From GEE to NPY

A GEE python-api script for downloading parcel-level Sentinel-1 / Sentinel-2 time series as NumPy

Returns array of size T x C x N

• T --> number of acquisitions
• C --> number of channels/bands
• N --> number of pixels within parcel

Setup

Install earthengine-api using

pip install earthengine-api

Follow instructions here to authenticate

General processing workflow

• filter collection by aoi, date, cloud-cover (for Sentinel-2), bands (10 S2 bands @10-20m, 2 S1 bands VV-VH)
• alternatively filter by footprint ID (eg granule ID for S2 or orbit number for S1)
• optionally pre-compute NDVI and add to bands
• apply speckle filter (S1 only). Options --> ['mean', 'median', 'temporal']
• co-register (align S1 with S2 pixels)
• normalize (min-max @ 2nd and 98th percentile)
• overlap analysis --> discard no data, repeating observations from overlapping scenes, incomplete image coverage
• save time series array as .npy per parcel
• save dates of acquisition + parcel label in separate files

Example

Requirements

• packages : earthengine-api + tqdm
• input parcel : geojson file containing parcel geometry with crop label column e.g. 'CODE_GROUP' and crop ID column e.g. 'ID_PARCEL'

# Sentinel-1 
get_data.py --rpg_file sample_farm.geojson --label_names ['CODE_GROUP'] --id_field ID_PARCEL --output_dir C:/downloads/s1_data --col_id COPERNICUS/S1_GRD --footprint_id [154] --start_date 2021-01-01 --end_date 2021-01-31 --speckle_filter mean 

# Sentinel-2
get_data.py --rpg_file sample_farm.geojson --label_names ['CODE_GROUP'] --id_field ID_PARCEL --output_dir C:/downloads/s2_data --col_id COPERNICUS/S2_SR  --footprint_id ["30UVU"] --start_date 2021-01-01 --end_date 2021-01-31 

Notes

Footprint argument is set to None by default. However to avoid using partly covered scenes when one can have full Sentinel-1/2 scenes, pre-run Example_findFootprint.ipynb

Contributor

• Stella Ofori-Ampofo
• Dr. Charlotte Pelletier

Credits

• Multi-temporal despeckling from WeiyingZhao
• Parcel data preprocessing from VSainteuf
• Sample parcels obtained from IGN Registre parcellaire graphique (RPG)