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<HTML><HEAD>
<TITLE>HDF5 Tutorial - Reading from and Writing to a Dataset
</TITLE>
</HEAD>
<body bgcolor="#ffffff">
<!-- BEGIN MAIN BODY -->
[ <A HREF="title.html"><I>HDF5 Tutorial Top</I></A> ]
<H1>
<BIG><BIG><BIG><FONT COLOR="#c101cd">Reading from and Writing to a Dataset</FONT>
</BIG></BIG></BIG></H1>
<hr noshade size=1>
<BODY>
<H2>Contents:</H2>
<UL>
<LI><A HREF="#rdwr">Reading from and Writing to a Dataset</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="rdwr">
<H2>Reading from and Writing to a Dataset</h2>
<P>
During a dataset I/O operation, the library transfers raw data between memory
and the file. The data in memory can have a datatype different from that of
the file and can also be of a different size
(i.e., the data in memory is a subset of the dataset elements, or vice versa).
Therefore, to perform read or write operations, the application
program must specify:
<UL>
<LI> The dataset
<LI> The dataset's datatype in memory
<LI> The dataset's dataspace in memory
<LI> The dataset's dataspace in the file
<LI>The dataset transfer property list
(The dataset transfer property list controls various aspects of the
I/O operations, such as the number of processes participating in a
collective I/O request or hints to the library to control caching of
raw data. In this tutorial, we use the default dataset transfer
property list.)
<LI> The data buffer
</UL>
<P>
The steps to read from or write to a dataset are
as follows:
<OL>
<LI> Obtain the dataset identifier.
<LI> Specify the memory datatype.
<LI> Specify the memory dataspace.
<LI> Specify the file dataspace.
<LI> Specify the transfer properties.
<LI> Perform the desired operation on the dataset.
<LI> Close the dataset.
<LI> Close the dataspace, datatype, and property list if necessary.
</OL>
To read from or write to a dataset,
the <code>H5Dread</code>/<code>h5dread_f</code> and
<code>H5Dwrite</code>/<code>h5dwrite_f</code>
routines are used. <P>
<I>C</I>:
<PRE>
status = H5Dread (set_id, mem_type_id, mem_space_id, file_space_id,
xfer_prp, buf );
status = H5Dwrite (set_id, mem_type_id, mem_space_id, file_space_id,
xfer_prp, buf);
</PRE>
<I>FORTRAN</I>:
<PRE>
CALL h5dread_f(dset_id, mem_type_id, buf, error, &
mem_space_id=mspace_id, file_space_id=fspace_id, &
xfer_prp=xfer_plist_id)
<font face=times><i>or</i></font>
CALL h5dread_f(dset_id, mem_type_id, buf, error)
CALL h5dwrite_f(dset_id, mem_type_id, buf, error, &
mem_space_id=mspace_id, file_space_id=fspace_id, &
xfer_prp=xfer_plist_id)
<font face=times><i>or</i></font>
CALL h5dwrite_f(dset_id, mem_type_id, buf, error)
</PRE>
<P>
<H2> Programming Example</H2>
<A NAME="desc">
<H3><U>Description</U></H3>
The following example shows how to read and write an existing dataset.
It opens the file created in the previous example, obtains the dataset
identifier for the dataset <code>/dset</code>,
writes the dataset to the file, then reads the dataset back from
memory. It then closes the dataset and file. <BR>
<UL>
[ <A HREF="examples/h5_rdwt.c">C Example</A> ] - <code>h5_rdwt.c</code> <BR>
[ <A HREF="examples/rwdsetexample.f90">FORTRAN Example</A> ] - <code>rwdsetexample.f90</code><BR>
[ <A HREF="examples/java/DatasetRdWt.java">Java Example</A> ] - <code>DatasetRdWt.java</code> <BR>
</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.
</PRE>
<A NAME="rem">
<H3><U>Remarks</U></H3>
<UL>
<LI><code>H5Fopen</code>/<code>h5fopen_f</code> opens an existing file and
returns a file identifier.
<PRE>
<I>C</I>:
hid_t H5Fopen (const char *name, unsigned access_mode, hid_t access_prp)
<I>FORTRAN</I>:
h5fopen_f (name, access_mode, file_id, hdferr, access_prp)
name CHARACTER(LEN=*)
access_mode INTEGER
(Possible values: H5F_ACC_RDWR_F, H5F_ACC_RDONLY_F)
file_id INTEGER(HID_T)
hdferr INTEGER
(Possible values: 0 on success and -1 on failure)
access_prp INTEGER(HID_T), OPTIONAL
</PRE>
<UL>
<LI> The argument <I>name</I> is the filename.
<P>
<LI> The <I>access_mode</I> parameter is the file access mode.
<code>H5F_ACC_RDWR</code> in C
(<code>H5F_ACC_RDWR_F</code> in FORTRAN)
allows read/write access
while <code>H5F_ACC_RDONLY</code> in C
(<code>H5F_ACC_RDONLY_F</code> in FORTRAN)
allows read-only access.
<P>
<LI> The <I>access_prp</I> parameter identifies the file access property list.
<code>H5P_DEFAULT</code> in C and <code>H5P_DEFAULT_F</code> in FORTRAN
specify the default file access property list.
This parameter is optional in FORTRAN; if it is omitted, the default file
access property list is used.
<P>
<LI>In FORTRAN, the return code is passed back in the <I>hdferr</I>
parameter: 0 if successful, -1 if not. In C, the function returns
the file identifier if successful, and a negative value otherwise.
</UL>
<P>
<LI> <code>H5Dopen</code>/<code>h5dopen_f</code> opens an existing dataset
with the name specified by <i>name</i> at the location specified by
<i>loc_id</i>.
For FORTRAN, the return value is passed in the <I>hdferr</I> parameter:
0 if successful, -1 if not. For C, the function returns the dataset
identifier if successful, and a negative value if not.
<P>
<I>C</I>:
<PRE>
hid_t H5Dopen (hid_t loc_id, const char *name)
</PRE>
<I>FORTRAN</I>:
<PRE>
h5dopen_f(loc_id, name, hdferr)
loc_id INTEGER(HID_T)
name CHARACTER(LEN=*)
hdferr INTEGER
(Possible values: 0 on success and -1 on failure)
</PRE>
<P>
<LI><code>H5Dwrite</code>/<code>h5dwrite_f</code> writes raw data
from an application buffer to the specified
dataset, converting from the datatype and dataspace of the dataset in
memory to the datatype and dataspace of the dataset in the file.
<P>
<I>C</I>:
<PRE>
herr_t H5Dwrite (hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t xfer_prp, const void * buf)
</PRE>
<I>FORTRAN</I>:
<PRE>
h5dwrite_f (dset_id, mem_type_id, buf, hdferr, mem_space_id, &
file_space_id, xfer_prp)
dset_id INTEGER(HID_T)
mem_type_id INTEGER(HID_T)
buf(*,...*) TYPE
hdferr INTEGER
(Possible values: 0 on success and -1 on failure)
mem_space_id INTEGER(HID_T), OPTIONAL
(Default value: H5S_ALL_F)
file_space_id INTEGER(HID_T), OPTIONAL
(Default value: H5S_ALL_F)
xfer_prp INTEGER(HID_T), OPTIONAL
(Default value: H5P_DEFAULT_F)
</PRE>
<UL>
<LI> The <I>dset_id</I> is the dataset identifier.
<P>
<LI> The <I>mem_type_id</I> parameter is the identifier of the dataset's
memory datatype. <code>H5T_NATIVE_INT</code> in C
(<code>H5T_NATIVE_INTEGER</code> in FORTRAN) is an integer datatype
for the machine on which the library was compiled.
<P>
<LI> The <I>mem_space_id</I> parameter is the identifier of the dataset's
memory dataspace. <code>H5S_ALL</code> in C (<code>H5S_ALL_F</code>
in FORTRAN) is the default value and indicates that the whole dataspace
in memory is selected for the I/O operation.
This parameter is optional in FORTRAN; if it is omitted, the default
will be used.
<P>
<LI> The <I>file_space_id</I> parameter is the identifier of the
dataset's file dataspace.
<code>H5S_ALL</code> in C (<code>H5S_ALL_F</code> in FORTRAN)
is the default value and indicates that the entire dataspace of
the dataset in the file is selected for the I/O operation.
This parameter is optional in FORTRAN; if it is omitted, the default
will be used.
<P>
<LI> The <I>xfer_prp</I> parameter is the data transfer propery list
identifier.
<code>H5P_DEFAULT</code> in C
(<code>H5P_DEFAULT_F</code> in FORTRAN) is the default value and
indicates that the default data transfer property list is used.
This parameter is optional in FORTRAN; if it is omitted, the default
will be used.
<P>
<LI> The <I>buf</I> parameter is the data buffer to write.
<P>
<LI> In FORTRAN, the <I>hdferr</I> parameter is for the error code
passed back: 0 if successful, -1 if not. In C, this function
returns a non-negative value if successful; otherwise it returns
a negative value.
</UL>
<P>
<LI><code>H5Dread</code>/<code>h5dread_f</code> reads raw data from the
specified dataset to an application buffer,
converting from the file datatype and dataspace to the memory datatype and
dataspace.
<P>
<I>C</I>:
<PRE>
herr_t H5Dread (hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t xfer_prp, void * buf)
</PRE>
<I>FORTRAN</I>:
<PRE>
h5dread_f (dset_id, mem_type_id, buf, hdferr, mem_space_id, &
file_space_id, xfer_prp)
dset_id INTEGER(HID_T)
mem_type_id INTEGER(HID_T)
buf(*,...*) TYPE
hdferr INTEGER
(Possible values: 0 on success and -1 on failure)
mem_space_id INTEGER(HID_T), OPTIONAL
(Default value: H5S_ALL_F)
file_space_id INTEGER(HID_T), OPTIONAL
(Default value: H5S_ALL_F)
xfer_prp INTEGER(HID_T), OPTIONAL
(Default value: H5P_DEFAULT_F)
</PRE>
<p>
<UL>
<LI>The <I>dset_id</I> parameter is the dataset identifier.
<P>
<LI>The <I>mem_type_id</I> parameter is the identifier of the dataset's
memory datatype. <code>H5T_NATIVE_INT</code> in C
(<code>H5T_NATIVE_INTEGER</code> in FORTRAN) is an integer datatype
for the machine on which the library was compiled.
<P>
<LI>The <I>mem_space_id</I> parameter is the identifier of the dataset's
memory dataspace. <code>H5S_ALL</code> in C (<code>H5S_ALL_F</code>
in FORTRAN) is the default value and indicates that the whole dataspace
in memory is selected for the I/O operation.
This parameter is optional in FORTRAN; if it is omitted, the default
will be used.
<P>
<LI>The <I>file_space_id</I> parameter is the identifier of the
dataset's file dataspace.
<code>H5S_ALL</code> in C (<code>H5S_ALL_F</code> in FORTRAN)
is the default value and indicates that the entire dataspace of
the dataset in the file is selected for the I/O operation.
This parameter is optional in FORTRAN; if it is omitted, the default
will be used.
<P>
<LI>The <I>xfer_prp</I> parameter is the data transfer propery list
identifier.
<code>H5P_DEFAULT</code> in C
(<code>H5P_DEFAULT_F</code> in FORTRAN) is the default value and
indicates that the default data transfer property list is used.
This parameter is optional in FORTRAN; if it is omitted, the default
will be used.
<P>
<LI> The <I>buf</I> parameter is the data buffer to read into.
<P>
<LI> In FORTRAN, the <I>hdferr</I> parameter is for the error code
passed back: 0 if successful, -1 if not. In C, this function
returns a non-negative value if successful; otherwise it returns
a negative value.
</UL>
</UL>
<A NAME="fc">
<H3><U>File Contents</U></H3>
Figure 6.1a shows the contents of <code>dset.h5</code> (created by the C program).
<BR>
Figure 6.1b shows the contents of <code>dsetf.h5</code> (created by the FORTRAN
program).
<P>
<B>Fig. 6.1a</B> <I><code>dset.h5</code> in DDL</I>
<PRE>
HDF5 "dset.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 4, 6 ) / ( 4, 6 ) }
DATA {
1, 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24
}
}
}
}
</PRE>
<P>
<B>Fig. 6.1b</B> <I><code>dsetf.h5</code> in DDL</I>
<PRE>
HDF5 "dsetf.h5" {
GROUP "/" {
DATASET "dset" {
DATATYPE { H5T_STD_I32BE }
DATASPACE { SIMPLE ( 6, 4 ) / ( 6, 4 ) }
DATA {
1, 7, 13, 19,
2, 8, 14, 20,
3, 9, 15, 21,
4, 10, 16, 22,
5, 11, 17, 23,
6, 12, 18, 24
}
}
}
}
</PRE>
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<BR> <H6>Last Modified: June 22, 2001</H6><BR>
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