Table of Contents
- tldr: SatExtractor gets all revisits in a date range from a given geojson region from any public satellite constellation and store it in a cloud friendly format.
The large amount of image data makes it difficult to create datasets to train models quickly and reliably. Existing methods for extracting satellite images take a long time to process and have user quotas that restrict access.
Therefore, we created an open source extraction tool SatExtractor to perform worldwide datasets extractions using serverless providers such as Google Cloud Platform or AWS and based on a common existing standard: STAC.
The tool scales horizontally as needed, extracting revisits and storing them in zarr format to be easily used by deep learning models.
It is fully configurable using Hydra.
SatExtractor needs a cloud provider to work. Before you start using it, you'll need to create and configure a cloud provider account.
We provide the implementation to work with Google Cloud, but SatExtractor is implemented to be easily extensible to other providers.
The package is structured in a modular and configurable approach. It is basically a pipeline containing 6 important steps (separated in modules).
-
Builder: contains the logic to build the container that will run the extraction.
more info
SatExtractor is based on a docker container. The Dockerfile in the root dir is used to build the core package and a reference in it to the specific provider extraction logic should be explicitly added (see the gcp example in directory providers/gcp).This is done by setting
ENV PROVIDERvar to point the provider directory. In the default Dockerfile it is set to gcp:ENV PROVIDER providers/gcp.
- Stac: converts a public constellation to the STAC standard.
more info
If the original constellation is not already in STAC standard it should be converted. To do so, you have to implement the constellation specific STAC conversor. Sentinel 2 and Landsat 7/8 examples can be found insrc/satextractor/stac. The function that is actually called to perform the conversion to the STAC standard is set in stac hydra config file (conf/stac/gcp.yaml)
- Tiler: Creates tiles of the given region to perform the extraction.
more info
The Tiler split the region in UTM tiles using SentinelHub splitter . There will be one Extraction Task per Tile. The config about the tiler can be found inconf/tiler/utm.yaml. There, the size of the tiles can be specified. Take into account that these tiles are not the actual patches that are later stored in your cloud provider, this is just the unit from where the (smaller) patches will be extracted.
-
Scheduler: Decides how those tiles are going to be scheduled creating extractions tasks.
more info
The Scheduler takes the resulting tiles from the Tiler and creates the actual patches (called also tiles) to be extracted.For example, if the Tiler splitted the region in 10000x10000 tiles, now the scheduler can be set to extract from each of the tiles smaller patches of, say, 1000x1000. Also, the scheduler calculates the intersection between the patches and the constellation STAC assets. At the end, you'll have and object called
ExtractionTaskwith the information to extract one revisit, one band and one tile splitted in multiple patches. ThisExtractionTaskwill be send to the cloud provider to perform the actual extraction.The config about the scheduler can be found in
conf/scheduler/utm.yaml.
-
Preparer: Prepare the files in the cloud storage.
more info
The Preparer creates the cloud file structure. It creates the needed zarr groups and arrays in order to later store the extracted patches.The gcp preparer config can be found in
conf/preparer/gcp.yaml.
- Deployer: Deploy the extraction tasks created by the scheduler to perform the extraction.
more info
The Deployer sends one message per ExtractionTask to the cloud provider to perform the actal extraction. It works by publishing messages to a PubSub queue where the extraction is subscribed to. When a new message (ExtractionTask) arrives it will be automatically run on the cloud autoscaling. The gcp deployer config can be found inconf/deployer/gcp.yaml.
All the steps are optional and the user decides which to run the main config file.
In order to run SatExtractor we recommend to have a virtual env and a cloud provider user should already been created.
- Clone the repo
git clone https://github.com/FrontierDevelopmentLab/sat-extractor
- Install python packages
pip install .
🔴🔴🔴
- WARNING!!!!:
Running SatExtractor will use your billable cloud provider services.
We strongly recommend testing it with a small region to get acquainted
with the process and have a first sense of your cloud provider costs
for the datasets you want to generate. Be sure you are running all your
cloud provider services in the same region to avoid extra costs.🔴🔴🔴
Once a cloud provider user is set and the package is installed you'll need to grab the GeoJSON region you want (you can get it from the super-cool tool geojson.io) and change the config files.
- Choose a region name (eg
cordobabelow) and create an output directory for it:
mkdir output/cordoba
- Save the region GeoJSON as
aoi.geojsonand store it in the folder you just created. - Open the
config.yamland you'll see something like this:
dataset_name: cordoba
output: ./output/${dataset_name}
log_path: ${output}/main.log
credentials: ${output}/token.json
gpd_input: ${output}/aoi.geojson
item_collection: ${output}/item_collection.geojson
tiles: ${output}/tiles.pkl
extraction_tasks: ${output}/extraction_tasks.pkl
start_date: 2020-01-01
end_date: 2020-02-01
constellations:
- sentinel-2
- landsat-5
- landsat-7
- landsat-8
defaults:
- stac: gcp
- tiler: utm
- scheduler: utm
- deployer: gcp
- builder: gcp
- cloud: gcp
- preparer: gcp
- _self_
tasks:
- build
- stac
- tile
- schedule
- prepare
- deploy
hydra:
run:
dir: .The important here is to set the dataset_name to <your_region_name>, define the start_date and end_date for your revisits, your constellations and the tasks to be run (you would want to run the build only one time and the comment it out.)
Important: the token.json contains the needed credentials to access you cloud provider. In this example case it contains the gcp credentials. You can see instructions for getting it below in the Authentication instructions.
-
Open the
cloud/<provider>.yamland add there your account info as in the default provided file. (optional): you can choose different configurations by changing modules configs:builder,stac,tiler,scheduler,preparer, etc. There you can change things like patch_size, chunk_size. -
Run
python src/satextractor/cli.pyand enjoy!
See the open issues for a full list of proposed features (and known issues).
To get the token.json for Google Cloud, the recommended approach is to create a service account:
- Go to Credentials
- Click
Create Credentialsand chooseService account - Enter a name (e.g.
sat-extractor) and clickDone(you may also want to modify permissions and users) - Choose the account from the list and then to to the
Keystab - Click
Add key->Create new key->JSONand save the file that gets downloaded - Rename to
token.jsonand you're done!
You may also need to run gcloud config set project your-proj-name for sat-extractor to work properly.
Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.
If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!
- Fork the Project
- Create your Feature Branch (
git checkout -b feature/AmazingFeature) - Commit your Changes (
git commit -m 'Add some AmazingFeature') - Push to the Branch (
git push origin feature/AmazingFeature) - Open a Pull Request
Distributed under the BSD 2 License. See LICENSE.txt for more information.
If you want to use this repo please cite:
@software{dorr_francisco_2021_5609657,
author = {Dorr, Francisco and
Kruitwagen, Lucas and
Ramos, Raúl and
García, Dolores and
Gottfriedsen, Julia and
Kalaitzis, Freddie},
title = {SatExtractor},
month = oct,
year = 2021,
publisher = {Zenodo},
version = {v0.1.0},
doi = {10.5281/zenodo.5609657},
url = {https://doi.org/10.5281/zenodo.5609657}
}
This work is the result of the 2021 ESA Frontier Development Lab World Food Embeddings team. We are grateful to all organisers, mentors and sponsors for providing us this opportunity. We thank Google Cloud for providing computing and storage resources to complete this work.