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<div class="headertitle"><div class="title">Use Case: Examining a JPSS NPP File With HDF5 Tools</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="_view_tools_command.html">Command-line Tools</a> </p><hr />
<h1><a class="anchor" id="secViewToolsJPSSTOC"></a>
Contents</h1>
<ul>
<li>
<a class="el" href="#secViewToolsJPSSDeter">Determining File Contents</a> </li>
<li>
<a class="el" href="#secViewToolsJPSSView">Viewing the User Block</a> </li>
<li>
<a class="el" href="#secViewToolsJPSSExam">Examining a Granule</a> </li>
</ul>
<p>This tutorial illustrates how to use the HDF5 tools to examine NPP files from the JPSS project. The following files are discussed: </p><div class="fragment"><div class="line">SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5 (<a href=<span class="stringliteral">"https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5.gz"</span>>gzipped file</a>)</div>
<div class="line">SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5 (<a href=<span class="stringliteral">"https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5.gz"</span>>gzipped file</a>)</div>
</div><!-- fragment --><h1><a class="anchor" id="secViewToolsJPSSDeter"></a>
Determining File Contents</h1>
<p>The first thing you may want to do is determine what is in your file. You can use the command-line tools or HDFView to do this: </p><ul>
<li><a class="el" href="#subsecViewToolsJPSSDeter_h5dump">h5dump</a> </li>
<li><a class="el" href="#subsecViewToolsJPSSDeter_h5ls">h5ls</a> </li>
<li><a class="el" href="#subsecViewToolsJPSSDeter_HDFView">HDFView</a></li>
</ul>
<p>JPSS NPP files all contain two root level groups: </p><table class="doxtable">
<tr>
<th>Group</th><th>Description </th></tr>
<tr>
<td>/All_Data </td><td>Contains the raw data and optional geo-location information. </td></tr>
<tr>
<td>/Data_Products </td><td>Contains a dataset ending in <code style="background-color:whitesmoke;">Aggr</code> with references to objects in the <code style="background-color:whitesmoke;">/All_Data</code> group. Contains granules (datasets with a name ending in <code style="background-color:whitesmoke;">Gran_#</code>) with references to selected regions in datasets under <code style="background-color:whitesmoke;">/All_Data</code>. </td></tr>
</table>
<h2><a class="anchor" id="subsecViewToolsJPSSDeter_h5dump"></a>
h5dump</h2>
<p>With <code style="background-color:whitesmoke;">h5dump</code> you can see a list of the objects in the file using the <code style="background-color:whitesmoke;">-n</code> option: </p><div class="fragment"><div class="line">h5dump -n <file></div>
</div><!-- fragment --><p>For example: </p><div class="fragment"><div class="line">$ h5dump -n SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5</div>
<div class="line">HDF5 <span class="stringliteral">"SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5"</span> {</div>
<div class="line">FILE_CONTENTS {</div>
<div class="line"> group /</div>
<div class="line"> group /All_Data</div>
<div class="line"> group /All_Data/VIIRS-M9-SDR_All</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/ModeGran</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/ModeScan</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/NumberOfBadChecksums</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/NumberOfDiscardedPkts</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/NumberOfMissingPkts</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/NumberOfScans</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/PadByte1</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/QF1_VIIRSMBANDSDR</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/QF2_SCAN_SDR</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/QF3_SCAN_RDR</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/QF4_SCAN_SDR</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/QF5_GRAN_BADDETECTOR</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/Radiance</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/RadianceFactors</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/Reflectance</div>
<div class="line"> dataset /All_Data/VIIRS-M9-SDR_All/ReflectanceFactors</div>
<div class="line"> group /Data_Products</div>
<div class="line"> group /Data_Products/VIIRS-M9-SDR</div>
<div class="line"> dataset /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Aggr</div>
<div class="line"> dataset /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0</div>
<div class="line"> dataset /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_1</div>
<div class="line"> dataset /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_2</div>
<div class="line"> dataset /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_3</div>
<div class="line"> }</div>
<div class="line">}</div>
</div><!-- fragment --><p>In the output above you can see that there are four granules (ending in <code style="background-color:whitesmoke;">Gran_#</code>) in the <code style="background-color:whitesmoke;">/Data_Products/VIIRS-M9-SDR/</code> group.</p>
<h2><a class="anchor" id="subsecViewToolsJPSSDeter_h5ls"></a>
h5ls</h2>
<p>With <code style="background-color:whitesmoke;">h5ls</code> you can see a list of the objects in the file using the <code style="background-color:whitesmoke;">-lr</code> options. The <code style="background-color:whitesmoke;">h5ls</code> utility also shows shape and size (dataspace) information about datasets. </p><div class="fragment"><div class="line">h5ls -lr <file></div>
</div><!-- fragment --><p>For example: </p><div class="fragment"><div class="line">$ h5ls -lr SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5</div>
<div class="line">/ Group</div>
<div class="line">/All_Data Group</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All Group</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/ModeGran Dataset {4/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/ModeScan Dataset {192/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/NumberOfBadChecksums Dataset {192/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/NumberOfDiscardedPkts Dataset {192/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/NumberOfMissingPkts Dataset {192/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/NumberOfScans Dataset {4/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/PadByte1 Dataset {12/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/QF1_VIIRSMBANDSDR Dataset {3072/Inf, 3200/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/QF2_SCAN_SDR Dataset {192/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/QF3_SCAN_RDR Dataset {192/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/QF4_SCAN_SDR Dataset {3072/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/QF5_GRAN_BADDETECTOR Dataset {64/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/Radiance Dataset {3072/Inf, 3200/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/RadianceFactors Dataset {8/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/Reflectance Dataset {3072/Inf, 3200/Inf}</div>
<div class="line">/All_Data/VIIRS-M9-SDR_All/ReflectanceFactors Dataset {8/Inf}</div>
<div class="line">/Data_Products Group</div>
<div class="line">/Data_Products/VIIRS-M9-SDR Group</div>
<div class="line">/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Aggr Dataset {16/Inf}</div>
<div class="line">/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0 Dataset {16/Inf}</div>
<div class="line">/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_1 Dataset {16/Inf}</div>
<div class="line">/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_2 Dataset {16/Inf}</div>
<div class="line">/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_3 Dataset {16/Inf}</div>
</div><!-- fragment --><p> Note that the <code style="background-color:whitesmoke;">Inf</code> indicates that those datasets are appendable or unlimited in size.</p>
<h2><a class="anchor" id="subsecViewToolsJPSSDeter_HDFView"></a>
HDFView</h2>
<p>If you open the file in HDFView, it will display the file and the root level groups within it in the TreeView on the left. An HDF5 file is a folder with a "5" in the middle, followed by the file name. There are two folders (groups) within the JPSS file (<code style="background-color:whitesmoke;">All_Data/</code> and <code style="background-color:whitesmoke;">Data Products/</code>), which you can select to see their contents: </p><table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-tree.png" alt=""/>
</div>
</td></tr>
</table>
<p>If you click twice with the left-mouse button on a folder or group in the TreeView, the contents of the folder will be listed. If you click twice on an object such as a dataset, a window with the object's values will be displayed.</p>
<p>Underneath the <code style="background-color:whitesmoke;">VIIRS-M1-SDR</code> folder are what HDF5 calls datasets. The scarlet letter <code style="background-color:whitesmoke;">"A"</code> attached to the group and datasets under <code style="background-color:whitesmoke;">Data_Products/</code> indicates that there are attributes associated with them.</p>
<h1><a class="anchor" id="secViewToolsJPSSView"></a>
Viewing the User Block</h1>
<p>All JPSS files contain a user block in XML with information about the file. The user block is an optional space allocated at the beginning of an HDF5 file that is not interpreted by the HDF5 library. Its size is a multiple of 512.</p>
<p>Since the user block in JPSS files is stored in ASCII and it is stored at the beginning of an HDF5 file, you could use a text editor or viewer to examine it. However, there are HDF5 utilities that can help with this: </p><table class="doxtable">
<tr>
<th>Utility</th><th>Description </th></tr>
<tr>
<td>h5unjam </td><td>Extracts a user block from an HDF5 file </td></tr>
<tr>
<td>h5dump </td><td>The -B (–superblock) option displays the size of the user block in an HDF5 file </td></tr>
</table>
<h2><a class="anchor" id="subsecViewToolsJPSSView_h5unjam"></a>
h5unjam</h2>
<p>The <a class="el" href="_view_tools_edit.html#secViewToolsEditAdd">Add or Remove User Block from File</a> tutorial topic discusses the use of the <code style="background-color:whitesmoke;">h5jam</code> and <code style="background-color:whitesmoke;">h5unjam</code> utilities for adding or removing a user block from a file. An input HDF5 file (<code style="background-color:whitesmoke;">-i</code>), output HDF5 file (<code style="background-color:whitesmoke;">-o</code>), and user block text file (<code style="background-color:whitesmoke;">-u</code>) can be specified with these tools. You can use the <code style="background-color:whitesmoke;">h5unjam</code> tool to extract and view the user block in a JPSS file: </p><div class="fragment"><div class="line">h5unjam -i <Input HDF5 File> -o <Output HDF5 File> -u <User Block File></div>
</div><!-- fragment --><p>For example this command will extract the user block into the file UB.xml: </p><div class="fragment"><div class="line">$ h5unjam -i SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5 </div>
<div class="line"> -o svm09-noUB.h5 -u UB.xml</div>
</div><!-- fragment --><p>The input HDF5 file remains unchanged. The output HDF5 file will not contain the user block. The <code style="background-color:whitesmoke;">UB.xml</code> file contains the user block which can be viewed with a browser.</p>
<h2><a class="anchor" id="subsecViewToolsJPSSView_h5dump"></a>
h5dump</h2>
<p>The h5dump utility has the <code style="background-color:whitesmoke;">-B (–superblock)</code> option for displaying the superblock in an HDF5 file. The superblock contains information about the file such as the file signature, file consistency flags, the number of bytes to store addresses and size of an object, as well as the size of the user block: </p><div class="fragment"><div class="line">h5dump -B (--superblock)</div>
</div><!-- fragment --><p>Below is an example (Unix): </p><div class="fragment"><div class="line">$ h5dump -B -H SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5 | more</div>
<div class="line">HDF5 <span class="stringliteral">"SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5"</span> {</div>
<div class="line">SUPER_BLOCK {</div>
<div class="line"> SUPERBLOCK_VERSION 0</div>
<div class="line"> FREELIST_VERSION 0</div>
<div class="line"> SYMBOLTABLE_VERSION 0</div>
<div class="line"> OBJECTHEADER_VERSION 0</div>
<div class="line"> OFFSET_SIZE 8</div>
<div class="line"> LENGTH_SIZE 8</div>
<div class="line"> BTREE_RANK 16</div>
<div class="line"> BTREE_LEAF 4</div>
<div class="line"> ISTORE_K 32</div>
<div class="line"> USER_BLOCK {</div>
<div class="line"> USERBLOCK_SIZE 1024</div>
<div class="line"> }</div>
<div class="line">}</div>
</div><!-- fragment --><p>Once you have the size of the user block, you can extract it from the file using system commands. For example, on Unix platforms you can use the head command-line tool: </p><div class="fragment"><div class="line">head -c <USERBLOCK_SIZE> <JPSS File> >& USERBLOCK.xml</div>
</div><!-- fragment --><p>There are Unix tools for Windows that may work, such as <a href="http://gnuwin32.sourceforge.net/packages/coreutils.htm">CoreUtils for Windows</a>.</p>
<h1><a class="anchor" id="secViewToolsJPSSExam"></a>
Examining a Granule</h1>
<ul>
<li>
<a class="el" href="#subsecViewToolsJPSSExam_h5dump">h5dump</a><br />
<ul>
<li>
<a class="el" href="#subsubsecViewToolsJPSSExam_h5dumpRegRef">Viewing a Region Reference</a> </li>
<li>
<a class="el" href="#subsubsecViewToolsJPSSExam_h5dumpQuality">Viewing a Quality Flag</a> </li>
<li>
<a class="el" href="#subsubsecViewToolsJPSSExam_h5dumpProps">Properties</a> </li>
</ul>
</li>
<li>
<a class="el" href="#subsecViewToolsJPSSExamr_HDFView">HDFView</a> </li>
</ul>
<h2><a class="anchor" id="subsecViewToolsJPSSExam_h5dump"></a>
h5dump</h2>
<p>There are several options that you may first want to use when examining a granule with h5dump: </p><table class="doxtable">
<tr>
<th>Option</th><th>Description </th></tr>
<tr>
<td>-H, –header </td><td>Prints header (metadata) information only </td></tr>
<tr>
<td>-d D, –dataset=D </td><td>Specifies the granule dataset </td></tr>
<tr>
<td>-A 0, –onlyattr=0 </td><td>Suppresses attributes </td></tr>
<tr>
<td>-p, –properties </td><td>Show properties of datasets (See Properties) </td></tr>
</table>
<p>You would specify the dataset (<code style="background-color:whitesmoke;">-d D</code>) and the <code style="background-color:whitesmoke;">-H</code> options to view the metadata associated with a specific granule. There are many attributes associated with a granule and <code style="background-color:whitesmoke;">-A 0</code> can be used to suppress those.</p>
<p>For example: </p><div class="fragment"><div class="line">h5dump -H -A 0 -d <span class="stringliteral">"/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0"</span> </div>
<div class="line"> SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5</div>
</div><!-- fragment --><p>This command displays: </p><div class="fragment"><div class="line">HDF5 <span class="stringliteral">"SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5"</span> {</div>
<div class="line">DATASET <span class="stringliteral">"/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0"</span> {</div>
<div class="line"> DATATYPE <a class="code hl_enumvalue" href="_h5_tpublic_8h.html#a071841985f647f69516dbe77d93167f2a5850e0b9353a5e7aeb615fb943d4e9cd">H5T_REFERENCE</a> { <a class="code hl_define" href="group___p_d_t_s_t_d.html#gaf5cb0d5cec3d40d8b3ac27512f86895e">H5T_STD_REF_DSETREG</a> }</div>
<div class="line"> DATASPACE SIMPLE { ( 16 ) / ( <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a> ) }</div>
<div class="line">}</div>
<div class="line">}</div>
<div class="ttc" id="a_h5_spublic_8h_html_a5af9ab788797b2ea9a4843857674ac18"><div class="ttname"><a href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a></div><div class="ttdeci">#define H5S_UNLIMITED</div><div class="ttdef"><b>Definition</b> H5Spublic.h:48</div></div>
<div class="ttc" id="a_h5_tpublic_8h_html_a071841985f647f69516dbe77d93167f2a5850e0b9353a5e7aeb615fb943d4e9cd"><div class="ttname"><a href="_h5_tpublic_8h.html#a071841985f647f69516dbe77d93167f2a5850e0b9353a5e7aeb615fb943d4e9cd">H5T_REFERENCE</a></div><div class="ttdeci">@ H5T_REFERENCE</div><div class="ttdef"><b>Definition</b> H5Tpublic.h:39</div></div>
<div class="ttc" id="agroup___p_d_t_s_t_d_html_gaf5cb0d5cec3d40d8b3ac27512f86895e"><div class="ttname"><a href="group___p_d_t_s_t_d.html#gaf5cb0d5cec3d40d8b3ac27512f86895e">H5T_STD_REF_DSETREG</a></div><div class="ttdeci">#define H5T_STD_REF_DSETREG</div><div class="ttdef"><b>Definition</b> H5Tpublic.h:410</div></div>
</div><!-- fragment --><p>To see the actual contents of the granule remove the <code style="background-color:whitesmoke;">-H</code> option: </p><div class="fragment"><div class="line">h5dump -A 0 -d <span class="stringliteral">"/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0"</span> </div>
<div class="line"> SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5</div>
</div><!-- fragment --><p>The above command displays: </p><div class="fragment"><div class="line">HDF5 <span class="stringliteral">"SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5"</span> {</div>
<div class="line">DATASET <span class="stringliteral">"/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0"</span> {</div>
<div class="line"> DATATYPE <a class="code hl_enumvalue" href="_h5_tpublic_8h.html#a071841985f647f69516dbe77d93167f2a5850e0b9353a5e7aeb615fb943d4e9cd">H5T_REFERENCE</a> { <a class="code hl_define" href="group___p_d_t_s_t_d.html#gaf5cb0d5cec3d40d8b3ac27512f86895e">H5T_STD_REF_DSETREG</a> }</div>
<div class="line"> DATASPACE SIMPLE { ( 16 ) / ( <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a> ) }</div>
<div class="line"> DATA {</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/Radiance {(0,0)-(767,3199)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/Reflectance {(0,0)-(767,3199)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/ModeScan {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/ModeGran {(0)-(0)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/PadByte1 {(0)-(2)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfScans {(0)-(0)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfMissingPkts {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfBadChecksums {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfDiscardedPkts {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/QF1_VIIRSMBANDSDR {(0,0)-(767,3199)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/QF2_SCAN_SDR {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/QF3_SCAN_RDR {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/QF4_SCAN_SDR {(0)-(767)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/QF5_GRAN_BADDETECTOR {(0)-(15)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/RadianceFactors {(0)-(1)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M9-SDR_All/ReflectanceFactors {(0)-(1)}</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line">}</div>
</div><!-- fragment --><p>As you can see in the output above, the datatype for this dataset is: </p><div class="fragment"><div class="line">DATATYPE <a class="code hl_enumvalue" href="_h5_tpublic_8h.html#a071841985f647f69516dbe77d93167f2a5850e0b9353a5e7aeb615fb943d4e9cd">H5T_REFERENCE</a> { <a class="code hl_define" href="group___p_d_t_s_t_d.html#gaf5cb0d5cec3d40d8b3ac27512f86895e">H5T_STD_REF_DSETREG</a> }</div>
</div><!-- fragment --><p>This indicates that it is a dataset specifically for storing references to regions (or subsets) in other datasets. The dataset contains 16 such references, and more can be added to it, as indicated by the dataspace (in other words it is unlimited): </p><div class="fragment"><div class="line">DATASPACE SIMPLE { ( 16 ) / ( <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a> ) }</div>
</div><!-- fragment --><h3><a class="anchor" id="subsubsecViewToolsJPSSExam_h5dumpRegRef"></a>
Viewing a Region Reference</h3>
<p>What if we wanted to look at the <code style="background-color:whitesmoke;">NumberOfScans</code> data for a specific granule in a file?</p>
<p>First, we may be interested in determining whether the scans were done at night or in the day. If a scan was at night, there will be no data.</p>
<p>The attribute <code style="background-color:whitesmoke;">N_Day_Night_Flag</code> is used to determine when the scan was done. If you don't know where this attribute is located, you can use the <code style="background-color:whitesmoke;">-N</code> option to search for it in the file. If you were to run this command on the <code style="background-color:whitesmoke;">SVM09</code> file used above, you would see that the <code style="background-color:whitesmoke;">N_Day_Night_Flag</code> attribute has a value of <code style="background-color:whitesmoke;">Night</code> for the four granules in the file. Indeed, if you actually examine the <code style="background-color:whitesmoke;">NumberOfScans</code> data, you will see that only fill values are written.</p>
<p>For that reason we will examine the <code style="background-color:whitesmoke;">NumberOfScans</code> data for the <code style="background-color:whitesmoke;">SVMO1</code> file below, as it was obtained during the day: </p><div class="fragment"><div class="line">h5dump -N N_Day_Night_Flag SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5</div>
</div><!-- fragment --><p>It displays: </p><div class="fragment"><div class="line">HDF5 <span class="stringliteral">"SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5"</span> {</div>
<div class="line">ATTRIBUTE <span class="stringliteral">"N_Day_Night_Flag"</span> {</div>
<div class="line"> DATATYPE <a class="code hl_enumvalue" href="_h5_tpublic_8h.html#a071841985f647f69516dbe77d93167f2a2de5d7919fe54466b7cf6a6c0b4265fa">H5T_STRING</a> {</div>
<div class="line"> STRSIZE 4;</div>
<div class="line"> STRPAD <a class="code hl_enumvalue" href="_h5_tpublic_8h.html#ad2ab726f3bd28222a2ffb91c6bbc3514a23c685afc240bbac4da23b36d8fd7e13">H5T_STR_NULLTERM</a>;</div>
<div class="line"> CSET <a class="code hl_enumvalue" href="_h5_tpublic_8h.html#a03755b8370672668ddc7063add28e71aa27383e03d1cad9b4c32d8611a145d663">H5T_CSET_ASCII</a>;</div>
<div class="line"> CTYPE <a class="code hl_define" href="group___p_d_t_s.html#ga7f6b6959fefe56d2e871659110936d2d">H5T_C_S1</a>;</div>
<div class="line"> }</div>
<div class="line"> DATASPACE SIMPLE { ( 1, 1 ) / ( 1, 1 ) }</div>
<div class="line"> DATA {</div>
<div class="line"> (0,0): <span class="stringliteral">"Day"</span></div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line">}</div>
<div class="ttc" id="a_h5_tpublic_8h_html_a03755b8370672668ddc7063add28e71aa27383e03d1cad9b4c32d8611a145d663"><div class="ttname"><a href="_h5_tpublic_8h.html#a03755b8370672668ddc7063add28e71aa27383e03d1cad9b4c32d8611a145d663">H5T_CSET_ASCII</a></div><div class="ttdeci">@ H5T_CSET_ASCII</div><div class="ttdef"><b>Definition</b> H5Tpublic.h:95</div></div>
<div class="ttc" id="a_h5_tpublic_8h_html_a071841985f647f69516dbe77d93167f2a2de5d7919fe54466b7cf6a6c0b4265fa"><div class="ttname"><a href="_h5_tpublic_8h.html#a071841985f647f69516dbe77d93167f2a2de5d7919fe54466b7cf6a6c0b4265fa">H5T_STRING</a></div><div class="ttdeci">@ H5T_STRING</div><div class="ttdef"><b>Definition</b> H5Tpublic.h:35</div></div>
<div class="ttc" id="a_h5_tpublic_8h_html_ad2ab726f3bd28222a2ffb91c6bbc3514a23c685afc240bbac4da23b36d8fd7e13"><div class="ttname"><a href="_h5_tpublic_8h.html#ad2ab726f3bd28222a2ffb91c6bbc3514a23c685afc240bbac4da23b36d8fd7e13">H5T_STR_NULLTERM</a></div><div class="ttdeci">@ H5T_STR_NULLTERM</div><div class="ttdef"><b>Definition</b> H5Tpublic.h:120</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 --><p>There is just one granule in this <code style="background-color:whitesmoke;">SVM01</code> file, as shown below: </p><div class="fragment"><div class="line">$ h5dump -n SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5</div>
<div class="line">HDF5 <span class="stringliteral">"SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5"</span> {</div>
<div class="line">FILE_CONTENTS {</div>
<div class="line"> group /</div>
<div class="line"> group /All_Data</div>
<div class="line"> group /All_Data/VIIRS-M1-SDR_All</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/ModeGran</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/ModeScan</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/NumberOfBadChecksums</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/NumberOfDiscardedPkts</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/NumberOfMissingPkts</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/NumberOfScans</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/PadByte1</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/QF2_SCAN_SDR</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/QF3_SCAN_RDR</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/QF4_SCAN_SDR</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/QF5_GRAN_BADDETECTOR</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/Radiance</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/RadianceFactors</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/Reflectance</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/ReflectanceFactors</div>
<div class="line"> group /Data_Products</div>
<div class="line"> group /Data_Products/VIIRS-M1-SDR</div>
<div class="line"> dataset /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Aggr</div>
<div class="line"> dataset /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0</div>
<div class="line"> }</div>
<div class="line">}</div>
</div><!-- fragment --><p>Now examine the references in the <code style="background-color:whitesmoke;">VIIRS-M1-SDR_Gran_0</code> granule </p><div class="fragment"><div class="line">$ h5dump -A 0 -d <span class="stringliteral">"/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0"</span> </div>
<div class="line"> SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5</div>
<div class="line">HDF5 <span class="stringliteral">"SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5"</span> {</div>
<div class="line">DATASET <span class="stringliteral">"/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0"</span> {</div>
<div class="line"> DATATYPE <a class="code hl_enumvalue" href="_h5_tpublic_8h.html#a071841985f647f69516dbe77d93167f2a5850e0b9353a5e7aeb615fb943d4e9cd">H5T_REFERENCE</a> { <a class="code hl_define" href="group___p_d_t_s_t_d.html#gaf5cb0d5cec3d40d8b3ac27512f86895e">H5T_STD_REF_DSETREG</a> }</div>
<div class="line"> DATASPACE SIMPLE { ( 16 ) / ( <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a> ) }</div>
<div class="line"> DATA {</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/Radiance {(0,0)-(767,3199)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/Reflectance {(0,0)-(767,3199)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/ModeScan {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/ModeGran {(0)-(0)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/PadByte1 {(0)-(2)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfScans {(0)-(0)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfMissingPkts {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfBadChecksums {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfDiscardedPkts {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR {(0,0)-(767,3199)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/QF2_SCAN_SDR {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/QF3_SCAN_RDR {(0)-(47)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/QF4_SCAN_SDR {(0)-(767)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/QF5_GRAN_BADDETECTOR {(0)-(15)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/RadianceFactors {(0)-(1)},</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/ReflectanceFactors {(0)-(1)}</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line">}</div>
</div><!-- fragment --><p>In the output above, you can see that the <code style="background-color:whitesmoke;">NumberOfScans</code> reference is the sixth reference in the granule counting from the top.</p>
<p>The list of references shown above is a 0-based index to the dataset. Therefore, to specify <code style="background-color:whitesmoke;">NumberOfScans</code>, enter a start offset of <code style="background-color:whitesmoke;">5</code> for the <code style="background-color:whitesmoke;">-s</code> option (the sixth reference minus 1). To see the region reference data, use the <code style="background-color:whitesmoke;">-R</code> option.</p>
<p>This command will display the data in the <code style="background-color:whitesmoke;">NumberOfScans</code> region reference: </p><div class="fragment"><div class="line">h5dump -A 0 -d <span class="stringliteral">"/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0"</span> -s 5 -R</div>
<div class="line"> SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5</div>
</div><!-- fragment --><p>It displays the number of scans (48): </p><div class="fragment"><div class="line">HDF5 <span class="stringliteral">"SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5"</span> {</div>
<div class="line">DATASET <span class="stringliteral">"/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0"</span> {</div>
<div class="line"> DATATYPE <a class="code hl_enumvalue" href="_h5_tpublic_8h.html#a071841985f647f69516dbe77d93167f2a5850e0b9353a5e7aeb615fb943d4e9cd">H5T_REFERENCE</a> { <a class="code hl_define" href="group___p_d_t_s_t_d.html#gaf5cb0d5cec3d40d8b3ac27512f86895e">H5T_STD_REF_DSETREG</a> }</div>
<div class="line"> DATASPACE SIMPLE { ( 16 ) / ( <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a> ) }</div>
<div class="line"> SUBSET {</div>
<div class="line"> START ( 5 );</div>
<div class="line"> STRIDE ( 1 );</div>
<div class="line"> COUNT ( 1 );</div>
<div class="line"> BLOCK ( 1 );</div>
<div class="line"> DATA {</div>
<div class="line"> (5): DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfScans {</div>
<div class="line"> (5): REGION_TYPE BLOCK (0)-(0)</div>
<div class="line"> (5): DATATYPE <a class="code hl_define" href="group___p_d_t_s_t_d.html#ga37e8a6be7ee64587c2a282b965019bb8">H5T_STD_I32BE</a></div>
<div class="line"> (5): DATASPACE SIMPLE { ( 1 ) / ( <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a> ) }</div>
<div class="line"> (5): DATA {</div>
<div class="line"> (0): 48</div>
<div class="line"> (5): }</div>
<div class="line"> (5): }</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line">}</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>The <code style="background-color:whitesmoke;">-s</code> option may be familiar as one of the options that was described in the <a class="el" href="_view_tools_view.html#secViewToolsViewSub">Dataset Subset</a> tutorial topic. The other subsetting options are not included, indicating that the default values are used.</p>
<p>If you leave off the <code style="background-color:whitesmoke;">-R</code> option, you will see the subset selection, but not the data: </p><div class="fragment"><div class="line">$ h5dump -A 0 -d <span class="stringliteral">"/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0"</span> -s 5 </div>
<div class="line"> SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5</div>
<div class="line">HDF5 <span class="stringliteral">"SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5"</span> {</div>
<div class="line">DATASET <span class="stringliteral">"/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0"</span> {</div>
<div class="line"> DATATYPE <a class="code hl_enumvalue" href="_h5_tpublic_8h.html#a071841985f647f69516dbe77d93167f2a5850e0b9353a5e7aeb615fb943d4e9cd">H5T_REFERENCE</a> { <a class="code hl_define" href="group___p_d_t_s_t_d.html#gaf5cb0d5cec3d40d8b3ac27512f86895e">H5T_STD_REF_DSETREG</a> }</div>
<div class="line"> DATASPACE SIMPLE { ( 16 ) / ( <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a> ) }</div>
<div class="line"> SUBSET {</div>
<div class="line"> START ( 5 );</div>
<div class="line"> STRIDE ( 1 );</div>
<div class="line"> COUNT ( 1 );</div>
<div class="line"> BLOCK ( 1 );</div>
<div class="line"> DATA {</div>
<div class="line"> DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfScans {(0)-(0)}</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line">}</div>
</div><!-- fragment --><h3><a class="anchor" id="subsubsecViewToolsJPSSExam_h5dumpQuality"></a>
Viewing a Quality Flag</h3>
<p>The quality flags in an NPP file can be viewed with h5dump using the <code style="background-color:whitesmoke;">-M</code> option. Quality flags are packed into each integer value in a quality flag dataset. Quality flag datasets in NPP files begin with the letters <code style="background-color:whitesmoke;">QF</code>.</p>
<p>In the following NPP file, there are five Quality Flag datasets (<code style="background-color:whitesmoke;">/All_Data/VIIRS-M1-SDR_All/QF*</code>): </p><div class="fragment"><div class="line">$ h5dump -n SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5</div>
<div class="line">HDF5 <span class="stringliteral">"SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5"</span> {</div>
<div class="line">FILE_CONTENTS {</div>
<div class="line"> group /</div>
<div class="line"> group /All_Data</div>
<div class="line"> group /All_Data/VIIRS-M1-SDR_All</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/ModeGran</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/ModeScan</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/NumberOfBadChecksums</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/NumberOfDiscardedPkts</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/NumberOfMissingPkts</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/NumberOfScans</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/PadByte1</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/QF2_SCAN_SDR</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/QF3_SCAN_RDR</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/QF4_SCAN_SDR</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/QF5_GRAN_BADDETECTOR</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/Radiance</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/RadianceFactors</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/Reflectance</div>
<div class="line"> dataset /All_Data/VIIRS-M1-SDR_All/ReflectanceFactors</div>
<div class="line"> group /Data_Products</div>
<div class="line"> group /Data_Products/VIIRS-M1-SDR</div>
<div class="line"> dataset /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Aggr</div>
<div class="line"> dataset /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0</div>
<div class="line"> }</div>
<div class="line">}</div>
</div><!-- fragment --><p>The flags in this particular dataset happen to be stored in every two bits of each quality flag dataset element, and the values range from 0 to 2. In other words, to see the quality flag values for this dataset, these bits would be examined: 0 and 1, 2 and 3, 4 and 5, or 6 and 7 (This information was obtained from the Product Profile XML File.)</p>
<p>For example, bits 0 and 1 in the <code style="background-color:whitesmoke;">VQF1_VIIRSMBANDSDR</code> dataset specify the flag that "Indicates calibration quality due to bad space view offsets, OBC view offsets, etc or use of a
previous calibration view". It has 3 values: Good (0), Poor (1), or No Calibration (2).</p>
<p>The <code style="background-color:whitesmoke;">-M</code> option is used to specify the quality flag bit offset (<code style="background-color:whitesmoke;">O</code>) and length (<code style="background-color:whitesmoke;">L</code>): </p><div class="fragment"><div class="line">h5dump -d DATASET -M O,L FILE</div>
</div><!-- fragment --><p>To view the first quality flag (0-1) in a 5 x 6 subset of the <code style="background-color:whitesmoke;">QF1_VIIRSMBANDSDR</code> dataset, specify: </p><div class="fragment"><div class="line">h5dump -d <span class="stringliteral">"/All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR[0,0;;5,6;]"</span> </div>
<div class="line"> -M 0,2 SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5</div>
</div><!-- fragment --><p>This outputs: </p><div class="fragment"><div class="line">HDF5 <span class="stringliteral">"SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5"</span> {</div>
<div class="line">DATASET <span class="stringliteral">"/All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR"</span> {</div>
<div class="line"> DATATYPE <a class="code hl_define" href="group___p_d_t_s_t_d.html#ga10b5774adca6e8432615dac892e13ed9">H5T_STD_U8BE</a></div>
<div class="line"> DATASPACE SIMPLE { ( 768, 3200 ) / ( <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a>, <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a> ) }</div>
<div class="line"> PACKED_BITS OFFSET=0 LENGTH=2</div>
<div class="line"> SUBSET {</div>
<div class="line"> START ( 0, 0 );</div>
<div class="line"> STRIDE ( 1, 1 );</div>
<div class="line"> COUNT ( 5, 6 );</div>
<div class="line"> BLOCK ( 1, 1 );</div>
<div class="line"> DATA {</div>
<div class="line"> (0,0): 2, 2, 2, 2, 2, 2,</div>
<div class="line"> (1,0): 2, 2, 2, 2, 2, 2,</div>
<div class="line"> (2,0): 0, 0, 0, 0, 0, 0,</div>
<div class="line"> (3,0): 0, 0, 0, 0, 0, 0,</div>
<div class="line"> (4,0): 0, 0, 0, 0, 0, 0</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line">}</div>
<div class="ttc" id="agroup___p_d_t_s_t_d_html_ga10b5774adca6e8432615dac892e13ed9"><div class="ttname"><a href="group___p_d_t_s_t_d.html#ga10b5774adca6e8432615dac892e13ed9">H5T_STD_U8BE</a></div><div class="ttdeci">#define H5T_STD_U8BE</div><div class="ttdef"><b>Definition</b> H5Tpublic.h:325</div></div>
</div><!-- fragment --><p>To view more than one quality flag at a time simply add the bit offset and length values to <code style="background-color:whitesmoke;">-M</code>, separated by commas. For example, this <code style="background-color:whitesmoke;">-M</code> option specifies bits 0-1 and 2-3: </p><div class="fragment"><div class="line">h5dump -d DATASET -M 0,2,2,2 FILE</div>
</div><!-- fragment --><h3><a class="anchor" id="subsubsecViewToolsJPSSExam_h5dumpProps"></a>
Properties</h3>
<p>To view properties of a specific dataset with <code style="background-color:whitesmoke;">h5dump</code> use the <code style="background-color:whitesmoke;">-p</code> option along with the <code style="background-color:whitesmoke;">-d</code> option. Depending on the number of attributes and the amount of data, the <code style="background-color:whitesmoke;">-A 0</code> and <code style="background-color:whitesmoke;">-H</code> options can also be specified to suppress printing of attributes and data values: </p><div class="fragment"><div class="line">h5dump -p -H -A 0 -d DATASET</div>
</div><!-- fragment --><p>The <code style="background-color:whitesmoke;">-p</code> option shows any compression filters associated with a dataset, as well as layout and fill value information. This option can be helpful in diagnosing performance and other issues.</p>
<p>As an example, examine the <code style="background-color:whitesmoke;">/All_Data/VIIRS-M1-SDR_All/Radiance</code> dataset in the <code style="background-color:whitesmoke;">SVM01</code> file: </p><div class="fragment"><div class="line">$ h5dump -p -H -A 0 -d <span class="stringliteral">"/All_Data/VIIRS-M1-SDR_All/Radiance"</span> </div>
<div class="line"> SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5</div>
<div class="line">HDF5 <span class="stringliteral">"SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5"</span> {</div>
<div class="line">DATASET <span class="stringliteral">"/All_Data/VIIRS-M1-SDR_All/Radiance"</span> {</div>
<div class="line"> DATATYPE <a class="code hl_define" href="group___p_d_t_s_t_d.html#ga10e46ab72ac0330c51ed6cf709db4697">H5T_STD_U16BE</a></div>
<div class="line"> DATASPACE SIMPLE { ( 768, 3200 ) / ( <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a>, <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a> ) }</div>
<div class="line"> STORAGE_LAYOUT {</div>
<div class="line"> CHUNKED ( 768, 3200 )</div>
<div class="line"> SIZE 4915200</div>
<div class="line"> }</div>
<div class="line"> FILTERS {</div>
<div class="line"> NONE</div>
<div class="line"> }</div>
<div class="line"> FILLVALUE {</div>
<div class="line"> FILL_TIME <a class="code hl_enumvalue" href="_h5_dpublic_8h.html#aa39293626c4e68dd28b06c0dc84bde4aa85b225308b0a277c4dd6fed7ee465a72">H5D_FILL_TIME_IFSET</a></div>
<div class="line"> VALUE 65529</div>
<div class="line"> }</div>
<div class="line"> ALLOCATION_TIME {</div>
<div class="line"> <a class="code hl_enumvalue" href="_h5_dpublic_8h.html#aab70b464cf3c5fc931dce0c4fe98b3d2ac898a96931fd3402d9e5646690c77636">H5D_ALLOC_TIME_INCR</a></div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line">}</div>
<div class="ttc" id="a_h5_dpublic_8h_html_aa39293626c4e68dd28b06c0dc84bde4aa85b225308b0a277c4dd6fed7ee465a72"><div class="ttname"><a href="_h5_dpublic_8h.html#aa39293626c4e68dd28b06c0dc84bde4aa85b225308b0a277c4dd6fed7ee465a72">H5D_FILL_TIME_IFSET</a></div><div class="ttdeci">@ H5D_FILL_TIME_IFSET</div><div class="ttdef"><b>Definition</b> H5Dpublic.h:104</div></div>
<div class="ttc" id="a_h5_dpublic_8h_html_aab70b464cf3c5fc931dce0c4fe98b3d2ac898a96931fd3402d9e5646690c77636"><div class="ttname"><a href="_h5_dpublic_8h.html#aab70b464cf3c5fc931dce0c4fe98b3d2ac898a96931fd3402d9e5646690c77636">H5D_ALLOC_TIME_INCR</a></div><div class="ttdeci">@ H5D_ALLOC_TIME_INCR</div><div class="ttdef"><b>Definition</b> H5Dpublic.h:79</div></div>
<div class="ttc" id="agroup___p_d_t_s_t_d_html_ga10e46ab72ac0330c51ed6cf709db4697"><div class="ttname"><a href="group___p_d_t_s_t_d.html#ga10e46ab72ac0330c51ed6cf709db4697">H5T_STD_U16BE</a></div><div class="ttdeci">#define H5T_STD_U16BE</div><div class="ttdef"><b>Definition</b> H5Tpublic.h:335</div></div>
</div><!-- fragment --><p>We can see that the chunk size for this dataset is 768 x 3200, and the storage size is 4915200.</p>
<p>What if the chunk size were smaller?</p>
<p>The dataset was modified to have a chunk size of 1 x 10, using the <code style="background-color:whitesmoke;">h5repack</code> utility, as shown below. </p><div class="fragment"><div class="line">$ h5repack -l /All_Data/VIIRS-M1-SDR_All/Radiance:CHUNK=1x10 </div>
<div class="line"> SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5 SVM01repack.h5</div>
<div class="line"> </div>
<div class="line">$ h5dump -p -H -A 0 -d <span class="stringliteral">"/All_Data/VIIRS-M1-SDR_All/Radiance"</span> SVM01repack.h5</div>
<div class="line">HDF5 <span class="stringliteral">"SVM01repack.h5"</span> {</div>
<div class="line">DATASET <span class="stringliteral">"/All_Data/VIIRS-M1-SDR_All/Radiance"</span> {</div>
<div class="line"> DATATYPE <a class="code hl_define" href="group___p_d_t_s_t_d.html#ga10e46ab72ac0330c51ed6cf709db4697">H5T_STD_U16BE</a></div>
<div class="line"> DATASPACE SIMPLE { ( 768, 3200 ) / ( <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a>, <a class="code hl_define" href="_h5_spublic_8h.html#a5af9ab788797b2ea9a4843857674ac18">H5S_UNLIMITED</a> ) }</div>
<div class="line"> STORAGE_LAYOUT {</div>
<div class="line"> CHUNKED ( 1, 10 )</div>
<div class="line"> SIZE 4915200</div>
<div class="line"> }</div>
<div class="line"> FILTERS {</div>
<div class="line"> NONE</div>
<div class="line"> }</div>
<div class="line"> FILLVALUE {</div>
<div class="line"> FILL_TIME <a class="code hl_enumvalue" href="_h5_dpublic_8h.html#aa39293626c4e68dd28b06c0dc84bde4aa85b225308b0a277c4dd6fed7ee465a72">H5D_FILL_TIME_IFSET</a></div>
<div class="line"> VALUE 65529</div>
<div class="line"> }</div>
<div class="line"> ALLOCATION_TIME {</div>
<div class="line"> <a class="code hl_enumvalue" href="_h5_dpublic_8h.html#aab70b464cf3c5fc931dce0c4fe98b3d2ac898a96931fd3402d9e5646690c77636">H5D_ALLOC_TIME_INCR</a></div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line">}</div>
</div><!-- fragment --><p>In this case, the storage size of the dataset is the same, but the size of the file almost doubled!: </p><div class="fragment"><div class="line">$ ls -1sh</div>
<div class="line">total 35M</div>
<div class="line">12M SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5</div>
<div class="line">23M SVM01repack.h5</div>
</div><!-- fragment --><p>In general, the smaller the chunk size, the more chunks that HDF5 has to keep track of, which increases the size of the file and can affect performance.</p>
<h2><a class="anchor" id="subsecViewToolsJPSSExamr_HDFView"></a>
HDFView</h2>
<p>As mentioned previously, the structure of an HDF5 file is displayed in the TreeView on the left side of the HDFView screen, and you can click on objects and have metadata information displayed on the right side.</p>
<p>To discover more about the granule <code style="background-color:whitesmoke;">/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0</code> in the <code style="background-color:whitesmoke;">SVM01</code> file shown below in the TreeView, position the mouse over the granule and click to select. Properties for the object is displayed on the right side of the HDFView screen. You can see Datatype and Dataspace information on the <code style="background-color:whitesmoke;">General Object Info</code> tab, any Attributes associated with the granulewill be on the <code style="background-color:whitesmoke;">Object Attribute Info</code> tab. In the <code style="background-color:whitesmoke;">General Object Info</code>, you can see that the dataset is a Region Reference dataset, and that there are sixteen Region References in this dataset: </p><table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-prop.png" alt=""/>
</div>
</td></tr>
</table>
<p>To examine the data in the granule, click twice on it with the left mouse button in the TreeView, and it will open in a new window.: </p><table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-regref.png" alt=""/>
</div>
</td></tr>
</table>
<p>If you click twice with the left mouse button on the fifth Region Reference <code style="background-color:whitesmoke;">/All_Data/VIIRS-M1-SDR_All/NumberOfScans</code> a window will pop up with the value(s) of the reference: </p><table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-regref2.png" alt=""/>
</div>
</td></tr>
</table>
<p>You can also set a user option to automatically show the value(s) in a Region Reference. Under the <code style="background-color:whitesmoke;">Tools</code> pull-down menu, select <code style="background-color:whitesmoke;">User Options</code> and then select <code style="background-color:whitesmoke;">HDF Settings</code> and then select <code style="background-color:whitesmoke;">Show RegRef Values</code> in the <code style="background-color:whitesmoke;">Data</code> section (see the middle of the image below): </p><table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-regrefval.png" alt=""/>
</div>
</td></tr>
</table>
<p>Then you will automatically see the values of the Region Reference when you open it and select an entry: </p><table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-regref1.png" alt=""/>
</div>
</td></tr>
</table>
<p>You can view and set quality flags by clicking the right mouse button over a quality flags dataset under <code style="background-color:whitesmoke;">All_Data</code> and selecting <code style="background-color:whitesmoke;">Open As</code> from the pop-up menu. In the middle of the window that pops up, you will see where you can specify <code style="background-color:whitesmoke;">Bitmask</code> options. </p><table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-qf.png" alt=""/>
</div>
</td></tr>
</table>
<hr />
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