exactextract

exactextract is a library for extracting and summarizing the values in the portion of a raster dataset that is covered by a polygon, often referred to as zonal statistics.

The goals of exactextract are to be:

fast - the algorithm used by exactextract outperforms many other implementations by avoiding point-in-polygon tests used to determine whether pixels are inside or outside the raster.
accurate - exactextract computes the fraction of each pixel that is covered by a polygon to determine if the pixel should be used and/or to weigh computations using this coverage fraction.
scalable - exactextract avoids the need to load polygon or raster datasets into memory at a single time, allowing it to be used on arbitrarily large datasets with fixed system resources.
convenient - exactextract provides efficient implementations of many common summary functions and allows the user to define their own functions in R or Python.

The library is developed in C++, with bindings for Python and R. It also includes a command-line interface.

Python

Most tasks can be accomplished using the single function exact_extract(), which provides a high-level interface:

from exactextract import exact_extract

rast = "elevation.tif"
polys = "watersheds.shp"

exact_extract(rast, polys, ["mean", "min", "max"], include_cols=["watershed_id"])

This will return a list of GeoJSON-like features with properties containing the values of the requested stats. Other output formats, such as pandas data frames and GDAL datasets can be requested. exact_extract() is able to work with inputs from many Python packages for spatial data, such as gdal, rasterio, fiona, geopandas, and xarray. The documentation for exact_extract() describes the various types of inputs and outputs that can be used.

For more information on the Python interface, see the Usage examples and API documentation.

R

Usage in R is very similar to Python and primarily consists of calls to the exact_extract function.

library(exactextractr)
library(terra)
library(sf)

elev <- rast("elevation.tif")
polys <- st_read("watersheds.shp")
exact_extract(rast, polys, c("mean", "min", "max"), append_cols='watershed_id')

The R package provides additional functionality, with adaptations of the exactextract algorithm to rasterize polygonal data or resample gridded data.

More information is available in R API documentation and usage examples.

Command-line

exactextract provides a simple command-line interface that uses GDAL to read a vector data source and one or more raster files, perform zonal statistics, and write output to a CSV, netCDF, or other tabular formats supported by GDAL.

 exactextract \
-r elevation.tif \
-p watersheds.shp \
-s "mean" \
-s "min" \
-s "max" \
-o mean_temperature.csv \
--include-col watershed_id

For more information, see Command-line usage examples.

Support

Development of exactextract has been supported by the following organizations: