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<div class="headertitle"><div class="title">Creating a Dataset</div></div>
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<div class="contents">
<div class="textblock"><p>Navigate back: <a class="el" href="index.html">Main</a> / <a class="el" href="_getting_started.html">Getting Started with HDF5</a> / <a class="el" href="_learn_basics.html">Learning the Basics</a> </p><hr />
<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 at which to create the dataset, the dataset name, the datatype and dataspace of the data array, and the property lists.</p>
<h1><a class="anchor" id="secLBDsetCreateDtype"></a>
Datatypes</h1>
<p>A datatype is a collection of 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.</p>
<p>There are two categories of datatypes in HDF5: </p><ul>
<li>
<b>Pre-defined</b>: These datatypes are opened and closed by HDF5.<br />
Pre-defined datatypes can be atomic or composite: <ul>
<li>
Atomic datatypes cannot be decomposed into smaller datatype units at the API level. For example: integer, float, reference, string. </li>
<li>
Composite datatypes are aggregations of one or more datatypes. For example: array, variable length, enumeration, compound.</li>
</ul>
</li>
<li>
<b>Derived</b>: These datatypes are created or derived from the pre-defined types.<br />
A simple example of creating a derived datatype is using the string datatype, H5T_C_S1, to create strings of more than one character:<br />
<div class="fragment"><div class="line"><a class="code hl_typedef" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a> strtype; <span class="comment">// Datatype ID</span></div>
<div class="line"><a class="code hl_typedef" href="_h5public_8h.html#a3b079ecf932a5c599499cf7e298af160">herr_t</a> status;</div>
<div class="line"> </div>
<div class="line">strtype = <a class="code hl_function" href="group___h5_t.html#gaec07efbab84f4e5b4ed22f010786be8e">H5Tcopy</a> (<a class="code hl_define" href="group___p_d_t_s.html#ga7f6b6959fefe56d2e871659110936d2d">H5T_C_S1</a>);</div>
<div class="line">status = <a class="code hl_function" href="group___h5_t.html#gae5f38bfd4a4c557496b3194b5180212c">H5Tset_size</a> (strtype, 5); <span class="comment">// create string of length 5</span></div>
<div class="ttc" id="a_h5_ipublic_8h_html_a0045db7ff9c22ad35db6ae91662e1943"><div class="ttname"><a href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a></div><div class="ttdeci">int64_t hid_t</div><div class="ttdef"><b>Definition</b> H5Ipublic.h:60</div></div>
<div class="ttc" id="a_h5public_8h_html_a3b079ecf932a5c599499cf7e298af160"><div class="ttname"><a href="_h5public_8h.html#a3b079ecf932a5c599499cf7e298af160">herr_t</a></div><div class="ttdeci">int herr_t</div><div class="ttdef"><b>Definition</b> H5public.h:235</div></div>
<div class="ttc" id="agroup___h5_t_html_gae5f38bfd4a4c557496b3194b5180212c"><div class="ttname"><a href="group___h5_t.html#gae5f38bfd4a4c557496b3194b5180212c">H5Tset_size</a></div><div class="ttdeci">herr_t H5Tset_size(hid_t type_id, size_t size)</div><div class="ttdoc">Sets size for a datatype.</div></div>
<div class="ttc" id="agroup___h5_t_html_gaec07efbab84f4e5b4ed22f010786be8e"><div class="ttname"><a href="group___h5_t.html#gaec07efbab84f4e5b4ed22f010786be8e">H5Tcopy</a></div><div class="ttdeci">hid_t H5Tcopy(hid_t type_id)</div><div class="ttdoc">Copies an existing datatype.</div></div>
<div class="ttc" id="agroup___p_d_t_s_html_ga7f6b6959fefe56d2e871659110936d2d"><div class="ttname"><a href="group___p_d_t_s.html#ga7f6b6959fefe56d2e871659110936d2d">H5T_C_S1</a></div><div class="ttdeci">#define H5T_C_S1</div><div class="ttdef"><b>Definition</b> H5Tpublic.h:476</div></div>
</div><!-- fragment --> </li>
</ul>
<p>Shown below is the HDF5 pre-defined datatypes. </p><div class="fragment"><div class="line"> +-- integer</div>
<div class="line"> +-- floating point</div>
<div class="line"> +---- atomic ----+-- date and time</div>
<div class="line"> | +-- character <span class="keywordtype">string</span></div>
<div class="line">HDF5 datatypes --| +-- bitfield</div>
<div class="line"> | +-- opaque</div>
<div class="line"> |</div>
<div class="line"> +---- compound</div>
</div><!-- fragment --><p>Some of the HDF5 predefined atomic datatypes are listed below.</p>
<table class="doxtable">
<caption>Examples of HDF5 predefined datatypes</caption>
<tr>
<th><b>Datatype</b> </th><th><b>Description</b> </th></tr>
<tr>
<th><b>H5T_STD_I32LE</b> </th><td>Four-byte, little-endian, signed, two's complement integer </td></tr>
<tr>
<th><b>H5T_STD_U16BE</b> </th><td>Two-byte, big-endian, unsigned integer </td></tr>
<tr>
<th><b>H5T_IEEE_F32BE</b> </th><td>Four-byte, big-endian, IEEE floating point </td></tr>
<tr>
<th><b>H5T_IEEE_F64LE</b> </th><td>Eight-byte, little-endian, IEEE floating point </td></tr>
<tr>
<th><b>H5T_C_S1</b> </th><td>One-byte, null-terminated string of eight-bit characters </td></tr>
</table>
<table class="doxtable">
<caption>Examples of HDF5 predefined native datatypes</caption>
<tr>
<th><b>Native Datatype</b> </th><th><b>Corresponding C or FORTRAN Type</b> </th></tr>
<tr>
<th span="2"><b>C</b> </th></tr>
<tr>
<th><b>H5T_NATIVE_INT</b> </th><td>int </td></tr>
<tr>
<th><b>H5T_NATIVE_FLOAT</b> </th><td>float </td></tr>
<tr>
<th><b>H5T_NATIVE_CHAR</b> </th><td>char </td></tr>
<tr>
<th><b>H5T_NATIVE_DOUBLE</b> </th><td>double </td></tr>
<tr>
<th><b>H5T_NATIVE_LDOUBLE</b> </th><td>long double </td></tr>
<tr>
<th span="2"><b>Fortran</b> </th></tr>
<tr>
<th><b>H5T_NATIVE_INTEGER</b> </th><td>integer </td></tr>
<tr>
<th><b>H5T_NATIVE_REAL</b> </th><td>real </td></tr>
<tr>
<th><b>H5T_NATIVE_DOUBLE</b> </th><td>double precision </td></tr>
<tr>
<th><b>H5T_NATIVE_CHARACTER</b> </th><td>character </td></tr>
</table>
<p>In this tutorial, we consider only HDF5 predefined integers.</p>
<p>For further information on datatypes, see <a class="el" href="_h5_t__u_g.html#sec_datatype">HDF5 Datatypes</a> in the <a class="el" href="_u_g.html">HDF5 User Guide</a>, in addition to the <a class="el" href="_l_b_datatypes.html">Datatype Basics</a> tutorial topic.</p>
<h1><a class="anchor" id="secLBDsetCreateDspace"></a>
Datasets and Dataspaces</h1>
<p>A dataspace describes the dimensionality of the data array. A dataspace is either a regular N-dimensional array of data points, called a simple dataspace, or a more general collection of data points organized in another manner, called a complex dataspace. In this tutorial, we only consider simple dataspaces.</p>
<p><em>HDF5 dataspaces</em> </p><div class="fragment"><div class="line"> +-- simple</div>
<div class="line">HDF5 dataspaces --|</div>
<div class="line"> +-- complex</div>
</div><!-- fragment --><p> The dimensions of a dataset can be fixed (unchanging), or they may be 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.</p>
<h1><a class="anchor" id="secLBDsetCreateProp"></a>
Property Lists</h1>
<p>Property lists are a mechanism for modifying the default behavior when creating or accessing objects. For more information on property lists see the <a class="el" href="_l_b_props_list.html">Property Lists Basics</a> tutorial topic.</p>
<p>The following property lists can be specified when creating a dataset: </p><ul>
<li>Dataset Creation Property List<br />
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, stored externally, etc. In this tutorial, we use the default dataset creation property list (contiguous storage layout and no compression). For more information about dataset creation property lists, see <a class="el" href="_h5_d__u_g.html#sec_dataset">HDF5 Datasets</a> in the <a class="el" href="_u_g.html">HDF5 User Guide</a>. </li>
<li>Link Creation Property List<br />
The link creation property list governs creation of the link(s) by which a new dataset is accessed and the creation of any intermediate groups that may be missing. </li>
<li>Dataset Access Property List<br />
Dataset access property lists are properties that can be specified when accessing a dataset.</li>
</ul>
<h1><a class="anchor" id="secLBDsetCreateSteps"></a>
Steps to Create a Dataset</h1>
<p>To create an empty dataset (no data written) the following steps need to be taken: </p><ol>
<li>
Obtain the location identifier where the dataset is to be created. </li>
<li>
Define or specify the dataset characteristics: <ol>
<li>
Define a datatype or specify a pre-defined datatype. </li>
<li>
Define a dataspace. </li>
<li>
Specify the property list(s) or use the default. </li>
</ol>
</li>
<li>
Create the dataset. </li>
<li>
Close the datatype, the dataspace, and the property list(s) if necessary. </li>
<li>
Close the dataset. </li>
</ol>
<p>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 the definition of the datatype and dataspace. In this tutorial, we use the HDF5 predefined datatypes (integer) and consider only simple dataspaces. Hence, only the creation of dataspace objects is needed.</p>
<h1><a class="anchor" id="secLBDsetCreateHL"></a>
High Level APIs</h1>
<p>The High Level <a class="el" href="group___h5_l_t.html">HDF5 Lite APIs (H5LT,H5LD)</a> include functions that simplify and condense the steps for creating datasets in HDF5. The examples in the following section use the standard APIs. For a quick start you may prefer to look at the <a class="el" href="group___h5_l_t.html">HDF5 Lite APIs (H5LT,H5LD)</a> at this time.</p>
<p>If you plan to work with images, please look at the High Level <a class="el" href="group___h5_i_m.html">HDF5 Images API (H5IM)</a>, as well.</p>
<h1><a class="anchor" id="secLBDsetCreateProg"></a>
Programming Example</h1>
<h2><a class="anchor" id="subsecLBDsetCreateProgDesc"></a>
Description</h2>
<p>See <a class="el" href="_l_b_examples.html">Examples from Learning the Basics</a> for the examples used in the <a class="el" href="_learn_basics.html">Learning the Basics</a> tutorial.</p>
<p>The example shows how to create an empty dataset. It creates a file called <code style="background-color:whitesmoke;">dset.h5</code> in the C version (<code style="background-color:whitesmoke;">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.</p>
<p>For details on compiling an HDF5 application: [ <a class="el" href="_l_b_compiling.html">Compiling HDF5 Applications</a> ]</p>
<h2><a class="anchor" id="subsecLBDsetCreateProgRem"></a>
Remarks</h2>
<p><a class="el" href="group___h5_s.html#ga8e35eea5738b4805856eac7d595254ae" title="Creates a new simple dataspace and opens it for access.">H5Screate_simple</a> creates a new simple dataspace and returns a dataspace identifier. <a class="el" href="group___h5_s.html#ga2b53128a39c8f104c1c9c2a91590fcc1" title="Releases and terminates access to a dataspace.">H5Sclose</a> releases and terminates access to a dataspace.</p>
<p><em>C</em> </p><div class="fragment"><div class="line">dataspace_id = <a class="code hl_function" href="group___h5_s.html#ga8e35eea5738b4805856eac7d595254ae">H5Screate_simple</a> (rank, dims, maxdims);</div>
<div class="line">status = <a class="code hl_function" href="group___h5_s.html#ga2b53128a39c8f104c1c9c2a91590fcc1">H5Sclose</a> (dataspace_id );</div>
<div class="ttc" id="agroup___h5_s_html_ga2b53128a39c8f104c1c9c2a91590fcc1"><div class="ttname"><a href="group___h5_s.html#ga2b53128a39c8f104c1c9c2a91590fcc1">H5Sclose</a></div><div class="ttdeci">herr_t H5Sclose(hid_t space_id)</div><div class="ttdoc">Releases and terminates access to a dataspace.</div></div>
<div class="ttc" id="agroup___h5_s_html_ga8e35eea5738b4805856eac7d595254ae"><div class="ttname"><a href="group___h5_s.html#ga8e35eea5738b4805856eac7d595254ae">H5Screate_simple</a></div><div class="ttdeci">hid_t H5Screate_simple(int rank, const hsize_t dims[], const hsize_t maxdims[])</div><div class="ttdoc">Creates a new simple dataspace and opens it for access.</div></div>
</div><!-- fragment --><p><em>FORTRAN</em> </p><div class="fragment"><div class="line">CALL h5screate_simple_f (rank, dims, dataspace_id, hdferr, maxdims=max_dims)</div>
<div class="line"> or</div>
<div class="line">CALL h5screate_simple_f (rank, dims, dataspace_id, hdferr)</div>
<div class="line"> </div>
<div class="line">CALL h5sclose_f (dataspace_id, hdferr)</div>
</div><!-- fragment --><p><a class="el" href="group___h5_d.html#ga0647ba4bbd26d5230cc07f3a5685b2cf">H5Dcreate</a> creates an empty dataset at the specified location and returns a dataset identifier. <a class="el" href="group___h5_d.html#gae47c3f38db49db127faf221624c30609" title="Closes the specified dataset.">H5Dclose</a> closes the dataset and releases the resource used by the dataset. This call is mandatory.</p>
<p><em>C</em> </p><div class="fragment"><div class="line">dataset_id = <a class="code hl_define" href="group___h5_d.html#ga0647ba4bbd26d5230cc07f3a5685b2cf">H5Dcreate</a>(file_id, <span class="stringliteral">"/dset"</span>, <a class="code hl_define" href="group___p_d_t_s_t_d.html#ga37e8a6be7ee64587c2a282b965019bb8">H5T_STD_I32BE</a>, dataspace_id, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>);</div>
<div class="line">status = <a class="code hl_function" href="group___h5_d.html#gae47c3f38db49db127faf221624c30609">H5Dclose</a> (dataset_id);</div>
<div class="ttc" id="a_h5_ppublic_8h_html_afa85e97bfbf9bf1c58e39263846c568f"><div class="ttname"><a href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a></div><div class="ttdeci">#define H5P_DEFAULT</div><div class="ttdef"><b>Definition</b> H5Ppublic.h:102</div></div>
<div class="ttc" id="agroup___h5_d_html_ga0647ba4bbd26d5230cc07f3a5685b2cf"><div class="ttname"><a href="group___h5_d.html#ga0647ba4bbd26d5230cc07f3a5685b2cf">H5Dcreate</a></div><div class="ttdeci">#define H5Dcreate</div><div class="ttdef"><b>Definition</b> H5version.h:892</div></div>
<div class="ttc" id="agroup___h5_d_html_gae47c3f38db49db127faf221624c30609"><div class="ttname"><a href="group___h5_d.html#gae47c3f38db49db127faf221624c30609">H5Dclose</a></div><div class="ttdeci">herr_t H5Dclose(hid_t dset_id)</div><div class="ttdoc">Closes the specified dataset.</div></div>
<div class="ttc" id="agroup___p_d_t_s_t_d_html_ga37e8a6be7ee64587c2a282b965019bb8"><div class="ttname"><a href="group___p_d_t_s_t_d.html#ga37e8a6be7ee64587c2a282b965019bb8">H5T_STD_I32BE</a></div><div class="ttdeci">#define H5T_STD_I32BE</div><div class="ttdef"><b>Definition</b> H5Tpublic.h:305</div></div>
</div><!-- fragment --><p><em>FORTRAN</em> </p><div class="fragment"><div class="line">CALL h5dcreate_f (loc_id, name, type_id, dataspace_id, dset_id, hdferr)</div>
<div class="line">CALL h5dclose_f (dset_id, hdferr)</div>
</div><!-- fragment --><p>Note that if using the pre-defined datatypes in FORTRAN, then a call must be made to initialize and terminate access to the pre-defined datatypes: </p><div class="fragment"><div class="line">CALL h5open_f (hdferr)</div>
<div class="line">CALL h5close_f (hdferr)</div>
</div><!-- fragment --><p>H5open must be called before any HDF5 library subroutine calls are made; H5close must be called after the final HDF5 library subroutine call.</p>
<p>See the programming example for an illustration of the use of these calls.</p>
<h2><a class="anchor" id="subsecLBDsetCreateContent"></a>
File Contents</h2>
<p>The contents of the file dset.h5 (dsetf.h5 for FORTRAN) are shown below: </p><table class="doxtable">
<caption>Contents of dset.h5 (dsetf.h5)</caption>
<tr>
<td><div class="image">
<img src="imgLBDsetCreate.gif" alt=""/>
</div>
</td></tr>
</table>
<table class="doxtable">
<tr>
<th>dset.h5 in DDL </th><th>dsetf.h5 in DDL </th></tr>
<tr>
<td><div class="fragment"><div class="line">HDF5 <span class="stringliteral">"dset.h5"</span> {</div>
<div class="line">GROUP <span class="stringliteral">"/"</span> {</div>
<div class="line"> DATASET <span class="stringliteral">"dset"</span> {</div>
<div class="line"> DATATYPE { <a class="code hl_define" href="group___p_d_t_s_t_d.html#ga37e8a6be7ee64587c2a282b965019bb8">H5T_STD_I32BE</a> }</div>
<div class="line"> DATASPACE { SIMPLE ( 4, 6 ) / ( 4, 6 ) }</div>
<div class="line"> DATA {</div>
<div class="line"> 0, 0, 0, 0, 0, 0,</div>
<div class="line"> 0, 0, 0, 0, 0, 0,</div>
<div class="line"> 0, 0, 0, 0, 0, 0,</div>
<div class="line"> 0, 0, 0, 0, 0, 0</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line">}</div>
</div><!-- fragment --> </td><td><div class="fragment"><div class="line">HDF5 <span class="stringliteral">"dsetf.h5"</span> {</div>
<div class="line">GROUP <span class="stringliteral">"/"</span> {</div>
<div class="line"> DATASET <span class="stringliteral">"dset"</span> {</div>
<div class="line"> DATATYPE { <a class="code hl_define" href="group___p_d_t_s_t_d.html#ga37e8a6be7ee64587c2a282b965019bb8">H5T_STD_I32BE</a> }</div>
<div class="line"> DATASPACE { SIMPLE ( 6, 4 ) / ( 6, 4 ) }</div>
<div class="line"> DATA {</div>
<div class="line"> 0, 0, 0, 0,</div>
<div class="line"> 0, 0, 0, 0,</div>
<div class="line"> 0, 0, 0, 0,</div>
<div class="line"> 0, 0, 0, 0,</div>
<div class="line"> 0, 0, 0, 0,</div>
<div class="line"> 0, 0, 0, 0</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line">}</div>
</div><!-- fragment --> </td></tr>
</table>
<p>Note in above that <a class="el" href="group___p_d_t_s_t_d.html#ga37e8a6be7ee64587c2a282b965019bb8">H5T_STD_I32BE</a>, a 32-bit Big Endian integer, is an HDF atomic datatype.</p>
<h2><a class="anchor" id="subsecLBDsetCreateProgDDL"></a>
Dataset Definition in DDL</h2>
<p>The following is the simplified DDL dataset definition: </p><div class="fragment"><div class="line"><dataset> ::= DATASET <span class="stringliteral">"<dataset_name>"</span> { <datatype></div>
<div class="line"> <dataspace></div>
<div class="line"> <data></div>
<div class="line"> <dataset_attribute>* }</div>
<div class="line"> </div>
<div class="line"><datatype> ::= DATATYPE { <atomic_type> }</div>
<div class="line"> </div>
<div class="line"><dataspace> ::= DATASPACE { SIMPLE <current_dims> / <max_dims> }</div>
<div class="line"> </div>
<div class="line"><dataset_attribute> ::= <attribute></div>
</div><!-- fragment --><hr />
<p> Navigate back: <a class="el" href="index.html">Main</a> / <a class="el" href="_getting_started.html">Getting Started with HDF5</a> / <a class="el" href="_learn_basics.html">Learning the Basics</a> </p>
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