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R Bloggers
Date(s): - Jun 4, 2015

Explore the Operational NEON HDF5 Format

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.

Background Materials

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

Data to Download

Download NEON Teaching Data Subset: Sample Tower Temperature - HDF5

These temperature data were collected by the National Ecological Observatory Network’s Flux Towers . The entire dataset can be accessed from the NEON website.

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 Experimental 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 from the NEON website.

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.

Click here to read more on the viewer in the HDFView: Exploring HDF5 Files in the Free HDFview Tool tutorial.

Please review the following:


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  

Useful HDF5 Resources

Python resources for HDF5:

  1. H5 Python Documentation
  2. O’Reilly book on Python and HDF5! The modern stamp of legitimacy for programming.
  3. Python examples from the HDF5 people themselves!

Python Code to Open HDF5 files

For sample python code to open HDF5 files, see the Opening HDF5 files with Python Sample Code tutorial .