (file_id, dsetnamer, H5T_STD_REF_DSETREG,
spacer_id, creation_prp);
</pre>
<P>
<I><B>FORTRAN:</B></I>
<pre>
CALL h5dcreate_f (file_id, dsetnamer, H5T_STD_REF_DSETREG, &
spacer_id, dset1, hdferr, creation_prp)
</pre>
<P>
<LI> This program uses hyperslab and point selections. We used the dataspace
identifier for the calls to <CODE>H5Sselect_hyperslab</CODE> /
<CODE>h5sselect_hyperslab_f</CODE> and
<CODE>H5Sselect_elements</CODE> / <CODE>h5sselect_elements_f</CODE>.
The identifier was obtained when the dataset was
created and it describes the dataset's dataspace. We did not close it when
the dataset was closed to decrease the number of function calls used
in the example.
In a real application program, one should open the dataset and determine
its dataspace using the <CODE>H5Dget_space</CODE> /
<CODE>h5dget_space_f</CODE> function.
<P>
<LI> <CODE>H5Rcreate</CODE> / <CODE>h5rcreate_f</CODE> is used to create a
dataset region reference. The signature of the function is as follows:
<P>
<I><B>C</B></I>:
<pre>
herr_t H5Rcreate (void *ref, hid_t loc_id, const char *name,
H5R_type_t ref_type, hid_t space_id)
</pre>
<P>
<I><B>FORTRAN</B></I>:
<pre>
h5rcreate_f (loc_id, name, space_id, ref, hdferr)
loc_id IN: INTEGER (HID_T)
name IN: CHARACTER (LEN=*)
space_id IN: INTEGER (HID_T)
ref_type OUT: TYPE(hdset_reg_ref_t_f)
hdferr OUT: INTEGER
</pre>
<P>
<UL>
<LI> The <em>ref</em> argument specifies the buffer in which
to store the reference.
<P>
<LI> The <I>loc_id</I> and <I>name</I> arguments specify the
referenced dataset.
<P>
<LI> In C, the <I>ref_type</I> argument specifies the reference type.
Since we are creating references to the dataset regions,
the <CODE>H5R_DATASET_REGION</CODE> datatype is used.
<P>
<LI> The <I>space_id</I> argument is a dataspace identifier.
This dataspace includes a selection in the referenced dataset.
<P>
<LI> In C, the function <CODE>H5Rcreate</CODE> returns a non-negative
value if successful and a negative value otherwise. In FORTRAN, the
return code from the <CODE>h5rcreate_f</CODE> subroutine is
returned in <I>hdferr</I>: 0 if succesful and -1 otherwise.
</UL>
<P>
<LI> The dataset with the region references was read by
<CODE>H5Dread</CODE> / <CODE>h5dread_f</CODE> with
the <CODE>H5T_STD_REF_DSETREG</CODE> datatype specified.
<P>
<LI> The read reference can be used to obtain the dataset identifier, as we
did with the following call:
<P>
<I><B>C:</B></I>
<pre>
dset2 = H5Rdereference (dset1, H5R_DATASET_REGION, &ref_out[0]);
</pre>
<P>
<I><B>FORTRAN:</B></I>
<pre>
CALL h5rdereference_f (dset1, ref_out(1), dset2, hdferr)
</pre>
<P>
or to obtain spacial information ( dataspace and selection ) with the call
to <CODE>H5Rget_region</CODE> / <CODE>h5rget_region_f</CODE>:
<P>
<I><B>C:</B></I>
<pre>
dspace2 = H5Rget_region (dset1, H5R_DATASET_REGION, &ref_out[0]);
</pre>
<P>
<I><B>FORTRAN:</B></I>
<pre>
CALL H5rget_region_f (dset1, ref_out(1), dspace2, hdferr)
</pre>
<P>
The reference to the dataset region has information for both the dataset
itself and its selection. In both calls,
<UL>
<LI> the <em>dset1</em> parameter is the identifier for the dataset
with the region references and
<P>
<LI> the <em>ref_out</em> parameter specifies the type of reference
stored. In this example a reference to the dataset region is stored.
</UL>
<P>
The C function returns the dataspace identifier or a
negative value if it is not successful.
In FORTRAN, the dataset identifier or dataspace identifier
is returned in <I>dset2</I> or <I>dspace2</I>
and the return code for the call is returned in <I>hdferr</I>:
0 if successful and -1 otherwise.
<P>
</UL>
</UL>
<A NAME="fc">
<H3><U>File Contents</U></H3>
<P>
<I><U>HDF5 File Created by C Example</U></I>
<P>
<B>Fig. A</B> <I><code>REF_REG.h5</code> in DDL</I>
<PRE>
HDF5 "REF_REG.h5" {
GROUP "/" {
DATASET "MATRIX" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 2, 9 ) / ( 2, 9 ) }
DATA {
1, 1, 2, 3, 3, 4, 5, 5, 6,
1, 2, 2, 3, 4, 4, 5, 6, 6
}
}
DATASET "REGION_REFERENCES" {
DATATYPE { H5T_REFERENCE }
DATASPACE { SIMPLE ( 2 ) / ( 2 ) }
DATA {
DATASET 0:744 {(0,3)-(1,5)}, DATASET 0:744 {(0,0), (1,6), (0,8)}
}
}
}
}
</PRE>
<I><U>HDF5 File Created by FORTRAN Example</U></I>:
<P>
<B>Fig. B</B> <I><code>FORTRAN.h5</code> in DDL</I>
<PRE>
HDF5 "FORTRAN.h5" {
GROUP "/" {
DATASET "MATRIX" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 9, 2 ) / ( 9, 2 ) }
DATA {
1, 1,
1, 2,
2, 2,
3, 3,
3, 4,
4, 4,
5, 5,
5, 6,
6, 6
}
}
DATASET "REGION_REFERENCES" {
DATATYPE { H5T_REFERENCE }
DATASPACE { SIMPLE ( 2 ) / ( 2 ) }
DATA {
DATASET 0:744 {(3,0)-(5,1)}, DATASET 0:744 {(0,0), (6,1), (8,0)}
}
}
}
}
</PRE>
Notice how the raw data in the dataset with the dataset regions is displayed.
Each element of the raw data consists of a reference to the dataset
(DATASET number1:number2) and its selected region.
If the selection is a hyperslab, the corner coordinates of the hyperslab
are displayed.
For the point selection, the coordinates of each point are displayed.
<!--
Since only two selections were stored, the third and fourth elements of the
dataset are set to NULL. This was done by the buffer
inizialization in the program.
-->
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<BR> <H6>Last Modified: March 16, 2001</H6><BR>
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