Running embeddings for Worldcover Sentinel-2 Composites

Running embeddings for Worldcover Sentinel-2 Composites#

This package is made to generate embeddings from the ESA Worldcover Sentinel-2 annual composites. The target region is all of the Contiguous United States.

We ran this script for 2020 and 2021.

The algorithm#

The run.py script will run through a column of image chips of 512x512 pixels. Each run is a column that spans the Contiguous United States from north to south. For each chip in that column, embeddings are generated and stored together in one geoparquet file. These files are then uploaded to the clay-worldcover-embeddings bucket on S3.

There are 1359 such columns to process in order to cover all of the Conus US.

The embeddings are stored alongside with the bbox of the data chip used for generating the embedding. To visualize the underlying data or an embedding the WMS and WMTS endpoints provided by the ESA Worldcover project can be used.

So the geoparquet files only have the following two columns

embeddings

bbox

[0.1, 0.4, … ]

POLYGON(…)

[0.2, 0.5, … ]

POLYGON(…)

[0.3, 0.6, … ]

POLYGON(…)

Exploring results#

The embeddings_db.py script provides a way to locally explore the embeddings. It will create a lancedb database and allow for search. The search results are visualizded by requesting the RGB image from the WMS endpoint for the bbox of each search result.

Running on Batch#

Upload package to fetch and run bucket#

This snippet will create the zip package that is used for the fetch-and-run instance in our ECR registry.

# Add clay src and scripts to zip file
zip -FSr batch-fetch-and-run-wc.zip src scripts -x *.pyc -x scripts/worldcover/wandb/**\*

# Add run to home dir, so that fetch-and-run can see it.
zip -uj batch-fetch-and-run-wc.zip scripts/worldcover/run.py

# Upload fetch-and-run package to S3
aws s3api put-object --bucket clay-fetch-and-run-packages --key "batch-fetch-and-run-wc.zip" --body "batch-fetch-and-run-wc.zip"

Push array job#

This command will send the array job to AWS batch to run all of the 1359 jobs to cover the US.

import boto3

batch = boto3.client("batch", region_name="us-east-1")
year = 2020
job = {
    "jobName": f"worldcover-conus-{year}",
    "jobQueue": "fetch-and-run",
    "jobDefinition": "fetch-and-run",
    "containerOverrides": {
        "command": ["run.py"],
        "environment": [
            {"name": "BATCH_FILE_TYPE", "value": "zip"},
            {
                "name": "BATCH_FILE_S3_URL",
                "value": "s3://clay-fetch-and-run-packages/batch-fetch-and-run-wc.zip",
            },
            {"name": "YEAR", "value": f"{year}"}
        ],
        "resourceRequirements": [
            {"type": "MEMORY", "value": "7500"},
            {"type": "VCPU", "value": "4"},
            # {"type": "GPU", "value": "1"},
        ],
    },
    "arrayProperties": {
        "size": int((125 - 67) * 12000 / 512)
    },
    "retryStrategy": {
      "attempts": 5,
      "evaluateOnExit": [
        {"onStatusReason": "Host EC2*", "action": "RETRY"},
        {"onReason": "*", "action": "EXIT"}
      ]
    },
}

print(batch.submit_job(**job))
Contents