shelterbelts 0.0.1

Using satellite imagery to identify shelterbelts and measure their impacts on agricultural productivity

shelterbelts

This repo is for using satellite imagery to map and categorise shelterbelts across Australia, in preparation for measuring impacts on agricultural productivity at scale.

Google Earth Engine App

You can visualise some results from the repo in this Earth Engine App:
https://christopher-bradley-phd.projects.earthengine.app/view/shelterbelts

My slides from the latest Australian National University Research School of Biology (ANU RSB) conference (22 Nov 2025) are here: https://docs.google.com/presentation/d/1_ItZhrtzTDuZXp-qzwP6mT8-nzrLUdA0sI959rIH5zs/edit?usp=sharing

My poster for the Ecology Society of Australia ESA 2025 is here: https://docs.google.com/presentation/d/1oC9jB2WT0nFkxfwlVgvFz6CeqZGZr4pwQr8kT_aS2-k/edit?usp=sharing

Current Methods & Upcoming Plans

The tree predictions come from annual Sentinel-2 imagery largely following a method by Stewart et al. (2025), using a tree/no-tree training dataset provided by Nicolas Pucino.

After the predictions, pixels were categorised using the following method:

• Assign trees from model confidence (50% threshold)
• Assign scattered trees to small groups (< 20 pixels)
• Assign core & buffers to big groups (> 3 pixels thick)
• Assign sheltered vs unsheltered pixels based on percent cover within 100m (10% threshold) , or wind direction (10 pixels leeward, 5 pixels upwind)
• Assign grassland, cropland, urban and water categories from WorldCover 2021
• Assign riparian and roads trees (3 pixel buffer)
• Assign linear vs non-linear patches by fitting an ellipse and skeleton to each group and applying length and width thresholds (the EE App currently has an outdated version of this)

Upcoming Plans

• Expand shelter categories to the rest of Australia, for each year 2017-2025
• Calculate summary statistics for different regions (states, local govdernment areas, IBRA regions)
• Cleanup demoes and tests and publish in the Journal of Open Source Software
• Include 1m canopy height for all of ACT & NSW
• Analyse effects on productivity & potential future benefits
• Add layers with opportunities for more trees

Parameter Reference

The main parameters for categorising shelterbelts are below:

Parameter	Default	Low Threshold	High Threshold	Description
min_patch_size	20	10	30	Minimum area (pixels) to classify as a patch rather than scattered trees
min_core_size	1000	100	10000	Minimum patch size (pixels) to classify as a core area
edge_size	3	1	5	Distance (pixels) defining the edge region around patch cores
max_gap_size	1	0	2	Maximum gap (pixels) to bridge when connecting tree clusters
buffer_width	3	1	5	Number of pixels away from the feature that still counts as within the buffer
distance_threshold	20	10	30	Distance from trees that counts as sheltered
density_threshold	5	3	10	Percentage tree cover within distance_threshold that counts as sheltered
wind_threshold	20	10	30	Wind speed threshold in km/h
wind_method	WINDWARD	MOST_COMMON	ALL	Method to determine primary wind direction
strict_core_area	strict	non-strict	strict	Whether to enforce strict connectivity for core areas
min_shelterbelt_length	15	10	30	Minimum skeleton length (in pixels) to classify a cluster as linear
max_shelterbelt_width	6	4	8	Maximum skeleton width (in pixels) to classify a cluster as linear

Parameters can be modified when calling functions directly in Python or via command-line arguments. For example:

python -m shelterbelts.indices.tree_categories input.tif --min_patch_size 30 --edge_size 5

Setup

Local Setup

1. Download and install Miniconda from https://www.anaconda.com/download/success
2. Add the miniconda filepath to your ~/.zhrc, e.g. export PATH="/opt/miniconda3/bin:$PATH"
3. git clone https://github.com/ChristopherBradley/shelterbelts.git
4. cd shelterbelts
5. conda env create -f environment.yml
6. conda activate shelterbelts

Setup on gadi at the National Computing Infrastructure (NCI)

1. Create an account and request access to the projects xe2 (Borevitz Lab), v10 (Digital Earth Australia modules), ka08 (Sentinel-2 Imagery), ob53 (BARRA Wind).
2. ssh {username}@nci.org.au and enter the password used to create your account.
3. git clone https://github.com/ChristopherBradley/shelterbelts.git
4. There are examples usage of the environments in pbs_scripts

Usage on NCI ARE (National Computing Infrastructure's Australian Research Environment)

1. Login here: https://are.nci.org.au/
2. Go to JupyterLab and create a session with 1 hour, queue normalbw, compute size small, project xe2, storage gdata/+gdata/xe2+gdata/v10+gdata/ka08+gdata/ob53, python environment base /g/data/xe2/cb8590/miniconda, conda environment /g/data/xe2/cb8590/miniconda/envs/shelterbelts. Alternatively, can use Module Dircetories /g/data/v10/public/modules/modulefiles and Modules: dea/20231204.
3. Right click any .py file and open as a jupyter notebook. Currently some debugging arguments are usually commented out at the bottom of each file. I'm planning to move these to tests/demos.

Examples

There are jupyter notebooks to demo the functionality of this repo in notebooks. Also, there are .pbs scripts for submitting jobs to gadi in pbs_scripts, along with .sh scripts to submit many jobs in parallel. The main python files are in src/shelterbelts and these can all be run from the command line as well. The tests have the same examples as notebooks but are more convenient to run all at once (but less convenient for demo-ing/understanding the functionality).

Testing

If on gadi: qsub -I -P xe2 -q copyq -l ncpus=1 -l mem=8GB -l walltime=02:00:00 -l storage=gdata/xe2+scratch/xe2 -l wd

Then: conda activate /g/data/xe2/cb8590/miniconda/envs/shelterbelts pytest tests

Documentation

Generate the html: make clean && make html

You can view the documenation locally in a browser by opening docs/build/index.html

Run the doctests: make doctest

Upload the html to github pages: ghp-import -n -p -f docs/build/html

You can view the published documentation at: https://christopherbradley.github.io/shelterbelts/index.html