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<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
<html>
  <head>
    <title>Dataset Interface (H5D)</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;
      Datasets&nbsp;&nbsp;
      <a href="Datatypes.html">Datatypes</a>&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;
      <br>
      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
</td></tr>
</table>
</center>
<hr>

    <h1>The Dataset Interface (H5D)</h1>

    <h2>1. Introduction</h2>

    <p>The purpose of the dataset interface is to provide a mechanism
      to describe properties of datasets and to transfer data between
      memory and disk.  A dataset is composed of a collection of raw
      data points and four classes of meta data to describe the data
      points.  The interface is hopefully designed in such a way as to
      allow new features to be added without disrupting current
      applications that use the dataset interface.

    <p>The four classes of meta data are:

    <dl>
      <dt>Constant Meta Data
      <dd>Meta data that is created when the dataset is created and
	exists unchanged for the life of the dataset.  For instance,
	the datatype of stored array elements is defined when the
	dataset is created and cannot be subsequently changed.
	
      <dt>Persistent Meta Data
      <dd>Meta data that is an integral and permanent part of a
	dataset but can change over time.  For instance, the size in
	any dimension can increase over time if such an increase is
	allowed when the dataset was created.

      <dt>Memory Meta Data
      <dd>Meta data that exists to describe how raw data is organized
	in the application's memory space.  For instance, the data
	type of elements in an application array might not be the same
	as the datatype of those elements as stored in the HDF5 file.

      <dt>Transport Meta Data
      <dd>Meta data that is used only during the transfer of raw data
	from one location to another.  For instance, the number of
	processes participating in a collective I/O request or hints
	to the library to control caching of raw data.
    </dl>

    <p>Each of these classes of meta data is handled differently by
      the library although the same API might be used to create them.
      For instance, the datatype exists as constant meta data and as
      memory meta data; the same API (the <code>H5T</code> API) is
      used to manipulate both pieces of meta data but they're handled
      by the dataset API (the <code>H5D</code> API) in different
      manners.



    <h2>2. Storage Layout Properties</h2>

    <p>The dataset API partitions these terms on three orthogonal axes
      (layout, compression, and external storage) and uses a
      <em>dataset creation property list</em> to hold the various
      settings and pass them through the dataset interface.  This is
      similar to the way HDF5 files are created with a file creation
      property list.  A dataset creation property list is always
      derived from the default dataset creation property list (use
      <code>H5Pcreate()</code> to get a copy of the default property
      list) by modifying properties with various
      <code>H5Pset_<em>property</em>()</code> functions.

    <dl>
      <dt><code>herr_t H5Pset_layout (hid_t <em>plist_id</em>,
	  H5D_layout_t <em>layout</em>)</code>
      <dd>The storage layout is a piece of constant meta data that
	describes what method the library uses to organize the raw
	data on disk. The default layout is contiguous storage.

	<br><br>
	<dl>
	  <dt><code>H5D_COMPACT</code>  &nbsp;&nbsp; <i><b>(Not yet implemented.)</b></i>
	  <dd>The raw data is presumably small and can be stored
	    directly in the object header.  Such data is
	    non-extendible, non-compressible, non-sparse, and cannot
	    be stored externally. Most of these restrictions are
	    arbitrary but are enforced because of the small size of
	    the raw data. Storing data in this format eliminates the
	    disk seek/read request normally necessary to read raw
	    data. 

	    <br><br>
	  <dt><code>H5D_CONTIGUOUS</code>
	  <dd>The raw data is large, non-extendible, non-compressible,
	    non-sparse, and can be stored externally.  This is the
	    default value for the layout property.  The term
	    <em>large</em> means that it may not be possible to hold
	    the entire dataset in memory.  The non-compressibility is
	    a side effect of the data being large, contiguous, and
	    fixed-size at the physical level, which could cause
	    partial I/O requests to be extremely expensive if
	    compression were allowed.

	    <br><br>
	  <dt><code>H5D_CHUNKED</code>
	  <dd>The raw data is large and can be extended in any
	    dimension at any time (provided the data space also allows
	    the extension). It may be sparse at the chunk level (each
	    chunk is non-sparse, but there might only be a few chunks)
	    and each chunk can be compressed and/or stored externally.
	    A dataset is partitioned into chunks so each chunk is the
	    same logical size.  The chunks are indexed by a B-tree and
	    are allocated on demand (although it might be useful to be
	    able to preallocate storage for parts of a chunked array
	    to reduce contention for the B-tree in a parallel
	    environment). The chunk size must be defined with
	    <code>H5Pset_chunk()</code>.

	    <br><br>
	  <dt><em>others...</em>
	  <dd>Other layout types may be defined later without breaking
	    existing code.  However, to be able to correctly read or
	    modify data stored with one of these new layouts, the
	    application will need to be linked with a new version of
	    the library.  This happens automatically on systems with
	    dynamic linking.
	</dl>
    </dl>

    <a name="Dataset_PSetChunk">
    <p>Once the general layout is defined, the user can define
    </a>
      properties of that layout.  Currently, the only layout that has
      user-settable properties is the <code>H5D_CHUNKED</code> layout,
      which needs to know the dimensionality and chunk size.
    <dl>
      <dt><code>herr_t H5Pset_chunk (hid_t <em>plist_id</em>, int
	  <em>ndims</em>, hsize_t <em>dim</em>[])</code>
      <dd>This function defines the logical size of a chunk for
	chunked layout.  If the layout property is set to
	<code>H5D_CHUNKED</code> and the chunk size is set to
	<em>dim</em>. The number of elements in the <em>dim</em> array
	is the dimensionality, <em>ndims</em>. One need not call
	<code>H5Dset_layout()</code> when using this function since
	the chunked layout is implied.
    </dl>

    <p>
      <center>
	<table border align=center width="100%">
	  <caption align=bottom><h4>Example: Chunked Storage</h4></caption>
	  <tr>
	    <td>
	      <p>This example shows how a two-dimensional dataset
		is partitioned into chunks.  The library can manage file
		memory by moving the chunks around, and each chunk could be
		compressed.  The chunks are allocated in the file on demand
		when data is written to the chunk.
	      <center>
		<img alt="Chunked Storage" src="chunk1.gif">
	      </center>

	      <p><code><pre>
size_t hsize[2] = {1000, 1000};
plist = H5Pcreate (H5P_DATASET_CREATE);
H5Pset_chunk (plist, 2, size);
	      </pre></code>
	    </td>
	  </tr>
	</table>
      </center>


    <p>Although it is most efficient if I/O requests are aligned on chunk
      boundaries, this is not a constraint.  The application can perform I/O
      on any set of data points as long as the set can be described by the
      data space.  The set on which I/O is performed is called the
      <em>selection</em>.

    <h2>3. Compression Properties</h2>

    <p>Chunked data storage 
      (see <a href="#Dataset_PSetChunk"><code>H5Pset_chunk</code></a>) 
      allows data compression as defined by the function 
      <code>H5Pset_deflate</code>.

<!--
    <dl>
      <dt><code>herr_t H5Pset_compression (hid_t <em>plist_id</em>,
	  H5Z_method_t <em>method</em>)</code>
      <dt><code>H5Z_method_t H5Pget_compression (hid_t
	  <em>plist_id</em>)</code>
      <dd>These functions set and query the compression method that
	is used to compress the raw data of a dataset.  The
	<em>plist_id</em> is a dataset creation property list.  The
	possible values for the compression method are:

	<br><br>
	<dl>
	  <dt><code>H5Z_NONE</code>
	  <dd>This is the default and specifies that no compression is
	    to be performed.

	    <br><br>
	  <dt><code>H5Z_DEFLATE</code>
	  <dd>This specifies that a variation of the Lempel-Ziv 1977
	    (LZ77) encoding is used, the same encoding used by the
	    free GNU <code>gzip</code> program.
	</dl>
-->

	<br><br>
      <dt><code>herr_t H5Pset_deflate (hid_t <em>plist_id</em>,
	  int <em>level</em>)</code>
      <dt><code>int H5Pget_deflate (hid_t <em>plist_id</em>)</code>
      <dd>These functions set or query the deflate level of
	dataset creation property list <em>plist_id</em>.  The
	<code>H5Pset_deflate()</code> sets the compression method to
	<code>H5Z_DEFLATE</code> and sets the compression level to
	some integer between one and nine (inclusive).  One results in
	the fastest compression while nine results in the best
	compression ratio.  The default value is six if
	<code>H5Pset_deflate()</code> isn't called.  The
	<code>H5Pget_deflate()</code> returns the compression level
	for the deflate method, or negative if the method is not the
	deflate method.
    </dl>

    <h2>4. External Storage Properties</h2>

    <p>Some storage formats may allow storage of data across a set of
      non-HDF5 files. Currently, only the <code>H5D_CONTIGUOUS</code> storage
      format allows external storage.  A set segments (offsets and sizes) in
      one or more files is defined as an external file list, or <em>EFL</em>,
      and the contiguous logical addresses of the data storage are mapped onto
      these segments.

    <dl>
      <dt><code>herr_t H5Pset_external (hid_t <em>plist</em>, const
	  char *<em>name</em>, off_t <em>offset</em>, hsize_t
	  <em>size</em>)</code>
      <dd>This function adds a new segment to the end of the external
	file list of the specified dataset creation property list.  The
	segment begins a byte <em>offset</em> of file <em>name</em> and
	continues for <em>size</em> bytes.  The space represented by this
	segment is adjacent to the space already represented by the external
	file list.  The last segment in a file list may have the size
	<code>H5F_UNLIMITED</code>, in which case the external file may be 
        of unlimited size and no more files can be added to the external files list.

	  <br><br>
      <dt><code>int H5Pget_external_count (hid_t <em>plist</em>)</code>
      <dd>Calling this function returns the number of segments in an
	external file list. If the dataset creation property list has no
	external data then zero is returned.

	<br><br>
      <dt><code>herr_t H5Pget_external (hid_t <em>plist</em>, int
	  <em>idx</em>, size_t <em>name_size</em>, char *<em>name</em>, off_t
	  *<em>offset</em>, hsize_t *<em>size</em>)</code>
      <dd>This is the counterpart for the <code>H5Pset_external()</code>
	function.  Given a dataset creation property list and a zero-based
	index into that list, the file name, byte offset, and segment size are
	returned through non-null arguments.  At most <em>name_size</em>
	characters are copied into the <em>name</em> argument which is not
	null terminated if the file name is longer than the supplied name
	buffer (this is similar to <code>strncpy()</code>).
    </dl>

    <p>
      <center>
	<table border align=center width="100%">
	  <caption align=bottom><h4>Example: Multiple Segments</h4></caption>
	  <tr>
	    <td>
	      <p>This example shows how a contiguous, one-dimensional dataset
		is partitioned into three parts and each of those parts is
		stored in a segment of an external file. The top rectangle
		represents the logical address space of the dataset
		while the bottom rectangle represents an external file.
	      <center>
		<img alt="Multiple Segments" src="extern1.gif">
	      </center>

	      <p><code><pre>
plist = H5Pcreate (H5P_DATASET_CREATE);
H5Pset_external (plist, "velocity.data", 3000, 1000);
H5Pset_external (plist, "velocity.data", 0, 2500);
H5Pset_external (plist, "velocity.data", 4500, 1500);
	      </pre></code>

	      <p>One should note that the segments are defined in order of the
		logical addresses they represent, not their order within the
		external file.  It would also have been possible to put the
		segments in separate files.  Care should be taken when setting
		up segments in a single file since the library doesn't
		automatically check for segments that overlap.
	    </td>
	  </tr>
	</table>
      </center>

    <p>
      <center>
	<table border align=center width="100%">
	  <caption align=bottom><h4>Example: Multi-Dimensional</h4></caption>
	  <tr>
	    <td>
	      <p>This example shows how a contiguous, two-dimensional dataset
		is partitioned into three parts and each of those parts is
		stored in a separate external file. The top rectangle
		represents the logical address space of the dataset
		while the bottom rectangles represent external files.
	      <center>
		<img alt="Multiple Dimensions" src="extern2.gif">
	      </center>

	      <p><code><pre>
plist = H5Pcreate (H5P_DATASET_CREATE);
H5Pset_external (plist, "scan1.data", 0, 24);
H5Pset_external (plist, "scan2.data", 0, 24);
H5Pset_external (plist, "scan3.data", 0, 16);
	      </pre></code>

	      <p>The library maps the multi-dimensional array onto a linear
		address space like normal, and then maps that address space
		into the segments defined in the external file list.
	    </td>
	  </tr>
	</table>
      </center>

    <p>The segments of an external file can exist beyond the end of the
      file. The library reads that part of a segment as zeros.  When writing
      to a segment that exists beyond the end of a file, the file is
      automatically extended. Using this feature, one can create a segment
      (or set of segments) which is larger than the current size of the
      dataset, which allows to dataset to be extended at a future time
      (provided the data space also allows the extension).

    <p>All referenced external data files must exist before performing raw
      data I/O on the dataset. This is normally not a problem since those
      files are being managed directly by the application, or indirectly
      through some other library.


    <h2>5. Datatype</h2>

    <p>Raw data has a constant datatype which describes the datatype
      of the raw data stored in the file, and a memory datatype that
      describes the datatype stored in application memory.  Both data
      types are manipulated with the <a
      href="Datatypes.html"><code>H5T</code></a> API.

    <p>The constant file datatype is associated with the dataset when
      the dataset is created in a manner described below.  Once
      assigned, the constant datatype can never be changed.

    <p>The memory datatype is specified when data is transferred
      to/from application memory.  In the name of data sharability,
      the memory datatype must be specified, but can be the same
      type identifier as the constant datatype.

    <p>During dataset I/O operations, the library translates the raw
      data from the constant datatype to the memory datatype or vice
      versa.  Structured datatypes include member offsets to allow
      reordering of struct members and/or selection of a subset of
      members and array datatypes include index permutation
      information to allow things like transpose operations (<b>the
      prototype does not support array reordering</b>) Permutations
      are relative to some extrinsic descritpion of the dataset.



    <h2>6. Data Space</h2>

    <p>The dataspace of a dataset defines the number of dimensions
      and the size of each dimension and is manipulated with the
      <code>H5S</code> API.  The <em>simple</em> dataspace consists of
      maximum dimension sizes and actual dimension sizes, which are
      usually the same.  However, maximum dimension sizes can be the
      constant <code>H5D_UNLIMITED</code> in which case the actual
      dimension size can be incremented with calls to
      <code>H5Dextend()</code>. The maximium dimension sizes are
      constant meta data while the actual dimension sizes are
      persistent meta data.  Initial actual dimension sizes are
      supplied at the same time as the maximum dimension sizes when
      the dataset is created.

    <p>The dataspace can also be used to define partial I/O
      operations. Since I/O operations have two end-points, the raw
      data transfer functions take two data space arguments: one which
      describes the application memory data space or subset thereof
      and another which describes the file data space or subset
      thereof.


    <h2>7. Setting Constant or Persistent Properties</h2>

    <p>Each dataset has a set of constant and persistent properties
      which describe the layout method, pre-compression
      transformation, compression method, datatype, external storage,
      and data space.  The constant properties are set as described
      above in a dataset creation property list whose identifier is
      passed to <code>H5Dcreate()</code>.

    <dl>
      <dt><code>hid_t H5Dcreate (hid_t <em>file_id</em>, const char
	  *<em>name</em>, hid_t <em>type_id</em>, hid_t
	  <em>space_id</em>, hid_t <em>create_plist_id</em>)</code>
      <dd>A dataset is created by calling <code>H5Dcreate</code> with
	a file identifier, a dataset name, a datatype, a dataspace,
	and constant properties.  The datatype and dataspace are the
	type and space of the dataset as it will exist in the file,
	which may be different than in application memory.  
        Dataset names within a group must be unique: 
        <code>H5Dcreate</code> returns an error if a dataset with the
        name specified in <code><em>name</em></code> already exists 
        at the location specified in <code><em>file_id</em></code>.
        The <em>create_plist_id</em> is a <code>H5P_DATASET_CREATE</code>
	property list created with <code>H5Pcreate()</code> and
	initialized with the various functions described above.
	<code>H5Dcreate()</code> returns a dataset handle for success
	or negative for failure. The handle should eventually be
	closed by calling <code>H5Dclose()</code> to release resources
	it uses.

	<br><br>
      <dt><code>hid_t H5Dopen (hid_t <em>file_id</em>, const char
	  *<em>name</em>)</code>
      <dd>An existing dataset can be opened for access by calling this
	function.  A dataset handle is returned for success or a
	negative value is returned for failure.  The handle should
	eventually be closed by calling <code>H5Dclose()</code> to
	release resources it uses.

	<br><br>
      <dt><code>herr_t H5Dclose (hid_t <em>dataset_id</em>)</code>
      <dd>This function closes a dataset handle and releases all
	resources it might have been using.  The handle should not be
	used in subsequent calls to the library.

	<br><br>
      <dt><code>herr_t H5Dextend (hid_t <em>dataset_id</em>,
	  hsize_t <em>dim</em>[])</code>
      <dd>This function extends a dataset by increasing the size in
	one or more dimensions.  Not all datasets can be extended.
    </dl>



    <h2>8. Querying Constant or Persistent Properties</h2>

    <p>Constant or persistent properties can be queried with a set of
      three functions.  Each function returns an identifier for a copy
      of the requested properties.  The identifier can be passed to
      various functions which modify the underlying object to derive a
      new object; the original dataset is completely unchanged.  The
      return values from these functions should be properly destroyed
      when no longer needed.

    <dl>
      <dt><code>hid_t H5Dget_type (hid_t <em>dataset_id</em>)</code>
      <dd>Returns an identifier for a copy of the dataset permanent
	datatype or negative for failure.

      <dt><code>hid_t H5Dget_space (hid_t <em>dataset_id</em>)</code>
      <dd>Returns an identifier for a copy of the dataset permanent
	data space, which also contains information about the current
	size of the dataset if the data set is extendable with
	<code>H5Dextend()</code>.

      <dt><code>hid_t H5Dget_create_plist (hid_t
	  <em>dataset_id</em>)</code>
      <dd>Returns an identifier for a copy of the dataset creation
	property list. The new property list is created by examining
	various permanent properties of the dataset.  This is mostly a
	catch-all for everything but type and space.
    </dl>



    <h2>9. Setting Memory and Transfer Properties</h2>

    <p>A dataset also has memory properties which describe memory
      within the application, and transfer properties that control
      various aspects of the I/O operations.  The memory can have a
      datatype different than the permanent file datatype (different
      number types, different struct member offsets, different array
      element orderings) and can also be a different size (memory is a
      subset of the permanent dataset elements, or vice versa).  The
      transfer properties might provide caching hints or collective
      I/O information. Therefore, each I/O operation must specify
      memory and transfer properties.

    <p>The memory properties are specified with <em>type_id</em> and
      <em>space_id</em> arguments while the transfer properties are
      specified with the <em>transfer_id</em> property list for the
      <code>H5Dread()</code> and <code>H5Dwrite()</code> functions
      (these functions are described below).

    <dl>
      <dt><code>herr_t H5Pset_buffer (hid_t <em>xfer_plist</em>,
	  hsize_t <em>max_buf_size</em>, void *<em>tconv_buf</em>, void
	  *<em>bkg_buf</em>)</code>
      <dt><code>hsize_t H5Pget_buffer (hid_t <em>xfer_plist</em>, void
	  **<em>tconv_buf</em>, void **<em>bkg_buf</em>)</code>
      <dd>Sets or retrieves the maximum size in bytes of the temporary
	buffer used for datatype conversion in the I/O pipeline.  An
	application-defined buffer can also be supplied as the
	<em>tconv_buf</em> argument, otherwise a buffer will be
	allocated and freed on demand by the library. A second
	temporary buffer <em>bkg_buf</em> can also be supplied and
	should be the same size as the <em>tconv_buf</em>.  The
	default values are 1MB for the maximum buffer size, and null
	pointers for each buffer indicating that they should be
	allocated on demand and freed when no longer needed. The
	<code>H5Pget_buffer()</code> function returns the maximum
	buffer size or zero on error.
    </dl>

    <p>If the maximum size of the temporary I/O pipeline buffers is
      too small to hold the entire I/O request, then the I/O request
      will be fragmented and the transfer operation will be strip
      mined.  However, certain restrictions apply to the strip
      mining.  For instance, when performing I/O on a hyperslab of a
      simple data space the strip mining is in terms of the slowest
      varying dimension.  So if a 100x200x300 hyperslab is requested,
      the temporary buffer must be large enough to hold a 1x200x300
      sub-hyperslab.

    <p>To prevent strip mining from happening, the application should
      use <code>H5Pset_buffer()</code> to set the size of the
      temporary buffer so it's large enough to hold the entire
      request.

    <p>
      <center>
	<table border align=center width="100%">
	  <caption align=bottom><h4>Example</h4></caption>
	  <tr>
	    <td>
	      <p>This example shows how to define a function that sets
		a dataset transfer property list so that strip mining
		does not occur.  It takes an (optional) dataset transfer
		property list, a dataset, a data space that describes
		what data points are being transfered, and a datatype
		for the data points in memory.  It returns a (new)
		dataset transfer property list with the temporary
		buffer size set to an appropriate value. The return
		value should be passed as the fifth argument to
		<code>H5Dread()</code> or <code>H5Dwrite()</code>.
	      <p><code><pre>
 1 hid_t
 2 disable_strip_mining (hid_t xfer_plist, hid_t dataset,
 3                       hid_t space, hid_t mem_type)
 4 {
 5     hid_t file_type;          /* File datatype */
 6     size_t type_size;         /* Sizeof larger type */
 7     size_t size;              /* Temp buffer size */
 8     hid_t xfer_plist;         /* Return value */
 9 
10     file_type = H5Dget_type (dataset);
11     type_size = MAX(H5Tget_size(file_type), H5Tget_size(mem_type));
12     H5Tclose (file_type);
13     size = H5Sget_npoints(space) * type_size;
14     if (xfer_plist&lt;0) xfer_plist = H5Pcreate (H5P_DATASET_XFER);
15     H5Pset_buffer(xfer_plist, size, NULL, NULL);
16     return xfer_plist;
17 }
	      </pre></code>
	    </td>
	  </tr>
	</table>
      </center>

      

    <h2>10. Querying Memory or Transfer Properties</h2>

    <p>Unlike constant and persistent properties, a dataset cannot be
      queried for it's memory or transfer properties.  Memory
      properties cannot be queried because the application already
      stores those properties separate from the buffer that holds the
      raw data, and the buffer may hold multiple segments from various
      datasets and thus have more than one set of memory properties.
      The transfer properties cannot be queried from the dataset
      because they're associated with the transfer itself and not with
      the dataset (but one can call
      <code>H5Pget_<em>property</em>()</code> to query transfer
      properties from a tempalate).


    <h2>11. Raw Data I/O</h2>

    <p>All raw data I/O is accomplished through these functions which
      take a dataset handle, a memory datatype, a memory data space,
      a file data space, transfer properties, and an application
      memory buffer.  They translate data between the memory datatype
      and space and the file datatype and space.  The data spaces can
      be used to describe partial I/O operations.
      
    <dl>
      <dt><code>herr_t H5Dread (hid_t <em>dataset_id</em>, hid_t
	  <em>mem_type_id</em>, hid_t <em>mem_space_id</em>, hid_t
	  <em>file_space_id</em>, hid_t <em>xfer_plist_id</em>,
	  void *<em>buf</em>/*out*/)</code>
      <dd>Reads raw data from the specified dataset into <em>buf</em>
	converting from file datatype and space to memory datatype
	and space.

	<br><br>
      <dt><code>herr_t H5Dwrite (hid_t <em>dataset_id</em>, hid_t
	  <em>mem_type_id</em>, hid_t <em>mem_space_id</em>, hid_t
	  <em>file_space_id</em>, hid_t <em>xfer_plist_id</em>,
	  const void *<em>buf</em>)</code>
      <dd>Writes raw data from an application buffer <em>buf</em> to
	the specified dataset converting from memory datatype and
	space to file datatype and space.
    </dl>


    <p>In the name of sharability, the memory datatype must be
      supplied.  However, it can be the same identifier as was used to
      create the dataset or as was returned by
      <code>H5Dget_type()</code>; the library will not implicitly
      derive memory datatypes from constant datatypes.

    <p>For complete reads of the dataset one may supply
      <code>H5S_ALL</code> as the argument for the file data space.
      If <code>H5S_ALL</code> is also supplied as the memory data
      space then no data space conversion is performed.  This is a
      somewhat dangerous situation since the file data space might be
      different than what the application expects.



    <h2>12. Examples</h2>

    <p>The examples in this section illustrate some common dataset
      practices.


    <p>This example shows how to create a dataset which is stored in
      memory as a two-dimensional array of native <code>double</code>
      values but is stored in the file in Cray <code>float</code>
      format using LZ77 compression.  The dataset is written to the
      HDF5 file and then read back as a two-dimensional array of
      <code>float</code> values.

    <p>
      <center>
	<table border align=center width="100%">
	  <caption align=bottom><h4>Example 1</h4></caption>
	  <tr>
	    <td>
	      <p><code><pre>
 1 hid_t file, data_space, dataset, properties;
 2 double dd[500][600];
 3 float ff[500][600];
 4 hsize_t dims[2], chunk_size[2];
 5 
 6 /* Describe the size of the array */
 7 dims[0] = 500;
 8 dims[1] = 600;
 9 data_space = H5Screate_simple (2, dims);
10 
11 
12 /*
13  * Create a new file using with read/write access,
14  * default file creation properties, and default file
15  * access properties.
16  */
17 file = H5Fcreate ("test.h5", H5F_ACC_RDWR, H5P_DEFAULT,
18                   H5P_DEFAULT);
19 
20 /* 
21  * Set the dataset creation plist to specify that
22  * the raw data is to be partitioned into 100x100 element
23  * chunks and that each chunk is to be compressed with
24  * LZ77.
25  */
26 chunk_size[0] = chunk_size[1] = 100;
27 properties = H5Pcreate (H5P_DATASET_CREATE);
28 H5Pset_chunk (properties, 2, chunk_size);
29 H5Pset_deflate (properties, 9);
30 
31 /*
32  * Create a new dataset within the file.  The datatype
33  * and data space describe the data on disk, which may
34  * be different than the format used in the application's
35  * memory.
36  */
37 dataset = H5Dcreate (file, "dataset", H5T_CRAY_FLOAT,
38                      data_space, properties);
39 
40 /*
41  * Write the array to the file.  The datatype and data
42  * space describe the format of the data in the `dd'
43  * buffer.  The raw data is translated to the format
44  * required on disk defined above.  We use default raw
45  * data transfer properties.
46  */
47 H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
48           H5P_DEFAULT, dd);
49 
50 /*
51  * Read the array as floats.  This is similar to writing
52  * data except the data flows in the opposite direction.
53  */
54 H5Dread (dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
55          H5P_DEFAULT, ff);
56 
64 H5Dclose (dataset);
65 H5Sclose (data_space);
66 H5Pclose (properties);
67 H5Fclose (file);
	      </pre></code>
	    </td>
	  </tr>
	</table>
      </center>

    <p>This example uses the file created in Example 1 and reads a
      hyperslab of the 500x600 file dataset.  The hyperslab size is
      100x200 and it is located beginning at element
      &lt;200,200&gt;. We read the hyperslab into an 200x400 array in
      memory beginning at element &lt;0,0&gt; in memory.  Visually,
      the transfer looks something like this: 

      <center>
	<img alt="Raw Data Transfer" src="dataset_p1.gif">
      </center>

    <p>
      <center>
	<table border align=center width="100%">
	  <caption align=bottom><h4>Example 2</h4></caption>
	  <tr>
	    <td>
	      <p><code><pre>
 1 hid_t file, mem_space, file_space, dataset;
 2 double dd[200][400];
 3 hssize_t offset[2];
 4 hsize size[2];
 5 
 6 /*
 7  * Open an existing file and its dataset.
 8  */
 9 file = H5Fopen ("test.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
10 dataset = H5Dopen (file, "dataset");
11 
12 /*
13  * Describe the file data space.
14  */
15 offset[0] = 200; /*offset of hyperslab in file*/
16 offset[1] = 200;
17 size[0] = 100;   /*size of hyperslab*/
18 size[1] = 200;
19 file_space = H5Dget_space (dataset);
20 H5Sset_hyperslab (file_space, 2, offset, size);
21 
22 /*
23  * Describe the memory data space.
24  */
25 size[0] = 200;  /*size of memory array*/
26 size[1] = 400;
27 mem_space = H5Screate_simple (2, size);
28 
29 offset[0] = 0;  /*offset of hyperslab in memory*/
30 offset[1] = 0;
31 size[0] = 100;  /*size of hyperslab*/
32 size[1] = 200;
33 H5Sset_hyperslab (mem_space, 2, offset, size);
34 
35 /*
36  * Read the dataset.
37  */
38 H5Dread (dataset, H5T_NATIVE_DOUBLE, mem_space,
39          file_space, H5P_DEFAULT, dd);
40 
41 /*
42  * Close/release resources.
43  */
44 H5Dclose (dataset);
45 H5Sclose (mem_space);
46 H5Sclose (file_space);
47 H5Fclose (file);
	      </pre></code>
	    </td>
	  </tr>
	</table>
      </center>

    <p>If the file contains a compound data structure one of whose
      members is a floating point value (call it "delta") but the
      application is interested in reading an array of floating point
      values which are just the "delta" values, then the application
      should cast the floating point array as a struct with a single
      "delta" member.

    <p>
      <center>
	<table border align=center width="100%">
	  <caption align=bottom><h4>Example 3</h4></caption>
	  <tr>
	    <td>
	      <p><code><pre>
 1 hid_t file, dataset, type;
 2 double delta[200];
 3 
 4 /*
 5  * Open an existing file and its dataset.
 6  */
 7 file = H5Fopen ("test.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
 8 dataset = H5Dopen (file, "dataset");
 9 
10 /*
11  * Describe the memory datatype, a struct with a single
12  * "delta" member.
13  */
14 type = H5Tcreate (H5T_COMPOUND, sizeof(double));
15 H5Tinsert (type, "delta", 0, H5T_NATIVE_DOUBLE);
16 
17 /*
18  * Read the dataset.
19  */
20 H5Dread (dataset, type, H5S_ALL, H5S_ALL,
21          H5P_DEFAULT, dd);
22 
23 /*
24  * Close/release resources.
25  */
26 H5Dclose (dataset);
27 H5Tclose (type);
28 H5Fclose (file);
	      </pre></code>
	    </td>
	  </tr>
	</table>
      </center>


<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;
      Datasets&nbsp;&nbsp;
      <a href="Datatypes.html">Datatypes</a>&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;
      <br>
      <a href="Ragged.html">Ragged Arrays</a>&nbsp;&nbsp;
</td></tr>
</table>
</center>



<hr>
<address>
<a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a>
</address>

<!-- Created: Tue Dec  2 09:17:09 EST 1997 -->
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Last modified:  7 April 2000
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<br>
Describes HDF5 Release 1.4 Beta, December 2000


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