Download Sentinel-1 & Sentinel-2 data cubes of huge-scale (larger-than-memory) on any machine with integrated cloud detection, snow masking, harmonization, merging, and temporal composites.

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Important Notes

1. This package is in early alpha stage. There will be bugs! If you encounter any error, warning, memory issue, etc. please open a GitHub issue with the code to reproduce.
2. This package is meant for large-scale processing and any area that is smaller than 8km in width and height will not run faster because of the underlying processing scheme.

Installing

This package is tested with Python 3.12.*. It may or may not work with other versions.

pip install sentle

or

git clone [email protected]:cmosig/sentle.git
cd sentle
pip install -e .

Guide

Process

There is only one important function: process. Here, you specify all parameters necessary for download and processing. Once this function is called, it immediately starts downloading and processing the data you specified into a zarr file.

from sentle import sentle
from rasterio.crs import CRS

sentle.process(
    zarr_store="mycube.zarr",
    target_crs=CRS.from_string("EPSG:32633"),
    bound_left=176000,
    bound_bottom=5660000,
    bound_right=216000,
    bound_top=5700000,
    datetime="2022-06-17/2023-06-17",
    target_resolution=10,
    S2_mask_snow=True,
    S2_cloud_classification=True,
    S2_cloud_classification_device="cuda",
    S1_assets=["vh_asc", "vh_desc", "vv_asc", "vv_desc"],
    S2_apply_snow_mask=True,
    S2_apply_cloud_mask=True,
    time_composite_freq="7d",
    num_workers=10,
)

This code downloads data for a 40km by 40km area with one year of both Sentinel-1 and Sentinel-2. Clouds and snow are detected and replaced with NaNs. Data is also averaged every 7 days.

Everything is parallelized across 10 workers and each worker immediately saves its results to the specified path to a zarr_store. This ensures you can download larger-than-memory cubes.

Visualize

Load the data with xarray.

import xarray as xr
da = xr.open_zarr("mycube.zarr").sentle
da

And visualize using the awesome lexcube package. Here, band B02 is visualized from the above example. One is able to spot the cloud gaps and the spotty coverage during winter.

import lexcube
lexcube.Cube3DWidget(da.load().sel(band="B02"), vmin=0, vmax=4000)

API Documentation

sentle.process

The package contains only one main function for retrieving and processing Sentinel data: process.

Required Parameters

Parameter	Type	Description
target_crs	rasterio.crs.CRS	Specifies the target CRS that all data will be reprojected to.
target_resolution	float	Determines the resolution that all data is reprojected to in the target_crs.
bound_left	float	Left bound of area that is supposed to be covered. Unit is in target_crs.
bound_bottom	float	Bottom bound of area that is supposed to be covered. Unit is in target_crs.
bound_right	float	Right bound of area that is supposed to be covered. Unit is in target_crs.
bound_top	float	Top bound of area that is supposed to be covered. Unit is in target_crs.
datetime	DatetimeLike	Specifies time range of data to be downloaded. This is forwarded to the respective STAC interface.
zarr_store	str or zarr.storage.Store	Path of where to create the zarr storage.

Optional Parameters

Parameter	Type	Default	Description
processing_spatial_chunk_size	int	4000	Size of spatial chunks across which parallelization is performed.
S1_assets	list[str]	["vh", "vv"]	Specify which bands to download for Sentinel-1. Only "vh" and "vv" are supported.
S2_mask_snow	bool	False	Whether to create a snow mask. Based on https://doi.org/10.1016/j.rse.2011.10.028.
S2_cloud_classification	bool	False	Whether to create cloud classification layer, where 0=clear sky, 2=thick cloud, 3=thin cloud, 4=shadow.
S2_cloud_classification_device	str	"cpu"	On which device to run cloud classification. Either "cpu" or "cuda".
S2_return_cloud_probabilities	bool	False	Whether to return raw cloud probabilities which were used to determine the cloud classes.
num_workers	int	1	Number of cores to scale computation across. Plan 2GiB of RAM per worker. -1 uses all available cores.
time_composite_freq	str	None	Rounding interval across which data is averaged.
S2_apply_snow_mask	bool	False	Whether to replace snow with NaN.
S2_apply_cloud_mask	bool	False	Whether to replace anything that is not clear sky with NaN.
overwrite	bool	False	Whether to overwrite existing zarr storage.
zarr_store_chunk_size	dict	{"time": 50, "x": 100, "y": 100}	Chunk sizes for zarr storage.

Notes

• If S2_apply_snow_mask is set to True, S2_mask_snow must also be True.
• If S2_apply_cloud_mask is set to True, S2_cloud_classification must also be True.
• If time_composite_freq is set and neither S2_apply_snow_mask nor S2_apply_cloud_mask is set, a warning will be issued as temporal aggregation may yield useless results for Sentinel-2 data.
• When S1_assets is supplied as an empty list, it will be converted to None, meaning no Sentinel-1 data will be downloaded.

Questions you may have

How do I scale this program?

Increase the number of workers using the num_workers parameter when calling sentle.process. With default spatial chunk size of 4000, specified by processing_spatial_chunk_size, you should plan with 2GiB per worker.

Contributing

Please submit issues or pull requests if you feel like something is missing or needs to be fixed.

License

This project is licensed under the MIT License - see the LICENSE.md file for details.

Acknowledgments

• Thank you to Cesar Aybar for his cloud detection model. All cloud detection in this package is performed using his model. The paper: link
• Thank you to David Montero for all the discussions and his awesome packages which inspired this.