ornldaac / gedi_tutorials

GEDI L3 and L4 Tutorials

Tutorials on GEDI Science Data Products

Author: ORNL DAAC
Date: August 26, 2021
Contact for the ORNL DAAC: [email protected]

Keywords: lidar, GEDI, AGBD, aboveground biomass

Overview

These tutorials demonstrate how to discover, access, and use GEDI science data products archived at the ORNL DAAC. GEDI L3, L4A, and L4B data products are available in various data tools and services.

Prerequisites

Requirements are in requirements.txt. To install the necessary Python libraries, you can copy the requirements.txt from this repository and run:

pip install -r requirements.txt

GEDI L4A Footprint Level Aboveground Biomass Density

📗 Jupyter Notebooks

1. Search and download GEDI L4A dataset: search and download GEDI L4A granules over an area of interest to a local machine
2. Subset GEDI L4A footprints: subset downloaded GEDI L4A granules to an area of interest
3. Explore GEDI L4A data structure: explore data structure, variables, and quality flags of the GEDI L4A dataset.
4. Direct S3 Access GEDI L4A from the NASA EarthData Cloud: retrieve the GEDI L4A dataset from NASA Earthdata Cloud using direct S3 access.
5. Access GEDI L4A dataset with NASA OPeNDAP in the Cloud: access selected variables for the GEDI L4A dataset within an area of interest using OPeNDAP Hyrax
6. Access GEDI L4A dataset with NASA Harmony API: direct access and subset the GEDI L4A variables using NASA Harmony API
7. Reproduce L4A AGBD estimates from GEDI L2A RH metrics: reconstruct L4A AGBD estimates using L2A relative height (RH) metrics
8. Apply correction to AGBD estimates for selected L4A shots, Version 2: apply AGBD correction to Version 1 (V001) GEDI L4A shots affected with the algorithm setting group 10 issue

💻 Python Scripts

1. Search and download GEDI L4A dataset: downloads GEDI L4A granules to a local directory based on GeoJSON polygon
2. Subset GEDI L4A footprints: subsets the downloaded GEDI L4A granules by a GeoJSON polygon file
3. Subset GEDI L4A with NASA OPeNDAP in the Cloud: accesses the GEDI L4A dataset using NASA's OPeNDAP Hyrax

GEDI L4B Gridded Aboveground Biomass Density

📗 Jupyter Notebooks

1. Access GEDI L4B Dataset with OGC Web Services: visualize and access the GEDI L4B dataset using the OGC WMS and WCS services

Related Resources

• NASA Earthdata Webinar: Explore NASA GEDI Aboveground Biomass Datasets, Services, and Tools at NASA's ORNL DAAC
• ESA Workshop: Synergistic Use of SAR and Lidar Data for Terrestrial Ecology Research

More resources related to ORNL DAAC data and web services can be found at the ORNL DAAC Learning page.

gedi_tutorials's Issues

Package Versions for Turorials

Hi,

First thank you so much for the tutorials and notebooks. They are really clear and helpful.
I was running 3_gedi_l4a_exploring_data.ipynb, which is good until

mt_leuser_3857_gdf = mt_leuser_gdf.to_crs(epsg=3857)

where an error is encountered (ProjError: x, y, z, and time must be same size).
I have tried using different versions of pyproj and proj, but still couldn't solve the problem.
Since there are many dependencies with the packages used in the tutorial, would it be possible for you to provide the package versions that you are using?

Thank you very much!

Not listed

This file (GEDI04_A_2019133103100_O02354_03_T00724_02_002_02_V002.h5) doesn't exist in the github page.

Feed error

I get an error as follows.

---

KeyError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_92/220220047.py in
41 granulesearch = cmrurl + 'granules.json'
42 response = requests.post(granulesearch, data=cmr_param, files=geojson)
---> 43 granules = response.json()['feed']['entry']
44
45 if granules:

KeyError: 'feed'

Parameters and their values in `model_data`

Hello,
When I run this line, I got 'NaN' value for all Predict_stratum, model_name, x_transform, y_transform, bia_correction, fit_stratum as follows. How can I fix this issue?

Feed word or doi value

Hi folks,

I was running your 3 notebooks, and they hook me, sadly I could not try it on my interest area, throwing an error related with word feed. I was thinking its cause could be that I use geojson instead of json file. Also, I though it could be related with doi value, maybe it just work for your area. Do you know if I can get a doi value for my area? if so, where can I get it?

doi = '10.3334/ORNLDAAC/1907'# GEDI L4A DOI
# CMR API base url
cmrurl='https://cmr.earthdata.nasa.gov/search/'
doisearch = cmrurl + 'collections.json?doi=' + doi
concept_id = requests.get(doisearch).json()['feed']['entry'][0]['id']
print(concept_id)
``
Any advice will be appreciated.
Thanks in advance, JL

AGBD linear models

Is the Table 3. AGBD Linear Models by Prediction Stratum provided in the tutorial https://github.com/ornldaac/gedi_tutorials/blob/main/3_gedi_l4a_exploring_data.ipynb
is the correct linear models used by GEDI to predict AGBD for all regions and PFT for every shot. If it is yes, than I found since they have with negative values in the model which makes most of the biomass calculation in negative values. For example, I tried with one shot with Rh values provided by L2a and use the model equation for that shot with DBT plant functional type but it comes in negative value. But for that shot predicted AGBD provided by L4A data is with different positive values.
Additionally, using RH values in the model equation gives directly the AGBD in mg/ha?
Please, provide me the information as I am doing study on comparing GEDI AGBD for North Asia region.

Subsetting only quality shots in the OpenDAP tutorial

Hello— I'm doing some Amazon wide research with GEDI L4A data, and because the data volume is enormous I've been using the "Accessing GEDI L4A Dataset with NASA OPeNDAP in the Cloud" tutorial to subset to only the necessary variables. I'm wondering if there is a way to only retrieve the data that has a value of 1 for the quality flag when downloading the science variables into a CSV. I know that might be beyond the scope of this tutorial, but if there are any quick methods of doing this, I would really appreciate the help. Thanks!

NetCDF: Unknown file format: b'hyrax' error message

Hi- when I try to download the subset data for the GEDI shots in my area of interest, I get the following error message. I'm fairly new to coding, and have not been able to resolve this issue. Any help would be much appreciated.

Two questions about the tutorial

Hi!
I've two questions about the tutorial and the AGBD calculation.

1. The document [1] and [2] specify that par[1] is always the intercept term but in the tutorial 3_gedi_l4a_exploring_data.ipynb say: The variable par gives model coefficients - the first element of the list is always the slope of the linear model. Which is the correct one?

2. Also, I have another question regarding the use of the existing model in ANCILLARY / model_data. For example, in the DBT_NAm case if the vertors are:
   predictor_id: [1 2 0 0 0 0 0 0]
   rh_index: [50 98 0 0 0 0 0 0]
   par: [-120.77709198 5.50771856 6.80801821 0. 0. ]

How use the information to make the model equation? The vectors index starts from 0 or 1?

Follow both [1] or [2] is some confusing the order of the parameters because I don't understand how I should combine the rh values as only have two values 1 and 2 within the prediction_id for rh50 and rh98 respectively but tree par coefficients.

I understand that a possible way can be:
AGBD = -120.77709198 + 5.50771856 * rh50 + 6.80801821 * rh98^2

Is this correct?

I hope my explanation has been understood.

Thank you very much for the tutorials.
Best regards
Santiago

[1] https://daac.ornl.gov/daacdata/gedi/GEDI_L4A_AGB_Density/comp/GEDI_L4A_Common_Queries.pdf
[2] https://daac.ornl.gov/GEDI/guides/GEDI_L4A_AGB_Density.html

polygons/harvard.json is missing

The tutorial "gedi_l4a_direct_s3_access.ipynb" no longer runs because the harvard.json file is not in the polygons folder.

Third GEDI tutorial

In GEDI Level 4 documentation or guidance, I saw a link to a third GEDI Level 4 tutorial that dealt with "exploration" of Level 4 data. Will this tutorial be available shortly?