NEON Brownbag: Intro to HDF5 at NEON

June 04, 2015
NEON

This NEON internal brownbag introduces the concept of Hierarchical Data Formats in the context of developing the NEON HDF5 operational file format. Look here to discover resources on HDF5, code snippets in R, Python and Matlab to use H5 files and some example H5 files for Remote Sensing Hyperspectral data and time series temperature data.

Things to do before the workshop

Please review, download and setup the following, prior to attending the brownbag.

Data to Download

Download NEON Teaching Data Subset: Imaging Spectrometer Data - HDF5

These hyperspectral remote sensing data provide information on the National Ecological Observatory Network's San Joaquin Exerimental Range field site. The data were collected over the San Joaquin field site located in California (Domain 17) and processed at NEON headquarters. The entire dataset can be accessed by request from the NEON Data Portal.

Download the Free H5 Viewer

The free H5 viewer will allow you to explore H5 data, using a graphic interface. HDF5 viewer can be downloaded from this page. More details on how to set up HDF5Viewer are at the end of this page.

Background Information

Schedule

Time Topic
12:00 Hand-on exploration of the HDF5 Data Format
12:20 Working with HDF5 in Python - live demo.
12:30 NEON HDF5 Format - what's next

Instructors

  • David Hulslander
  • Josh Elliot
  • Leah A. Wasser
  • Tristan Goulden

Additional Set Up Instructions

Install HDFView

The free HDFView application allows you to explore the contents of an HDF5 file.

To install HDFView:

  1. Click to go to the download page.

  2. From the section titled HDF-Java 2.1x Pre-Built Binary Distributions select the HDFView download option that matches the operating system and computer setup (32 bit vs 64 bit) that you have. The download will start automatically.

  3. Open the downloaded file.

    • Mac - You may want to add the HDFView application to your Applications directory.
    • Windows - Unzip the file, open the folder, run the .exe file, and follow directions to complete installation.
  4. Open HDFView to ensure that the program installed correctly.

Data Tip: The HDFView application requires Java to be up to date. If you are having issues opening HDFView, try to update Java first!

Time Topic
12:00 Hand-on exploration of the HDF5 Data Format
12:20 Working with HDF5 in Python - live demo.
12:30 NEON HDF5 Format - what's next

Tutorial: Hierarchical Data Formats - What is HDF5?

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

Tutorial: Open HDF5 files with Python Sample Code

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

Tutorial: HDFView: Exploring HDF5 Files in the Free HDFview Tool

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

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