cog-worker 0.3.0

Scalable geospatial analysis on Cloud Optimized GeoTIFFs.

Cog Worker

Scalable geospatial analysis on Cloud Optimized GeoTIFFs.

• Documentation: https://vizzuality.github.io/cog_worker
• PyPI: https://pypi.org/project/cog-worker

cog_worker is a simple library to help write scripts to conduct scaleable analysis of gridded data. It's intended to be useful for moderate- to large-scale GIS, remote sensing, and machine learning applications.

Installation

pip install cog_worker

Examples

See docs/examples for Jupyter notebook examples

Quick start

0. A simple cog_worker script

from rasterio.plot import show
from cog_worker import Manager

def my_analysis(worker):
    arr = worker.read('roads_cog.tif')
    return arr

manager = Manager(proj='wgs84', scale=0.083333)
arr, bbox = manager.preview(my_analysis)
show(arr)

1. Define an analysis function that recieves a cog_worker.Worker as the first parameter.

from cog_worker import Worker, Manager
import numpy as np

# Define an analysis function to read and process COG data sources
def MyAnalysis(worker: Worker) -> np.ndarray:

    # 1. Read a COG (reprojecting, resampling and clipping as necessary)
    array: np.ndarray = worker.read('roads_cog.tif')

    # 2. Work on the array
    # ...

    # 3. Return (or post to blob storage etc.)
    return array

2. Run your analysis in different scales and projections

import rasterio as rio

# Run your analysis using a cog_worker.Manager which handles chunking
manager = Manager(
    proj = 'wgs84',       # any pyproj string
    scale = 0.083333,  # in projection units (degrees or meters)
    bounds = (-180, -90, 180, 90),
    buffer = 128          # buffer pixels when chunking analysis
)

# preview analysis
arr, bbox = manager.preview(MyAnalysis, max_size=1024)
rio.plot.show(arr)

# preview analysis chunks
for bbox in manager.chunks(chunksize=1500):
    print(bbox)

# execute analysis chunks sequentially
for arr, bbox in manager.chunk_execute(MyAnalysis, chunksize=1500):
    rio.plot.show(arr)

# generate job execution parameters
for params in manager.chunk_params(chunksize=1500):
    print(params)

3. Write scale-dependent functions¶

import scipy

def focal_mean(
    worker: Worker,
    kernel_radius: float = 1000 # radius in projection units (meters)
) -> np.ndarray:

    array: np.ndarray = worker.read('sample-geotiff.tif')

    # Access the pixel size at worker.scale
    kernel_size = kernel_radius * 2 / worker.scale
    array = scipy.ndimage.uniform_filter(array, kernel_size)

    return array

4. Chunk your analysis and run it in a dask cluster

from cog_worker.distributed import DaskManager
from dask.distributed import LocalCluster, Client

# Set up a Manager with that connects to a Dask cluster
cluster = LocalCluster()
client = Client(cluster)
distributed_manager = DaskManager(
    client,
    proj = 'wgs84',
    scale = 0.083333,
    bounds = (-180, -90, 180, 90),
    buffer = 128
)

# Execute in worker pool and save chunks to disk as they complete.
distributed_manager.chunk_save('output.tif', MyAnalysis, chunksize=2048)