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<div class="headertitle"><div class="title">HDF5 Optimizations APIs (H5DO)</div></div>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<p><em>Bypassing default HDF5 behavior in order to optimize for specific use cases (H5DO)</em></p>
<p>HDF5 functions described is this section are implemented in the HDF5 High-level library as optimized functions. These functions generally require careful setup and testing as they enable an application to bypass portions of the HDF5 library's I/O pipeline for performance purposes.</p>
<p>These functions are distributed in the standard HDF5 distribution and are available any time the HDF5 High-level library is available.</p>
<ul>
<li><a class="el" href="#ga316caac160af15192e0c78228667341e">H5DOappend</a> <br />
Appends data to a dataset along a specified dimension.</li>
<li><a class="el" href="#gaaf8ec5a5623f93549e49c39f95c4abab">H5DOread_chunk</a> <br />
Reads a raw data chunk directly from a dataset in a file into a buffer (DEPRECATED)</li>
<li><a class="el" href="#gabc3c07ed2cf29dd34035194919fbeb31">H5DOwrite_chunk</a> <br />
Writes a raw data chunk from a buffer directly to a dataset in a file (DEPRECATED) </li>
</ul>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a id="func-members" name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:ga316caac160af15192e0c78228667341e" id="r_ga316caac160af15192e0c78228667341e"><td class="memItemLeft" align="right" valign="top">H5_HLDLL <a class="el" href="_h5public_8h.html#a3b079ecf932a5c599499cf7e298af160">herr_t</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="#ga316caac160af15192e0c78228667341e">H5DOappend</a> (<a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a> dset_id, <a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a> dxpl_id, unsigned axis, size_t extension, <a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a> memtype, const void *buf)</td></tr>
<tr class="memdesc:ga316caac160af15192e0c78228667341e"><td class="mdescLeft"> </td><td class="mdescRight">Appends data to a dataset along a specified dimension. <br /></td></tr>
<tr class="separator:ga316caac160af15192e0c78228667341e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:gabc3c07ed2cf29dd34035194919fbeb31" id="r_gabc3c07ed2cf29dd34035194919fbeb31"><td class="memItemLeft" align="right" valign="top">H5_HLDLL <a class="el" href="_h5public_8h.html#a3b079ecf932a5c599499cf7e298af160">herr_t</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="#gabc3c07ed2cf29dd34035194919fbeb31">H5DOwrite_chunk</a> (<a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a> dset_id, <a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a> dxpl_id, uint32_t filters, const <a class="el" href="_h5public_8h.html#a7f81cce70fb546af88da24d9285d3c1c">hsize_t</a> *offset, size_t data_size, const void *buf)</td></tr>
<tr class="memdesc:gabc3c07ed2cf29dd34035194919fbeb31"><td class="mdescLeft"> </td><td class="mdescRight">Writes a raw data chunk from a buffer directly to a dataset in a file. <br /></td></tr>
<tr class="separator:gabc3c07ed2cf29dd34035194919fbeb31"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:gaaf8ec5a5623f93549e49c39f95c4abab" id="r_gaaf8ec5a5623f93549e49c39f95c4abab"><td class="memItemLeft" align="right" valign="top">H5_HLDLL <a class="el" href="_h5public_8h.html#a3b079ecf932a5c599499cf7e298af160">herr_t</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="#gaaf8ec5a5623f93549e49c39f95c4abab">H5DOread_chunk</a> (<a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a> dset_id, <a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a> dxpl_id, const <a class="el" href="_h5public_8h.html#a7f81cce70fb546af88da24d9285d3c1c">hsize_t</a> *offset, uint32_t *filters, void *buf)</td></tr>
<tr class="memdesc:gaaf8ec5a5623f93549e49c39f95c4abab"><td class="mdescLeft"> </td><td class="mdescRight">Reads a raw data chunk directly from a dataset in a file into a buffer. <br /></td></tr>
<tr class="separator:gaaf8ec5a5623f93549e49c39f95c4abab"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<h2 class="groupheader">Function Documentation</h2>
<a id="ga316caac160af15192e0c78228667341e" name="ga316caac160af15192e0c78228667341e"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ga316caac160af15192e0c78228667341e">◆ </a></span>H5DOappend()</h2>
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<td class="memname">H5_HLDLL <a class="el" href="_h5public_8h.html#a3b079ecf932a5c599499cf7e298af160">herr_t</a> H5DOappend </td>
<td>(</td>
<td class="paramtype"><a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a></td> <td class="paramname"><span class="paramname"><em>dset_id</em>, </span></td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a></td> <td class="paramname"><span class="paramname"><em>dxpl_id</em>, </span></td>
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<td></td>
<td class="paramtype">unsigned</td> <td class="paramname"><span class="paramname"><em>axis</em>, </span></td>
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<td class="paramkey"></td>
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<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>extension</em>, </span></td>
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<td class="paramtype"><a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a></td> <td class="paramname"><span class="paramname"><em>memtype</em>, </span></td>
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<td class="paramkey"></td>
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<td class="paramtype">const void *</td> <td class="paramname"><span class="paramname"><em>buf</em></span> )</td>
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<p>Appends data to a dataset along a specified dimension. </p>
<hr />
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">dset_id</td><td>Dataset identifier </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">dxpl_id</td><td>Dataset transfer property list identifier </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">axis</td><td>Dataset Dimension (0-based) for the append </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">extension</td><td>Number of elements to append for the axis-th dimension </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">memtype</td><td>The memory datatype identifier </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">buf</td><td>Buffer with data for the append</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Returns a non-negative value if successful; otherwise, returns a negative value.</dd></dl>
<p>The <a class="el" href="#ga316caac160af15192e0c78228667341e" title="Appends data to a dataset along a specified dimension.">H5DOappend()</a> routine extends a dataset by <code>extension</code> number of elements along a dimension specified by a dimension <code>axis</code> and writes <code>buf</code> of elements to the dataset. Dimension <code>axis</code> is 0-based. Elements’ type is described by <code>memtype</code>.</p>
<p>This routine combines calling <a class="el" href="group___h5_d.html#gad31e1e0129f4520c531ce524de2a056f" title="Changes the sizes of a dataset's dimensions.">H5Dset_extent()</a>, <a class="el" href="group___h5_s.html#ga6adfdf1b95dc108a65bf66e97d38536d" title="Selects a hyperslab region to add to the current selected region.">H5Sselect_hyperslab()</a>, and <a class="el" href="group___h5_d.html#ga98f44998b67587662af8b0d8a0a75906" title="Writes raw data from a buffer to a dataset.">H5Dwrite()</a> into a single routine that simplifies application development for the common case of appending elements to an existing dataset.</p>
<p>For a multi-dimensional dataset, appending to one dimension will write a contiguous hyperslab over the other dimensions. For example, if a 3-D dataset has dimension sizes (3, 5, 8), extending the 0th dimension (currently of size 3) by 3 will append 3*5*8 = 120 elements (which must be pointed to by the <code>buffer</code> parameter) to the dataset, making its final dimension sizes (6, 5, 8).</p>
<p>If a dataset has more than one unlimited dimension, any of those dimensions may be appended to, although only along one dimension per call to <a class="el" href="#ga316caac160af15192e0c78228667341e" title="Appends data to a dataset along a specified dimension.">H5DOappend()</a>.</p>
<dl class="section since"><dt>Since</dt><dd>1.10.0 </dd></dl>
</div>
</div>
<a id="gaaf8ec5a5623f93549e49c39f95c4abab" name="gaaf8ec5a5623f93549e49c39f95c4abab"></a>
<h2 class="memtitle"><span class="permalink"><a href="#gaaf8ec5a5623f93549e49c39f95c4abab">◆ </a></span>H5DOread_chunk()</h2>
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<td class="memname">H5_HLDLL <a class="el" href="_h5public_8h.html#a3b079ecf932a5c599499cf7e298af160">herr_t</a> H5DOread_chunk </td>
<td>(</td>
<td class="paramtype"><a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a></td> <td class="paramname"><span class="paramname"><em>dset_id</em>, </span></td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a></td> <td class="paramname"><span class="paramname"><em>dxpl_id</em>, </span></td>
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<td></td>
<td class="paramtype">const <a class="el" href="_h5public_8h.html#a7f81cce70fb546af88da24d9285d3c1c">hsize_t</a> *</td> <td class="paramname"><span class="paramname"><em>offset</em>, </span></td>
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<td class="paramtype">uint32_t *</td> <td class="paramname"><span class="paramname"><em>filters</em>, </span></td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">void *</td> <td class="paramname"><span class="paramname"><em>buf</em></span> )</td>
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</div><div class="memdoc">
<p>Reads a raw data chunk directly from a dataset in a file into a buffer. </p>
<hr />
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">dset_id</td><td>Identifier for the dataset to be read </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">dxpl_id</td><td>Transfer property list identifier for this I/O operation </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">offset</td><td>Logical position of the chunk's first element in the dataspace </td></tr>
<tr><td class="paramdir">[in,out]</td><td class="paramname">filters</td><td>Mask for identifying the filters used with the chunk </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">buf</td><td>Buffer containing the chunk read from the dataset</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Returns a non-negative value if successful; otherwise, returns a negative value.</dd></dl>
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000003">Deprecated</a></b></dt><dd><p class="startdd">This function was deprecated in favor of the function <a class="el" href="group___h5_d.html#gac1092a63b718ec949d6539590a914b60" title="Reads a raw data chunk directly from a dataset in a file into a buffer.">H5Dread_chunk()</a> as of HDF5-1.10.3. In HDF5 1.10.3, the functionality of <a class="el" href="#gaaf8ec5a5623f93549e49c39f95c4abab" title="Reads a raw data chunk directly from a dataset in a file into a buffer.">H5DOread_chunk()</a> was moved to <a class="el" href="group___h5_d.html#gac1092a63b718ec949d6539590a914b60" title="Reads a raw data chunk directly from a dataset in a file into a buffer.">H5Dread_chunk()</a>. </p>
<p class="enddd">For compatibility, this API call has been left as a stub which simply calls <a class="el" href="group___h5_d.html#gac1092a63b718ec949d6539590a914b60" title="Reads a raw data chunk directly from a dataset in a file into a buffer.">H5Dread_chunk()</a>. New code should use <a class="el" href="group___h5_d.html#gac1092a63b718ec949d6539590a914b60" title="Reads a raw data chunk directly from a dataset in a file into a buffer.">H5Dread_chunk()</a>.</p>
</dd></dl>
<p>The <a class="el" href="#gaaf8ec5a5623f93549e49c39f95c4abab" title="Reads a raw data chunk directly from a dataset in a file into a buffer.">H5DOread_chunk()</a> reads a raw data chunk as specified by its logical <code>offset</code> in a chunked dataset <code>dset_id</code> from the dataset in the file into the application memory buffer <code>buf</code>. The data in <code>buf</code> is read directly from the file bypassing the library's internal data transfer pipeline, including filters.</p>
<p><code>dxpl_id</code> is a data transfer property list identifier.</p>
<p>The mask <code>filters</code> indicates which filters are used with the chunk when written. A zero value indicates that all enabled filters are applied on the chunk. A filter is skipped if the bit corresponding to the filter's position in the pipeline (<code>0 ≤ position < 32</code>) is turned on.</p>
<p><code>offset</code> is an array specifying the logical position of the first element of the chunk in the dataset's dataspace. The length of the offset array must equal the number of dimensions, or rank, of the dataspace. The values in <code>offset</code> must not exceed the dimension limits and must specify a point that falls on a dataset chunk boundary.</p>
<p><code>buf</code> is the memory buffer containing the chunk read from the dataset in the file.</p>
<dl class="section user"><dt>Example</dt><dd>The following code illustrates the use of <a class="el" href="#gaaf8ec5a5623f93549e49c39f95c4abab" title="Reads a raw data chunk directly from a dataset in a file into a buffer.">H5DOread_chunk()</a> to read a chunk from a dataset: <div class="fragment"><div class="line"> </div>
<div class="line"><span class="preprocessor">#include <zlib.h></span></div>
<div class="line"><span class="preprocessor">#include <math.h></span></div>
<div class="line"><span class="preprocessor">#define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s)) * 1.001) + 12)</span></div>
<div class="line"> :</div>
<div class="line"> :</div>
<div class="line"><span class="keywordtype">size_t</span> buf_size = CHUNK_NX*CHUNK_NY*<span class="keyword">sizeof</span>(int);</div>
<div class="line"> <span class="keyword">const</span> Bytef *z_src = (<span class="keyword">const</span> Bytef *)(direct_buf);</div>
<div class="line"> Bytef *z_dst; <span class="comment">/* Destination buffer */</span></div>
<div class="line"> uLongf z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);</div>
<div class="line"> uLong z_src_nbytes = (uLong)buf_size;</div>
<div class="line"> <span class="keywordtype">int</span> aggression = 9; <span class="comment">/* Compression aggression setting */</span></div>
<div class="line"> uint32_t filter_mask = 0;</div>
<div class="line"> <span class="keywordtype">size_t</span> buf_size = CHUNK_NX * CHUNK_NY * <span class="keyword">sizeof</span>(int);</div>
<div class="line"> <span class="comment">/* For H5DOread_chunk() */</span></div>
<div class="line"> <span class="keywordtype">void</span> *readbuf = NULL; <span class="comment">/* Buffer for reading data */</span></div>
<div class="line"> <span class="keyword">const</span> Bytef *pt_readbuf; <span class="comment">/* Point to the buffer for data read */</span></div>
<div class="line"> <a class="code hl_typedef" href="_h5public_8h.html#a7f81cce70fb546af88da24d9285d3c1c">hsize_t</a> read_chunk_nbytes; <span class="comment">/* Size of chunk on disk */</span></div>
<div class="line"> <span class="keywordtype">int</span> read_dst_buf[CHUNK_NX][CHUNK_NY]; <span class="comment">/* Buffer to hold un-compressed data */</span></div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Create the data space */</span></div>
<div class="line"> <span class="keywordflow">if</span> ((dataspace = <a class="code hl_function" href="group___h5_s.html#ga8e35eea5738b4805856eac7d595254ae">H5Screate_simple</a>(RANK, dims, maxdims)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Create a new file */</span></div>
<div class="line"> <span class="keywordflow">if</span> ((file = <a class="code hl_function" href="group___h5_f.html#gae64b51ee9ac0781bc4ccc599d98387f4">H5Fcreate</a>(FILE_NAME5, <a class="code hl_define" href="_h5_fpublic_8h.html#a5a2d6726f9ad8d2bca8df2b817e5ad6a">H5F_ACC_TRUNC</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>)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Modify dataset creation properties, i.e. enable chunking and compression */</span></div>
<div class="line"> <span class="keywordflow">if</span> ((cparms = <a class="code hl_function" href="group___p_l_c_r.html#gaf1b11da01d4d45d788c45f8bc5f0cbfa">H5Pcreate</a>(<a class="code hl_define" href="_h5_ppublic_8h.html#afcd7f8186c404f3a1d768632eacba102">H5P_DATASET_CREATE</a>)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> ((status = <a class="code hl_function" href="group___d_c_p_l.html#ga3584d592e377da3604b7604e266dcf5b">H5Pset_chunk</a>(cparms, RANK, chunk_dims)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> ((status = <a class="code hl_function" href="group___d_c_p_l.html#gaf1f569bfc54552bdb9317d2b63318a0d">H5Pset_deflate</a>(cparms, aggression)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Create a new dataset within the file using cparms creation properties */</span></div>
<div class="line"> <span class="keywordflow">if</span> ((dset_id = <a class="code hl_function" href="group___h5_d.html#gabf62045119f4e9c512d87d77f2f992df">H5Dcreate2</a>(file, DATASETNAME, <a class="code hl_define" href="group___p_d_t_n_a_t.html#ga3cf93ffc6782be68070ef8e00f219ec2">H5T_NATIVE_INT</a>, dataspace, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>, cparms,</div>
<div class="line"> <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Initialize data for one chunk */</span></div>
<div class="line"> <span class="keywordflow">for</span> (i = n = 0; i < CHUNK_NX; i++)</div>
<div class="line"> <span class="keywordflow">for</span> (j = 0; j < CHUNK_NY; j++)</div>
<div class="line"> direct_buf[i][j] = n++;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Allocate output (compressed) buffer */</span></div>
<div class="line"> outbuf = malloc(z_dst_nbytes);</div>
<div class="line"> z_dst = (Bytef *)outbuf;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Perform compression from the source to the destination buffer */</span></div>
<div class="line"> ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Check for various zlib errors */</span></div>
<div class="line"> <span class="keywordflow">if</span> (Z_BUF_ERROR == ret) {</div>
<div class="line"> fprintf(stderr, <span class="stringliteral">"overflow"</span>);</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span> <span class="keywordflow">if</span> (Z_MEM_ERROR == ret) {</div>
<div class="line"> fprintf(stderr, <span class="stringliteral">"deflate memory error"</span>);</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span> <span class="keywordflow">if</span> (Z_OK != ret) {</div>
<div class="line"> fprintf(stderr, <span class="stringliteral">"other deflate error"</span>);</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Write the compressed chunk data repeatedly to cover all the</span></div>
<div class="line"><span class="comment"> * * chunks in the dataset, using the direct write function. */</span></div>
<div class="line"> <span class="keywordflow">for</span> (i = 0; i < NX / CHUNK_NX; i++) {</div>
<div class="line"> <span class="keywordflow">for</span> (j = 0; j < NY / CHUNK_NY; j++) {</div>
<div class="line"> status = <a class="code hl_function" href="#gabc3c07ed2cf29dd34035194919fbeb31">H5DOwrite_chunk</a>(dset_id, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>, filter_mask, offset, z_dst_nbytes, outbuf);</div>
<div class="line"> offset[1] += CHUNK_NY;</div>
<div class="line"> }</div>
<div class="line"> offset[0] += CHUNK_NX;</div>
<div class="line"> offset[1] = 0;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> (<a class="code hl_function" href="group___h5_f.html#gae686870f0a276c4d06bbc667b2c24124">H5Fflush</a>(dataset, <a class="code hl_enumvalue" href="_h5_fpublic_8h.html#ac9db1b1211555797021daed9b54b8cdfa3d09ee2d1551f31b008a7dc7d80b42bd">H5F_SCOPE_LOCAL</a>) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> (<a class="code hl_function" href="group___h5_d.html#gae47c3f38db49db127faf221624c30609">H5Dclose</a>(dataset) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> ((dataset = <a class="code hl_function" href="group___h5_d.html#ga04198c4cf0b849ed3a8921f6c7169ee2">H5Dopen2</a>(file, DATASETNAME1, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> offset[0] = CHUNK_NX;</div>
<div class="line"> offset[1] = CHUNK_NY;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Get the size of the compressed chunk */</span></div>
<div class="line"> ret = <a class="code hl_function" href="group___h5_d.html#gaaeea958861de082db9051fc4bf215234">H5Dget_chunk_storage_size</a>(dataset, offset, &read_chunk_nbytes);</div>
<div class="line"> </div>
<div class="line"> readbuf = malloc(read_chunk_nbytes);</div>
<div class="line"> pt_readbuf = (<span class="keyword">const</span> Bytef *)readbuf;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Use H5DOread_chunk() to read the chunk back */</span></div>
<div class="line"> <span class="keywordflow">if</span> ((status = <a class="code hl_function" href="#gaaf8ec5a5623f93549e49c39f95c4abab">H5DOread_chunk</a>(dataset, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>, offset, &read_filter_mask, readbuf)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> ret =</div>
<div class="line"> uncompress((Bytef *)read_dst_buf, (uLongf *)&buf_size, pt_readbuf, (uLong)read_chunk_nbytes);</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Check for various zlib errors */</span></div>
<div class="line"> <span class="keywordflow">if</span> (Z_BUF_ERROR == ret) {</div>
<div class="line"> fprintf(stderr, <span class="stringliteral">"error: not enough room in output buffer"</span>);</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span> <span class="keywordflow">if</span> (Z_MEM_ERROR == ret) {</div>
<div class="line"> fprintf(stderr, <span class="stringliteral">"error: not enough memory"</span>);</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span> <span class="keywordflow">if</span> (Z_OK != ret) {</div>
<div class="line"> fprintf(stderr, <span class="stringliteral">"error: corrupted input data"</span>);</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Data verification here */</span></div>
<div class="line"> :</div>
<div class="line"> :</div>
<div class="ttc" id="a_h5_ppublic_8h_html_afcd7f8186c404f3a1d768632eacba102"><div class="ttname"><a href="_h5_ppublic_8h.html#afcd7f8186c404f3a1d768632eacba102">H5P_DATASET_CREATE</a></div><div class="ttdeci">#define H5P_DATASET_CREATE</div><div class="ttdef"><b>Definition</b> H5Ppublic.h:53</div></div>
<div class="ttc" id="agroup___h5_d_o_html_gaaf8ec5a5623f93549e49c39f95c4abab"><div class="ttname"><a href="#gaaf8ec5a5623f93549e49c39f95c4abab">H5DOread_chunk</a></div><div class="ttdeci">H5_HLDLL herr_t H5DOread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters, void *buf)</div><div class="ttdoc">Reads a raw data chunk directly from a dataset in a file into a buffer.</div></div>
<div class="ttc" id="agroup___h5_d_o_html_gabc3c07ed2cf29dd34035194919fbeb31"><div class="ttname"><a href="#gabc3c07ed2cf29dd34035194919fbeb31">H5DOwrite_chunk</a></div><div class="ttdeci">H5_HLDLL herr_t H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, size_t data_size, const void *buf)</div><div class="ttdoc">Writes a raw data chunk from a buffer directly to a dataset in a file.</div></div>
<div class="ttc" id="agroup___p_d_t_n_a_t_html_ga290b9655882754ee0ec9f31b42ac04f6"><div class="ttname"><a href="group___p_d_t_n_a_t.html#ga290b9655882754ee0ec9f31b42ac04f6">H5T_NATIVE_LONG</a></div><div class="ttdeci">#define H5T_NATIVE_LONG</div><div class="ttdef"><b>Definition</b> H5Tpublic.h:777</div></div>
</div><!-- fragment --></dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.10.3 Function deprecated in favor of H5Dread_chunk.</dd></dl>
<dl class="section since"><dt>Since</dt><dd>1.10.2, 1.8.19 </dd></dl>
</div>
</div>
<a id="gabc3c07ed2cf29dd34035194919fbeb31" name="gabc3c07ed2cf29dd34035194919fbeb31"></a>
<h2 class="memtitle"><span class="permalink"><a href="#gabc3c07ed2cf29dd34035194919fbeb31">◆ </a></span>H5DOwrite_chunk()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">H5_HLDLL <a class="el" href="_h5public_8h.html#a3b079ecf932a5c599499cf7e298af160">herr_t</a> H5DOwrite_chunk </td>
<td>(</td>
<td class="paramtype"><a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a></td> <td class="paramname"><span class="paramname"><em>dset_id</em>, </span></td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="_h5_ipublic_8h.html#a0045db7ff9c22ad35db6ae91662e1943">hid_t</a></td> <td class="paramname"><span class="paramname"><em>dxpl_id</em>, </span></td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">uint32_t</td> <td class="paramname"><span class="paramname"><em>filters</em>, </span></td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="_h5public_8h.html#a7f81cce70fb546af88da24d9285d3c1c">hsize_t</a> *</td> <td class="paramname"><span class="paramname"><em>offset</em>, </span></td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">size_t</td> <td class="paramname"><span class="paramname"><em>data_size</em>, </span></td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const void *</td> <td class="paramname"><span class="paramname"><em>buf</em></span> )</td>
</tr>
</table>
</div><div class="memdoc">
<p>Writes a raw data chunk from a buffer directly to a dataset in a file. </p>
<hr />
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">dset_id</td><td>Identifier for the dataset to write to </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">dxpl_id</td><td>Transfer property list identifier for this I/O operation </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">filters</td><td>Mask for identifying the filters in use </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">offset</td><td>Logical position of the chunk's first element in the dataspace </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">data_size</td><td>Size of the actual data to be written in bytes </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">buf</td><td>Buffer containing data to be written to the chunk</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Returns a non-negative value if successful; otherwise, returns a negative value.</dd></dl>
<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000002">Deprecated</a></b></dt><dd><p class="startdd">This function was deprecated in favor of the function <a class="el" href="group___h5_d.html#ga416ccd200929b11386a10e9024977109" title="Writes a raw data chunk from a buffer directly to a dataset in a file.">H5Dwrite_chunk()</a> of HDF5-1.10.3. The functionality of <a class="el" href="#gabc3c07ed2cf29dd34035194919fbeb31" title="Writes a raw data chunk from a buffer directly to a dataset in a file.">H5DOwrite_chunk()</a> was moved to <a class="el" href="group___h5_d.html#ga416ccd200929b11386a10e9024977109" title="Writes a raw data chunk from a buffer directly to a dataset in a file.">H5Dwrite_chunk()</a>. </p>
<p class="enddd">For compatibility, this API call has been left as a stub which simply calls <a class="el" href="group___h5_d.html#ga416ccd200929b11386a10e9024977109" title="Writes a raw data chunk from a buffer directly to a dataset in a file.">H5Dwrite_chunk()</a>. New code should use <a class="el" href="group___h5_d.html#ga416ccd200929b11386a10e9024977109" title="Writes a raw data chunk from a buffer directly to a dataset in a file.">H5Dwrite_chunk()</a>.</p>
</dd></dl>
<p>The <a class="el" href="#gabc3c07ed2cf29dd34035194919fbeb31" title="Writes a raw data chunk from a buffer directly to a dataset in a file.">H5DOwrite_chunk()</a> writes a raw data chunk as specified by its logical <code>offset</code> in a chunked dataset <code>dset_id</code> from the application memory buffer <code>buf</code> to the dataset in the file. Typically, the data in <code>buf</code> is preprocessed in memory by a custom transformation, such as compression. The chunk will bypass the library's internal data transfer pipeline, including filters, and will be written directly to the file.</p>
<p><code>dxpl_id</code> is a data transfer property list identifier.</p>
<p><code>filters</code> is a mask providing a record of which filters are used with the chunk. The default value of the mask is zero (<code>0</code>), indicating that all enabled filters are applied. A filter is skipped if the bit corresponding to the filter's position in the pipeline (<code>0 ≤ position < 32</code>) is turned on. This mask is saved with the chunk in the file.</p>
<p><code>offset</code> is an array specifying the logical position of the first element of the chunk in the dataset's dataspace. The length of the offset array must equal the number of dimensions, or rank, of the dataspace. The values in <code>offset</code> must not exceed the dimension limits and must specify a point that falls on a dataset chunk boundary.</p>
<p><code>data_size</code> is the size in bytes of the chunk, representing the number of bytes to be read from the buffer <code>buf</code>. If the data chunk has been precompressed, <code>data_size</code> should be the size of the compressed data.</p>
<p><code>buf</code> is the memory buffer containing data to be written to the chunk in the file.</p>
<dl class="section attention"><dt>Attention</dt><dd>Exercise caution when using <a class="el" href="#gaaf8ec5a5623f93549e49c39f95c4abab" title="Reads a raw data chunk directly from a dataset in a file into a buffer.">H5DOread_chunk()</a> and <a class="el" href="#gabc3c07ed2cf29dd34035194919fbeb31" title="Writes a raw data chunk from a buffer directly to a dataset in a file.">H5DOwrite_chunk()</a>, as they read and write data chunks directly in a file. <a class="el" href="#gabc3c07ed2cf29dd34035194919fbeb31" title="Writes a raw data chunk from a buffer directly to a dataset in a file.">H5DOwrite_chunk()</a> bypasses hyperslab selection, the conversion of data from one datatype to another, and the filter pipeline to write the chunk. Developers should have experience with these processes before using this function. Please see <a href="https://portal.hdfgroup.org/display/HDF5/Using+the+Direct+Chunk+Write+Function">Using the Direct Chunk Write Function</a> for more information.</dd></dl>
<dl class="section note"><dt>Note</dt><dd><a class="el" href="#gaaf8ec5a5623f93549e49c39f95c4abab" title="Reads a raw data chunk directly from a dataset in a file into a buffer.">H5DOread_chunk()</a> and <a class="el" href="#gabc3c07ed2cf29dd34035194919fbeb31" title="Writes a raw data chunk from a buffer directly to a dataset in a file.">H5DOwrite_chunk()</a> are not supported under parallel and do not support variable length types.</dd></dl>
<dl class="section user"><dt>Example</dt><dd>The following code illustrates the use of H5DOwrite_chunk to write an entire dataset, chunk by chunk: <div class="fragment"><div class="line"> </div>
<div class="line"><span class="preprocessor">#include <zlib.h></span></div>
<div class="line"><span class="preprocessor">#include <math.h></span></div>
<div class="line"><span class="preprocessor">#define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s)) * 1.001) + 12)</span></div>
<div class="line"> :</div>
<div class="line"> :</div>
<div class="line"><span class="keywordtype">size_t</span> buf_size = CHUNK_NX*CHUNK_NY*<span class="keyword">sizeof</span>(int);</div>
<div class="line"> <span class="keyword">const</span> Bytef *z_src = (<span class="keyword">const</span> Bytef *)(direct_buf);</div>
<div class="line"> Bytef *z_dst; <span class="comment">/* Destination buffer */</span></div>
<div class="line"> uLongf z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size);</div>
<div class="line"> uLong z_src_nbytes = (uLong)buf_size;</div>
<div class="line"> <span class="keywordtype">int</span> aggression = 9; <span class="comment">/* Compression aggression setting */</span></div>
<div class="line"> uint32_t filter_mask = 0;</div>
<div class="line"> <span class="keywordtype">size_t</span> buf_size = CHUNK_NX * CHUNK_NY * <span class="keyword">sizeof</span>(int);</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Create the data space */</span></div>
<div class="line"> <span class="keywordflow">if</span> ((dataspace = <a class="code hl_function" href="group___h5_s.html#ga8e35eea5738b4805856eac7d595254ae">H5Screate_simple</a>(RANK, dims, maxdims)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Create a new file */</span></div>
<div class="line"> <span class="keywordflow">if</span> ((file = <a class="code hl_function" href="group___h5_f.html#gae64b51ee9ac0781bc4ccc599d98387f4">H5Fcreate</a>(FILE_NAME5, <a class="code hl_define" href="_h5_fpublic_8h.html#a5a2d6726f9ad8d2bca8df2b817e5ad6a">H5F_ACC_TRUNC</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>)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Modify dataset creation properties, i.e. enable chunking and compression */</span></div>
<div class="line"> <span class="keywordflow">if</span> ((cparms = <a class="code hl_function" href="group___p_l_c_r.html#gaf1b11da01d4d45d788c45f8bc5f0cbfa">H5Pcreate</a>(<a class="code hl_define" href="_h5_ppublic_8h.html#afcd7f8186c404f3a1d768632eacba102">H5P_DATASET_CREATE</a>)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> ((status = <a class="code hl_function" href="group___d_c_p_l.html#ga3584d592e377da3604b7604e266dcf5b">H5Pset_chunk</a>(cparms, RANK, chunk_dims)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">if</span> ((status = <a class="code hl_function" href="group___d_c_p_l.html#gaf1f569bfc54552bdb9317d2b63318a0d">H5Pset_deflate</a>(cparms, aggression)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Create a new dataset within the file using cparms creation properties */</span></div>
<div class="line"> <span class="keywordflow">if</span> ((dset_id = <a class="code hl_function" href="group___h5_d.html#gabf62045119f4e9c512d87d77f2f992df">H5Dcreate2</a>(file, DATASETNAME, <a class="code hl_define" href="group___p_d_t_n_a_t.html#ga3cf93ffc6782be68070ef8e00f219ec2">H5T_NATIVE_INT</a>, dataspace, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>, cparms,</div>
<div class="line"> <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>)) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Initialize data for one chunk */</span></div>
<div class="line"> <span class="keywordflow">for</span> (i = n = 0; i < CHUNK_NX; i++)</div>
<div class="line"> <span class="keywordflow">for</span> (j = 0; j < CHUNK_NY; j++)</div>
<div class="line"> direct_buf[i][j] = n++;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Allocate output (compressed) buffer */</span></div>
<div class="line"> outbuf = malloc(z_dst_nbytes);</div>
<div class="line"> z_dst = (Bytef *)outbuf;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Perform compression from the source to the destination buffer */</span></div>
<div class="line"> ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Check for various zlib errors */</span></div>
<div class="line"> <span class="keywordflow">if</span> (Z_BUF_ERROR == ret) {</div>
<div class="line"> fprintf(stderr, <span class="stringliteral">"overflow"</span>);</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span> <span class="keywordflow">if</span> (Z_MEM_ERROR == ret) {</div>
<div class="line"> fprintf(stderr, <span class="stringliteral">"deflate memory error"</span>);</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span> <span class="keywordflow">if</span> (Z_OK != ret) {</div>
<div class="line"> fprintf(stderr, <span class="stringliteral">"other deflate error"</span>);</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Write the compressed chunk data repeatedly to cover all the</span></div>
<div class="line"><span class="comment"> * * chunks in the dataset, using the direct write function. */</span></div>
<div class="line"> <span class="keywordflow">for</span> (i = 0; i < NX / CHUNK_NX; i++) {</div>
<div class="line"> <span class="keywordflow">for</span> (j = 0; j < NY / CHUNK_NY; j++) {</div>
<div class="line"> status =</div>
<div class="line"> <a class="code hl_function" href="#gabc3c07ed2cf29dd34035194919fbeb31">H5DOwrite_chunk</a>(dset_id, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>, filter_mask, offset, z_dst_nbytes, outbuf);</div>
<div class="line"> offset[1] += CHUNK_NY;</div>
<div class="line"> }</div>
<div class="line"> offset[0] += CHUNK_NX;</div>
<div class="line"> offset[1] = 0;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Overwrite the first chunk with uncompressed data. Set the filter mask to</span></div>
<div class="line"><span class="comment"> * * indicate the compression filter is skipped */</span></div>
<div class="line"> filter_mask = 0x00000001;</div>
<div class="line"> offset[0] = offset[1] = 0;</div>
<div class="line"> <span class="keywordflow">if</span> (<a class="code hl_function" href="#gabc3c07ed2cf29dd34035194919fbeb31">H5DOwrite_chunk</a>(dset_id, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>, filter_mask, offset, buf_size, direct_buf) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Read the entire dataset back for data verification converting ints to longs */</span></div>
<div class="line"> <span class="keywordflow">if</span> (<a class="code hl_function" href="group___h5_d.html#ga8287d5a7be7b8e55ffeff68f7d26811c">H5Dread</a>(dataset, <a class="code hl_define" href="group___p_d_t_n_a_t.html#ga290b9655882754ee0ec9f31b42ac04f6">H5T_NATIVE_LONG</a>, <a class="code hl_define" href="_h5_spublic_8h.html#a5f96eeee84b987f18470737f85af0484">H5S_ALL</a>, <a class="code hl_define" href="_h5_spublic_8h.html#a5f96eeee84b987f18470737f85af0484">H5S_ALL</a>, <a class="code hl_define" href="_h5_ppublic_8h.html#afa85e97bfbf9bf1c58e39263846c568f">H5P_DEFAULT</a>, outbuf_long) < 0)</div>
<div class="line"> <span class="keywordflow">goto</span> error;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">/* Data verification here */</span></div>
<div class="line"> :</div>
<div class="line"> :</div>
<div class="line"> </div>
</div><!-- fragment --></dd></dl>
<dl class="section version"><dt>Version</dt><dd>1.10.3 Function deprecated in favor of H5Dwrite_chunk.</dd></dl>
<dl class="section since"><dt>Since</dt><dd>1.8.11 </dd></dl>
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