mirzacengic / fasterize

Fast vector <--> raster conversion for modern R spatial data 🚀🌏▦

fasterize

Fast sf-to-raster conversion

fasterize is high-performance replacement for the rasterize() function in the raster package.

Functionality is currently limited to rasterizing polygons in sf-type data frames.

Installation

Install fasterize with devtools. fasterize uses Rcpp and thus requires a compile toolchain to install. It also requires sf, which requires GDAL (>= 2.0.0), GEOS (>= 3.3.0), PROJ.4 (>= 4.8.0).

devtools::install_github("ecohealthalliance/fasterize")

Usage

The main function, fasterize(), takes the same inputs as raster::rasterize() but currently has fewer options and is currently limited to rasterizing polygons.

A method for creating empty rasters from sf objects is provided, and raster plot methods are re-exported.

library(raster)
library(fasterize)
library(sf)
p1 <- rbind(c(-180,-20), c(-140,55), c(10, 0), c(-140,-60), c(-180,-20))
hole <- rbind(c(-150,-20), c(-100,-10), c(-110,20), c(-150,-20))
p1 <- list(p1, hole)
p2 <- list(rbind(c(-10,0), c(140,60), c(160,0), c(140,-55), c(-10,0)))
p3 <- list(rbind(c(-125,0), c(0,60), c(40,5), c(15,-45), c(-125,0)))
pols <- st_sf(value = c(1,2,3),
             geometry = st_sfc(lapply(list(p1, p2, p3), st_polygon)))
r <- raster(pols, res = 1)
r <- fasterize(pols, r, field = "value", fun="sum")
plot(r)

Performance

Let's compare fasterize() to raster::rasterize():

pols_r <- as(pols, "Spatial")
bench <- microbenchmark::microbenchmark(
  rasterize = r <- raster::rasterize(pols_r, r, field = "value", fun="sum"),
  fasterize = f <- fasterize(pols, r, field = "value", fun="sum"),
  unit = "ms"
)
print(bench, digits = 3)

#> Unit: milliseconds
#>       expr     min      lq    mean  median      uq   max neval cld
#>  rasterize 333.292 349.469 379.997 362.640 416.768 559.0   100   b
#>  fasterize   0.283   0.304   0.546   0.334   0.411   4.2   100  a

How does fasterize() do on a large set of polygons? Here I download the IUCN shapefile for the ranges of all terrestrial mammals and generate a 1/6 degree world map of mammalian biodiversity by rasterizing all the layers.

download.file(
  "http://spatial-data.s3.amazonaws.com/groups/TERRESTRIAL_MAMMALS.zip",
  destfile = "Mammals_Terrestrial.zip") # <-- 383 MB
unzip("Mammals_Terrestrial.zip", exdir = "Mammals_Terrestrial")

mammal_shapes <- st_read("Mammals_Terrestrial")

#> Reading layer `Mammals_Terrestrial' from data source `/Users/noamross/Dropbox (EHA)/projects/fasterize/Mammals_Terrestrial' using driver `ESRI Shapefile'
#> converted into: MULTIPOLYGON
#> Simple feature collection with 42714 features and 27 fields
#> geometry type:  MULTIPOLYGON
#> dimension:      XY
#> bbox:           xmin: -180 ymin: -85.58276 xmax: 180 ymax: 89.99999
#> epsg (SRID):    4326
#> proj4string:    +proj=longlat +datum=WGS84 +no_defs

mammal_raster <- raster(mammal_shapes, res = 1/6)
bench2 <- microbenchmark::microbenchmark(
  mammals = mammal_raster <- fasterize(mammal_shapes, mammal_raster, fun="sum"),
  times=20, unit = "s")
print(bench2, digits=3)

#> Unit: seconds
#>     expr   min   lq mean median   uq max neval
#>  mammals 0.856 0.87  0.9  0.897 0.92   1    20

par(mar=c(0,0.5,0,0.5))
plot(mammal_raster, axes=FALSE, box=FALSE)

About

fasterize is developed openly at EcoHealth Alliance. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.