Hazard indicator intro

from dotenv import load_dotenv
from affine import Affine
import os
import numpy as np
import pathlib
from pathlib import PurePosixPath
from pyproj import Transformer
import s3fs
import zarr

# load bucket credentials as environment variables
dotenv_dir = os.environ.get("CREDENTIAL_DOTENV_DIR", os.getcwd())
dotenv_path = pathlib.Path(dotenv_dir) / "credentials.env"
if os.path.exists(dotenv_path):
    load_dotenv(dotenv_path=dotenv_path, override=True)

import s3fs

bucket = os.environ.get("OSC_S3_BUCKET_DEV")
s3 = s3fs.S3FileSystem(
    key=os.environ.get("OSC_S3_ACCESS_KEY_DEV", None),
    secret=os.environ.get("OSC_S3_SECRET_KEY_DEV", None),
)

group_path = str(PurePosixPath(bucket, "hazard/hazard.zarr"))
scenario = "historical"
year = "1985"
full_path = str(
    PurePosixPath(
        bucket,
        f"hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_{scenario}_{year}",
    )
)

The Zarr group is located at path physrisk-hazard-indicators-dev01/hazard/hazard.zarr. The particular array is located at path physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985.

print(f"Contents of 'driectory' {full_path}:")
contents = s3.ls(full_path)
print(f"{len(contents)} files")
print(contents)

Contents of 'driectory' physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985:
765 files
['physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/.zarray', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/.zattrs', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.0.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.0.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.0.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.0.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.1.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.1.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.1.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.1.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.1.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.1.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.1.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.14', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.15', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.16', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.17', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.29', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.10.30', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.14', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.15', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.16', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.17', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.29', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.11.30', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.14', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.15', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.16', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.17', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.29', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.30', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.12.31', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.14', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.15', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.16', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.17', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.29', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.30', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.31', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.6', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.7', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.8', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.13.9', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.14', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.15', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.16', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.17', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.29', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.30', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.31', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.7', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.8', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.14.9', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.14', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.15', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.16', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.17', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.29', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.15.30', 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'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.36.4', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.36.5', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.36.6', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.36.7', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.36.8', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.2', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.3', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.32', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.37', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.38', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.4', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.5', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.6', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.37.7', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.38.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.38.2', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.38.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.38.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.38.31', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.38.37', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.39.29', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.39.30', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.39.31', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.1', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.2', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.3', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.4', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.4.5', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.1', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.2', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.3', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.4', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.5.5', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.2', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.3', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.6.4', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.17', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.29', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.7.30', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.16', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.17', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.29', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.30', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.8.31', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.15', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.16', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.17', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.18', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.19', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.20', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.21', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.22', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.23', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.24', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.25', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.26', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.27', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.28', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.29', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.30', 'physrisk-hazard-indicators-dev01/hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985/0.9.31']

Note that this comprises files .zarray, .zattrs, and the (non-empty) chunks which have filenames in the format {chunk_z, chunk_y, chunk_x}, e.g. 0.1.21

with s3.open(full_path + "/.zarray") as f:
    print(f.read().decode())

{
    "chunks": [
        5,
        1000,
        1000
    ],
    "compressor": {
        "blocksize": 0,
        "clevel": 5,
        "cname": "lz4",
        "id": "blosc",
        "shuffle": 1
    },
    "dtype": "<f4",
    "fill_value": "NaN",
    "filters": null,
    "order": "C",
    "shape": [
        5,
        39420,
        38374
    ],
    "zarr_format": 2
}

The array is (5 returns) x (39420 spatial y coordinates) x (38374 spatial x coordinates). The array is split into chunks where each chunk is 5 x 1000 x 1000.

with s3.open(full_path + "/.zattrs") as f:
    print(f.read().decode())

{
    "crs": "+proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs=True",
    "dimensions": [
        "index",
        "latitude",
        "longitude"
    ],
    "index_name": "return period (years)",
    "index_values": [
        10,
        30,
        100,
        300,
        1000
    ],
    "transform_mat3x3": [
        100.0,
        0.0,
        2648099.999999999,
        0.0,
        -99.99999999999999,
        5404499.999999997,
        0.0,
        0.0,
        1.0
    ]
}

This defines the dimensions, gives the CRS for the spatial dimensions (x/longitude and y/latitude), defines the index values for the z dimension (which contains each return period).

Transform_mat3x3 provides the affine transform needed to find pixels from latitude and longitude.

# For accessing

store = s3fs.S3Map(root=group_path, s3=s3, check=False)
root = zarr.group(store=store)
z = root["inundation/river_tudelft/v2/flood_depth_unprot_historical_1985"]

t = z.attrs["transform_mat3x3"]
crs = z.attrs["crs"]
transform = Affine(t[0], t[1], t[2], t[3], t[4], t[5])
lat, lon = (51.7426, -1.2669)
transproj = Transformer.from_crs("epsg:4326", crs, always_xy=True)
x, y = transproj.transform([lon], [lat])

px, py = ~transform * (x[0], y[0])
print(f"pixel values x/y for longitude/latitude are {px}/{py}")

pixel values x/y for longitude/latitude are 8982.571352041778/21631.33479974286

print(z[:, int(py), int(px)])

[2.2507873 2.4166772 2.5981872 2.7464173 2.8810973]

# some code to do the same thing but fast for a large number of x and y coordinates

coords = np.vstack((x, y, np.ones(len(x))))  # type: ignore
inv_trans = ~transform
mat = np.array(inv_trans).reshape(3, 3)
frac_image_coords = mat @ coords
print(frac_image_coords)
index_values = z.attrs.get("index_values", [0])
image_coords = np.floor(frac_image_coords).astype(int)
iy = np.repeat(image_coords[1, :], len(index_values))
ix = np.repeat(image_coords[0, :], len(index_values))
iz = np.tile(np.arange(z.shape[0]), image_coords.shape[1])
data = z.get_coordinate_selection((iz, iy, ix))
print(data)

[[8.98257135e+03]
 [2.16313348e+04]
 [1.00000000e+00]]
[2.2507873 2.4166772 2.5981872 2.7464173 2.8810973]

# doing the same thing locally

test_output_dir = "/Users/joemoorhouse/Code/hazard/tests/test_output/"  # this contains a copy of hazard/hazard.zarr/inundation/river_tudelft/v2/flood_depth_unprot_historical_1985
local_store = zarr.DirectoryStore(
    os.path.join(test_output_dir, "hazard", "hazard.zarr")
)
root_local = zarr.group(store=local_store)
z_local = root_local["inundation/river_tudelft/v2/flood_depth_unprot_historical_1985"]

print(z_local[:, int(py), int(px)])

[2.2507873 2.4166772 2.5981872 2.7464173 2.8810973]

A note on performance. When we request a set of coordinates from Zarr, Zarr works out which chunks it needs to obtain, decompress and which pixels it needs to look up from those chunks. The only non-trivial parts in terms of performance are: 1) getting the chunk into memory 2) decompressing the chunk

For an S3 store, 1 takes most of the time and it is important that the machine doing the decompression and look-up has a fast connection to the bucket (as I write, I am running this on a laptop with a broadband connection in a different continent to the bucket, an example of a slow connection!).

S3 is generally ‘fast enough’ in that requesting order 100,000 coordinates takes order ~10s (depending on clustering of lats/lons) but of course we can get orders of magnitude faster than this, e.g. storing on a solid state hard disk, or distributed memory containing uncompressed tiles.

Moreover, Zarr provides a number of stores (we have used only the S3 and local so far) to manage the chunks. https://zarr.readthedocs.io/en/stable/api/storage.html