<commit_before>---
layout: post
title: "HDFView: Exploring HDF5 Files in the Free HDFview Tool"
date:   2015-1-30 20:49:52
lastModified:   2015-1-10 20:49:52
createdDate:   2014-11-19 20:49:52
estimatedTime: 0.25 - 0.5 Hours
packagesLibraries: HDFview
authors: <NAME>
categories: [coding-and-informatics]
category: coding-and-informatics
tags: [HDF5]
mainTag: HDF5
description: "Explore HDF5 files and the groups and datasets contained within, using the free HDFview tool. See how HDF5 files can be structured and explore metadata. Explore both spatial and temporal data stored in HDF5!"
code1: 
image:
  feature: hierarchy_folder_green.png
  credit: <NAME> NEON, Inc.
  creditlink: http://www.neoninc.org
permalink: /HDF5/Exploring-Data-HDFView
---
<section id="table-of-contents" class="toc">
  <header>
    <h3>Contents</h3>
  </header>
<div id="drawer" markdown="1">
*  Auto generated table of contents
{:toc}
</div>
</section><!-- /#table-of-contents -->


<div id="objectives">
<h3>Learning Goals</h3>
After completing this activity, you will:
<ol>
<li>Understand how data can be structured and stored in HDF5.</li>
<li>Understand how metadata can be added to an HDF5 file, making it "self describing"</li>
<li>Know how to explore HDF5 files using the free HDF Viewer</li>
</ol>

<h3>Tools you'll Need</h3>
<ul>
<li>Install the free HDFview application. This application allows you to explore the contents of an HDF5 file easily. <a href="http://www.hdfgroup.org/products/java/release/download.html" target="_blank">Click HERE to go to the download page. </a></li>
</ul>
<h3>Data to Download</h3>
<ul>
<li><a href="{{ site.baseurl }}/data/NEON_TowerDataD3_D10.hdf5" class="btn btn-success">Download the National Ecological Observatory Network (NEON) Flux Tower Temperature data HERE.</a> </li>
<li>Download the <a href="http://neonhighered.org/Data/HDF5/SJER_140123_chip.h5" class="btn btn-success">NEON Airborne Observation Platform Spectrometer Data HDF5 File.</a> </li>
</ul>
NOTE: The second file downloaded above has an ".h5" extension while the first has an HDF5 extension. Both extensions represent the HDF5 data type.
</div>

###About Installing HDFView
Select the HDFView download option that matches the operating system and computer
 setup (32 bit vs 64 bit) that you have. If you are using a windows machine, you 
can click on the VS 2012 version. Click on the operating system name (ie Windows 
or Mac).


##Review: Hierarchical Data Format 5 - HDF5

We learned previously that the Hierarchical Data Format version 5 (HDF5), is an open file format that supports large, complex, heterogeneous data. Some key points about HDF5:

-  HDF5 uses a "file directory" like structure. The HDF5 data models organizes information using `Groups`. Each group may contain one or more `datasets`.
-  HDF5 is a self describing file format. This means that the metadata for the data contained within the HDF5 file, are built into the file itself.
-  One HDF5 file may contain several heterogeneous data types (e.g. images, numeric data, data stored as strings) <commit_msg>fixed text in download button<commit_after>---
layout: post
title: "HDFView: Exploring HDF5 Files in the Free HDFview Tool"
date:   2015-1-30 20:49:52
lastModified:   2015-1-10 20:49:52
createdDate:   2014-11-19 20:49:52
estimatedTime: 0.25 - 0.5 Hours
packagesLibraries: HDFview
authors: <NAME>
categories: [coding-and-informatics]
category: coding-and-informatics
tags: [HDF5]
mainTag: HDF5
description: "Explore HDF5 files and the groups and datasets contained within, using the free HDFview tool. See how HDF5 files can be structured and explore metadata. Explore both spatial and temporal data stored in HDF5!"
code1: 
image:
  feature: hierarchy_folder_green.png
  credit: <NAME> NEON, Inc.
  creditlink: http://www.neoninc.org
permalink: /HDF5/Exploring-Data-HDFView
---
<section id="table-of-contents" class="toc">
  <header>
    <h3>Contents</h3>
  </header>
<div id="drawer" markdown="1">
*  Auto generated table of contents
{:toc}
</div>
</section><!-- /#table-of-contents -->


<div id="objectives">
<h3>Learning Goals</h3>
After completing this activity, you will:
<ol>
<li>Understand how data can be structured and stored in HDF5.</li>
<li>Understand how metadata can be added to an HDF5 file, making it "self describing"</li>
<li>Know how to explore HDF5 files using the free HDF Viewer</li>
</ol>

<h3>Tools you'll Need</h3>
<ul>
<li>Install the free HDFview application. This application allows you to explore the contents of an HDF5 file easily. <a href="http://www.hdfgroup.org/products/java/release/download.html" target="_blank">Click HERE to go to the download page. </a></li>
</ul>
<h3>Data to Download</h3>
<ul>
<li><a href="{{ site.baseurl }}/data/NEON_TowerDataD3_D10.hdf5" class="btn btn-success">Download the National Ecological Observatory Network (NEON) Flux Tower Temperature data HERE.</a> </li>
<li><a href="http://neonhighered.org/Data/HDF5/SJER_140123_chip.h5" class="btn btn-success">Download the NEON Airborne Observation Platform Spectrometer Data HDF5 File.</a> </li>
</ul>
NOTE: The second file downloaded above has an ".h5" extension while the first has an HDF5 extension. Both extensions represent the HDF5 data type.
</div>

###About Installing HDFView
Select the HDFView download option that matches the operating system and computer
 setup (32 bit vs 64 bit) that you have. If you are using a windows machine, you 
can click on the VS 2012 version. Click on the operating system name (ie Windows 
or Mac).


##Review: Hierarchical Data Format 5 - HDF5

We learned previously that the Hierarchical Data Format version 5 (HDF5), is an open file format that supports large, complex, heterogeneous data. Some key points about HDF5:

-  HDF5 uses a "file directory" like structure. The HDF5 data models organizes information using `Groups`. Each group may contain one or more `datasets`.
-  HDF5 is a self describing file format. This means that the metadata for the data contained within the HDF5 file, are built into the file itself.
-  One HDF5 file may contain several heterogeneous data types (e.g. images, numeric data, data stored as strings) 
{'fraction_non_alphanumeric': 0.10285528877352369, 'fraction_numerical': 0.03244646333549643, 'mean_word_length': 4.640439158279963, 'pattern_counts': {'":': 0, '<': 89, '<?xml version=': 0, '>': 89, 'https://': 0, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 15, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2765037', 'n_tokens_mistral': 2049, 'n_tokens_neox': 1902, 'n_words': 792}