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<div class="title">Learning HDF5 with HDFView </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> </p><hr />
<p>This tutorial enables you to get a feel for HDF5 by using the HDFView browser. It does NOT require any programming experience.</p>
<h1><a class="anchor" id="sec_learn_hv_install"></a>
HDFView Installation</h1>
<ul>
<li>Download and install HDFView. It can be downloaded from the <a href="https://portal.hdfgroup.org/display/support/Download+HDFView">Download HDFView</a> page. </li>
<li>Obtain the <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> text file, used in the tutorial.</li>
</ul>
<h1><a class="anchor" id="sec_learn_hv_begin"></a>
Begin Tutorial</h1>
<p>Once you have HDFView installed, bring it up and you are ready to begin the tutorial.</p>
<table style="background-color:#FAFAD2">
<caption>Unable to complete tutorial because fields are greyed out? </caption>
<tr>
<td><p class="starttd">This tutorial requires that the default HDFView File Access Mode be Read / Write. If fields are greyed out so that you cannot select them, then the File Access Mode is Read Only.</p>
<p class="endtd">To change the File Access Mode follow these steps: </p><ul>
<li>
Bring up HDFView </li>
<li>
Left-mouse click on the Tools pull-down menu and select User Options. </li>
<li>
A Preferences window pops up with the General Settings tab selected. About half-way down you will see Default File Access Mode. Select Read / Write. </li>
<li>
Click on Apply and Close at the bottom of the window. </li>
<li>
Close down HDFView. </li>
<li>
Bring HDFView back up and try the tutorial again. PLEASE BE AWARE that selecting a File Access Mode of Read / Write can result in changes to the timestamp of HDF files that are viewed with HDFView. In general, a File Access Mode of Read Only should be used to ensure that this does not occur. </li>
</ul>
</td></tr>
</table>
<h2><a class="anchor" id="subsec_learn_hv_begin_topics"></a>
Topics Covered</h2>
<p>Following are the topics covered in the tutorial. The first topic creates the file that is used in the subsequent topics. </p><ul>
<li>
<a class="el" href="_learn_h_d_f_view.html#subsec_learn_hv_topics_file">Creating a New HDF5 File with a Contiguous Dataset</a> </li>
<li>
<a class="el" href="_learn_h_d_f_view.html#subsec_learn_hv_topics_image">Displaying a Dataset as an Image</a> </li>
<li>
<a class="el" href="_learn_h_d_f_view.html#subsec_learn_hv_topics_attr">Creating Attributes</a> </li>
<li>
<a class="el" href="_learn_h_d_f_view.html#subsec_learn_hv_topics_compress">Creating a Compressed and Chunked Dataset</a> </li>
<li>
<a class="el" href="_learn_h_d_f_view.html#subsec_learn_hv_topics_subset">Creating an Image and a Subset</a> </li>
<li>
<a class="el" href="_learn_h_d_f_view.html#subsec_learn_hv_topics_table">Creating a Table (Compound Dataset)</a> </li>
</ul>
<h1><a class="anchor" id="sec_learn_hv_topics"></a>
Topics</h1>
<h2><a class="anchor" id="subsec_learn_hv_topics_file"></a>
Creating a New HDF5 File with a Contiguous Dataset</h2>
<p>The steps below describe how to create a file (storm.h5), group (/Data), and a contiguous dataset (/Data/Storm) using HDFView. A group is an HDF5 object that allows objects to be collected together. A dataset is an array of data values. A contiguous dataset is one that is stored as a single block in the HDF5 file. </p><ul>
<li>
Select the <em>File</em> pull-down menu at the top left, and then select <em>New -> HDF5</em>. </li>
<li>
Specify a location and type in <em>storm.h5</em> for the name of your file, and click on the <em>Save</em> button. You will see the <em>storm.h5</em> file in the TableView: <table class="doxtable">
<tr>
<td><div class="image">
<img src="storm.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Right click on <em>storm.h5</em>, and select <em>New -> Group</em>. </li>
<li>
Enter <em>Data</em> for the name of the group and then click the <em>Ok</em> button. You will see the group <em>Data</em> in the TableView. <table class="doxtable">
<tr>
<td><div class="image">
<img src="DataGroup.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Right click on the group <em>Data</em> and select <em>New -> Dataset</em>. </li>
<li>
A window pops up on the right. Fill in the information as follows, and then click <em>Ok</em> (leave the Datatype information as is): <table class="doxtable">
<tr>
<th>Dataset Name </th><td><em>Storm</em> </td></tr>
<tr>
<th>Under Dataspace, Current size </th><td>57x57 </td></tr>
<tr>
<th>Layout </th><td><em>Contiguous</em> (default) </td></tr>
</table>
</li>
<li>
Click to expand the <em>Data</em> group in the tree view to see the <em>Storm</em> dataset: <table class="doxtable">
<tr>
<td><div class="image">
<img src="StormDataset.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Double left click on the <em>Storm</em> dataset in the tree view. A window with an empty spreadsheet pops open. </li>
<li>
<p class="startli">Copy the data from the <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> file into the dataset.</p>
<p class="interli">If you downloaded <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a>, then click on the <em>Import/Export Data</em> menu and select <em>Import Data from -> Text File</em>. Specify a location, select <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> and click on the <em>Open</em> button. Answer <em>Yes</em> in the dialog box that pops up (which asks if you wish to paste the selected data).</p>
<p class="interli">Alternately, you can copy/paste directly. Select and copy the data in a separate window. Position your cursor at (0,0) in your table, and select <em>Paste</em> from the <em>Table</em> menu.</p>
<p class="endli">The values will be entered into the spreadsheet. </p><table class="doxtable">
<tr>
<td><div class="image">
<img src="datasetwdata.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
<em>Table -> Close</em> the dataset, and save the data. </li>
</ul>
<h2><a class="anchor" id="subsec_learn_hv_topics_image"></a>
Displaying a Dataset as an Image</h2>
<p>Any dataset can be viewed as an image in HDFView. Below are the steps that demonstrate this. </p><ul>
<li>
Right click on <em>Storm</em> in the tree view, and select <em>Open As</em>. </li>
<li>
Select the <em>Image</em> button under <em>Display As</em> (near the top) in the Dataset Selection window that pops up. Then click <em>OK</em> at the bottom of the window to display the image. <table class="doxtable">
<tr>
<td><div class="image">
<img src="showasimage.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
The rainbow icon brings you to the Image Palette window. Click on that to play with the palette (GrayWave probably is the best choice). Close. </li>
</ul>
<h2><a class="anchor" id="subsec_learn_hv_topics_attr"></a>
Creating Attributes</h2>
<p>Additional information to describe an object can be stored in attributes. An attribute can be added to a group or dataset with HDFView.</p>
<p>The following illustrates how to add an attribute to the group <em>/Data</em>: </p><ul>
<li>
Click on the <em>/Data</em> folder in the tree view. You will see two tabs, <em>Object Attribute Info</em> and <em>General Object Info</em>, in the pane on the right site of the HDFView window. <table class="doxtable">
<tr>
<td><div class="image">
<img src="noattrs.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
With the left mouse button, select the <em>Add Attribute</em> button. </li>
<li>
Select the <em>Add Attribute</em> button to add an attribute with these values: <table class="doxtable">
<tr>
<th>Name </th><td><em>BatchID</em> </td></tr>
<tr>
<th>Type </th><td>INTEGER </td></tr>
<tr>
<th>Size (bits) </th><td>32 </td></tr>
</table>
</li>
<li>
Select the <em>Ok</em> button. The attribute will show up under the <em>Object Attribute Info</em> tab. </li>
<li>
Double-click the BatchID attribute line to open the data table for BatchID. </li>
<li>
Click in the first cell and enter <em>3343</em> followed by the enter key. </li>
<li>
<em>Table -> Close</em>, answer <em>Yes</em> in the dialog box that pops up (which asks if you wish to paste the selected data). </li>
</ul>
<p>Adding an attribute to a dataset is very similar to adding an attribute to a group. For example, the following adds an attribute to the <em>/Storm</em> dataset: </p><ul>
<li>
Left mouse click on the <em>/Storm</em> dataset in the tree view. You will see the <em>Object Attribute Info</em> and <em>General Object Info</em> tabs on the right </li>
<li>
In the <em>Object Attribute Info</em> pane select the <em>Add Attribute</em> button and enter an attribute with these values. (Be sure to add a <em>String Length</em> or the string will be truncated to one character!): <table class="doxtable">
<tr>
<th>Name </th><td><em>Units</em> </td></tr>
<tr>
<th>Type </th><td>STRING </td></tr>
<tr>
<th>String Length </th><td>3 </td></tr>
</table>
</li>
<li>
Select the <em>Ok</em> button. The attribute will show up under the <em>Object Attribute Info</em> tab. </li>
<li>
Double-click the Units attribute line to open the data table for Units. </li>
<li>
Click in the first cell and enter <em>m/s</em> followed by the enter key. </li>
<li>
<em>Table -> Close</em>, answer <em>Yes</em> in the dialog box that pops up (which asks if you wish to paste the selected data). <table class="doxtable">
<tr>
<td><div class="image">
<img src="scarletletter.png" alt=""/>
</div>
</td></tr>
</table>
</li>
</ul>
<h2><a class="anchor" id="subsec_learn_hv_topics_compress"></a>
Creating a Compressed and Chunked Dataset</h2>
<p>A chunked and compressed dataset can be created using HDFView. A compressed dataset is a dataset whose size has been compressed to take up less space. In order to compress an HDF5 dataset, the dataset must be stored with a chunked dataset layout (as multiple <em>chunks</em> that are stored separately in the file).</p>
<p>Please note that the chunk sizes used in this topic are for demonstration purposes only. For information on chunking and specifying an appropriate chunk size, see the <a href="https://confluence.hdfgroup.org/display/HDF5/Chunking+in+HDF5">Chunking in HDF5</a> documentation.</p>
<p>Also see the HDF5 Tutorial topic on <a class="el" href="_l_b_com_dset.html#secLBComDsetCreate">Creating a Compressed Dataset</a>. </p><ul>
<li>
Right click on storm.h5. Select <em>New -> Group</em>. </li>
<li>
Enter <em>Image</em> for the name of the group, and click the <em>OK</em> button to create the group. <table class="doxtable">
<tr>
<td><div class="image">
<img src="newgroupimage.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Right click on the <em>Image</em> group, and select <em>New -> Dataset</em>. </li>
<li>
Enter the following information for the dataset. Leave the <em>Datatype</em> as is (INTEGER): <table class="doxtable">
<tr>
<th>Dataset name </th><td><em>Another Storm</em> </td></tr>
<tr>
<th>Under Dataspace, Current size </th><td>57x57 </td></tr>
<tr>
<th>Storage Layout </th><td>Chunked </td></tr>
<tr>
<th>Chunk Size </th><td>20x20 </td></tr>
<tr>
<th>Compression </th><td>gzip </td></tr>
<tr>
<th>Compression Level </th><td>9 </td></tr>
</table>
You will see the <em>Another Storm</em> dataset in the <em>Image</em> group: <table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-anthrstrm.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Double left-mouse click on the <em>Another Storm</em> dataset to display the spreadsheet: <table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-anthrstrm-sprdsht.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Copy the data from the <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> file into the dataset. (See the previous topic for copying <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> into a dataset.) </li>
<li>
<em>Table -> Close</em>, and save the data. </li>
<li>
Right click on <em>Another Storm</em>, and select <em>Open As</em>. </li>
<li>
Select the <em>Image</em> button in the Dataset Selection window that pops up. Click the <em>Ok</em> button at the bottom of the window to view the dataset as an image. <table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-anthrstrm-img.png" alt=""/>
</div>
</td></tr>
</table>
</li>
</ul>
<h2><a class="anchor" id="subsec_learn_hv_topics_subset"></a>
Creating an Image and a Subset</h2>
<p>A previous topic demonstrated how to view any dataset as an image in HDFView. With HDFView you can also create an image to begin with, as is shown below. </p><ul>
<li>
Right click on the <em>Data</em> group and select <em>New -> Image</em>. </li>
<li>
<p class="startli">A window pops up on the right. Enter the following and then click <em>Ok</em>: </p><table class="doxtable">
<tr>
<th>Image name </th><td><em>Storm Image</em> </td></tr>
<tr>
<th>Height </th><td>57 </td></tr>
<tr>
<th>Width </th><td>57 </td></tr>
</table>
<p class="endli"></p>
</li>
<li>
Close the dataset. </li>
<li>
Expand the <em>Data</em> group to see its contents. You will see the <em>Storm Image</em> dataset. <table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-imgicon.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Add data to the <em>Storm Image</em> dataset as was shown previously: <ul>
<li>
Right click on <em>Storm Image</em>, and select <em>Open As</em> to open the Dataset Selection window. </li>
<li>
Click on the <em>Spreadsheet</em> button at the top left of the Dataset Selection window to view the image as a spreadsheet. </li>
<li>
Copy the data from the <a href="https://support.hdfgroup.org/ftp/HDF5/examples/files/tutorial/storm1.txt">storm1.txt</a> file into the dataset. </li>
<li>
Close the dataset and save the data. </li>
</ul>
</li>
<li>
Left double click on <em>Storm Image</em> to see the image. Close the dataset. </li>
<li>
Right click on <em>Storm Image</em> and select <em>Open As</em> to bring up the Data Selection window. </li>
<li>
Select a subset by clicking the left mouse on the image in the window and dragging the mouse. Notice that the Height and Width values change. Select to display it as an image. Click <em>Ok</em>. <table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-imgsubset.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Position the cursor in the middle of the image. Press Shift+Left Mouse button and hold, and then drag the mouse to select another subset. </li>
<li>
Select <em>Image->Write Selection to Image</em>. Enter <em>Subset</em> for the new image name. Click <em>Ok</em>. The <em>Subset</em> image will appear in the tree view on the left. </li>
<li>
Left double click on the image <em>Subset</em> to bring it up on the right. <table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-newimgsubset.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Close the <em>Subset</em> image. </li>
</ul>
<h2><a class="anchor" id="subsec_learn_hv_topics_table"></a>
Creating a Table (Compound Dataset)</h2>
<p>A dataset with a compound datatype contains data elements that consist of multiple fields. If the dataspace for the compound dataset is one-dimensional, then the dataset can be viewed as a table in HDFView, as is shown below. </p><ul>
<li>
Right button click on the group <em>Data</em>. Select <em>New -> Compound DS</em>. </li>
<li>
<p class="startli">A window pops up. Only fill in the following fields: </p><table class="doxtable">
<tr>
<th>Dataset name </th><td>Table </td></tr>
<tr>
<th>Dataspace (Current size only) </th><td>4 </td></tr>
<tr>
<th>Compound Datatype Properties: <br />
Number of Members </th><td>3 </td></tr>
<tr>
<th>Compound Datatype Properties: <br />
<em>Name</em> / Datatype / Size </th><td><em>Description</em> / string / 4 <br />
<em>Temperature</em> / float / 1 <br />
<em>Pressure</em> / double / 1 </td></tr>
</table>
<table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-newcmpd.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Click Ok at the bottom. </li>
<li>
Open the Data group (if it is not open) and double left click on the Table object. <table class="doxtable">
<tr>
<td><div class="image">
<img src="hdfview-table.png" alt=""/>
</div>
</td></tr>
</table>
</li>
<li>
Close the dataset. </li>
</ul>
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