Scripts for extracting NASA PACE OCI vegetation index (LandVI) and Chlorophyll a data to GeoTIF format

R scripts for converting PACE LandVI and chlorophyll a concentration data from the original NetCDF to GeoTIF

Description: Why do I need these scripts?

Scenario: You are a regular GIS user. You have downloaded particularly large PACE OCI vegetation index or chlorophyll-a concentration files in NetCDF (.NC) format from NASA EarthData or the NASA OB.DAAC and you just want to extract the data in GeoTIF for use in ArcGIS or QGIS. You could process the NetCDF files individually, but you would prefer to batch process them. 😉

Required software

You will need R or R Studio to use the script[s], and you will need the dependencies specified (i.e., ncdf4 and raster).

Workflow (suggested)

1. Get PACE OCI LandVI data from the NASA OB.DAAC's Level 3 & Level 4 browser (https://oceandata.sci.gsfc.nasa.gov/l3/):

2. You will need to select Provisional from Product Status, PACE-OCI from Instrument, and Land Vegetation Indices from Product:

3. You will also need to click the blue Extract or Download Data button in the top right:

4. After that, you can select which Period of data you want to download (i.e., daily, 8-day, or monthly), and you will want to select the [spatial] resolution (i.e., 2km, 4km, or 0.1 degree), and to select the Mapped option under Type. Next, click the green Dowload button at the bottom:

5. This will generate a list of NetCDF (.NC) files that can be downloaded:

6. To download the data, you will need to login with your NASA EarthData credentials:

7. After downloading the data, you will be able to run the script using R:

Notes

1. The standard vegetation indices provided for the provisional, version 3 of the PACE OCI data include:

   (i) Normalized Difference Vegetation Index (NDVI),

   (ii) Enhanced Vegetation Index (EVI),

   (iii) Normalized Difference Water Index (NDWI),

   (iv) Normalized Difference Infrared Index (NDII),

   (v) Chlorophyll-Carotenoid Index (CCI),

   (vi) Normalized Difference Snow Index (NDSI),

   (vii) Photochemical Reflectance Index (PRI),

   (viii) Chlorophyll Index Red Edge (CIRE),

   (ix) Carotenoid content index (CAR), and

   (x) modified Anthocyanin Reflectance Index (mARI).

2. Descriptions of these indices can be found in the following presentation by Dr. K. Fred Huemmrich (NASA / UMBC) of the PACE Science & Applications Team: https://pace.oceansciences.org/docs/03-c-Huemmrich_PACE_Terrestrial.pdf.

3. If you would like to skip processing the PACE OCI data on your desktop system and just work with the data in the cloud, check out the PACE OCI toolkit for Google Earth Engine (GEE): https://github.com/BzGEO/pace_oci_toolkit.

Acknowledgements

This work is being led by researchers from the Lab for Applied Science of the Earth System Science Center of the University of Alabama in Huntsville and has been supported by the NASA Earth Action / NASA Marshall Space Flight Center. This work is being done in the context of an Early Adopters project for PACE. The PACE Mission Applications Lead, Dr. Morgaine McKibben (NASA / SSAI), is acknowledged for her support, as are Skye Caplan (NASA / SSAI) of the PACE mission, and Dr. K. Fred Huemmrich of the PACE Science & Applications Team (NASA / UMBC). Kudos are also due to Kelsey Herndon (NASA / UAH), Dr. Africa-Flores-Anderson (NASA), Eric Anderson (NASA), Dr. Kevin Horn (NASA), Dr. Ashutosh Limaye (NASA), and Dan Irwin (NASA) of NASA MSFC.

Contact information

If you have any questions, feel free to contact Emil Cherrington by 📩 email: emil.cherrington [at] uah.edu.