使用世界地图数据进行测试

Question

gIntersects()包中用于测试点是否位于多边形中的函数rgeos非常慢。有没有一种加速计算的好方法？

Answer 1

我尝试了评论中已经提到的sp::point.in.polygon，sp::over和rgeos::gIntersects()之间的速度比较。请注意point.in.poly中还有一个{spatialEco}函数，但它似乎只是sp::over的包装。

我意识到sp::point.in.polygon不能很好地处理多部分多边形（也指向here）并且需要提供原始坐标（所以我认为对于多部分多边形需要用于循环）。请注意，sp::point.in.polygon仅在方形多边形的情况下它比其他所有其他更快，这使我认为只有更简单的形状才会更快。总而言之，无论何时遇到速度问题，juts都会尝试测试您的具体情况。对于我具体选择的例子，sp::over似乎是一个更好的选择，但我不会概括。希望我的例子没问题，否则请随意纠正我。

由于没有提供数据，我在下面使用了一些例子。

使用世界地图数据进行测试

准备数据＆amp;功能

library(rgeos)
library(sp)
library(microbenchmark)
library(ggplot2)
library(maps)
library(maptools)
library(raster)
# Get world map data
# (conversion code from "Applied Spatial Data Analysis with R")
worldmap      <- maps::map("world", fill=TRUE, plot=FALSE)
# transform to SpatialPolygons
worldmapPolys <- maptools::map2SpatialPolygons(worldmap,
                                               IDs=sapply(strsplit(worldmap$names, ":"), "[", 1L), 
                                               proj4string=CRS("+proj=longlat +datum=WGS84"))
# Generate random points for entire world
set.seed(2017)
pts <- sp::spsample(worldmapPolys, n=10^5, type="random")

# Define functions to test for speed
gIntersects_tst <- function(my.pts, my.poly){
    rgeos::gIntersects(spgeom1 = my.pts, 
                       spgeom2 = my.poly, 
                       byid    = TRUE)
}

over_tst <- function(my.pts, my.poly){
    sp::over(x = my.pts, y = my.poly)
}

point.in.polygon_tst <- function(my.pts, my.poly){
    # get coordinates from polygon
    XY <- raster::geom(my.poly)
    sp::point.in.polygon(point.x = my.pts@coords[,1],
                         point.y = my.pts@coords[,2],
                         pol.x = XY[,5],
                         pol.y = XY[,6],
                         mode.checked = TRUE)
}

测试单部分多边形

# Micro-benchmarking
# The idea is to test which points fall into a selected polygon (country)
res <- microbenchmark(TF1 <- gIntersects_tst(pts, worldmapPolys[183,]),
                      TF2 <- gIntersects_tst(worldmapPolys[183,], pts),
                      idx <- over_tst(pts, worldmapPolys[183,]),
                      codes <- point.in.polygon_tst(pts, worldmapPolys[183,]))
print(res)
## Unit: milliseconds
##                                                      expr       min
##         TF1 <- gIntersects_tst(pts, worldmapPolys[183, ]) 142.61992
##         TF2 <- gIntersects_tst(worldmapPolys[183, ], pts) 125.99551
##                idx <- over_tst(pts, worldmapPolys[183, ])  50.72425
##  codes <- point.in.polygon_tst(pts, worldmapPolys[183, ]) 224.57961
##         lq      mean    median        uq      max neval cld
##  153.46915 174.42346 162.90885 177.69223 338.2691   100  b 
##  136.13762 158.88218 144.89180 156.91664 352.3276   100  b 
##   55.50899  69.67542  63.80366  78.12026 132.8704   100 a  
##  243.12288 276.71458 257.38068 275.46144 589.9082   100   c

ggplot2::autoplot(res) + ggtitle("single-polygon: 100 evaluations")

请注意，对于gIntersects()，参数的顺序似乎很重要。结果的速度和结构存在差异。

identical(TF1,TF2)
## [1] FALSE
identical(TF1[,1:length(pts)], TF2[1:length(pts),])
## [1] TRUE
class(TF1); str(TF1)
## [1] "matrix"
##  logi [1, 1:100000] FALSE FALSE FALSE FALSE FALSE FALSE ...
##  - attr(*, "dimnames")=List of 2
##   ..$ : chr "Romania"
##   ..$ : chr [1:100000] "1" "2" "3" "4" ...
class(TF2); str(TF2)
## [1] "matrix"
##  logi [1:100000, 1] FALSE FALSE FALSE FALSE FALSE FALSE ...
##  - attr(*, "dimnames")=List of 2
##   ..$ : chr [1:100000] "1" "2" "3" "4" ...
##   ..$ : chr "Romania"
# Subset world points
pts.gI1 <- pts[TF1,]
pts.gI2 <- pts[TF2,]
pts.ovr <- pts[!is.na(idx),]
pts.PiP <- pts[as.logical(codes),]

# All subsets are identical
identical(pts.gI1, pts.gI2)
## [1] TRUE
identical(pts.gI2, pts.ovr)
## [1] TRUE
identical(pts.ovr, pts.PiP)
## [1] TRUE

更简单的形状 - 使用两个方形多边形进行测试

# Generate two square polygons
grd <- sp::GridTopology(c(1,1), c(1,1), c(2,1))
polys <- sp::as.SpatialPolygons.GridTopology(grd)
# Generate some random points
set.seed(2017)
pts2 <- sp::spsample(polys, n=10^5, type="random")

# Micro-benchmarking
# Test only for those points falling in first square
res <- microbenchmark(TF1 <- gIntersects_tst(pts2, polys[1,]),
                      TF2 <- gIntersects_tst(polys[1,], pts2),
                      idx <- over_tst(pts2, polys[1,]),
                      codes <- point.in.polygon_tst(pts2, polys[1,]))
print(res)
## Unit: milliseconds
##                                             expr       min        lq
##         TF1 <- gIntersects_tst(pts2, polys[1, ]) 151.35336 165.23526
##         TF2 <- gIntersects_tst(polys[1, ], pts2) 123.26241 135.90883
##                idx <- over_tst(pts2, polys[1, ])  54.84891  63.89454
##  codes <- point.in.polygon_tst(pts2, polys[1, ])   9.39330  10.66513
##       mean    median        uq       max neval  cld
##  189.67848 177.62808 190.89566 365.92728   100    d
##  157.47151 148.50073 160.37567 314.02700   100   c 
##   76.42608  70.66998  79.81225 240.55570   100  b  
##   14.09199  11.37738  16.88741  46.19245   100 a

ggplot2::autoplot(res) + ggtitle("square polygon: 100 evaluations")

pts2.gI1 <- pts2[TF1,]
pts2.gI2 <- pts2[TF2,]
pts2.ovr <- pts2[!is.na(idx),]
pts2.PiP <- pts2[as.logical(codes),]
# All subsets are identical
identical(pts2.gI1, pts2.gI2)
## [1] TRUE
identical(pts2.gI2, pts2.ovr)
## [1] TRUE
identical(pts2.ovr, pts2.PiP)
## [1] TRUE

会话信息

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] raster_2.5-8           mapview_1.2.0          leaflet_1.1.0          maptools_0.9-2         maps_3.1.1            
[6] ggplot2_2.2.1          microbenchmark_1.4-2.1 sp_1.2-4               rgeos_0.3-23

R点在多边形速度慢

1 个答案:

使用世界地图数据进行测试

准备数据＆amp;功能

测试单部分多边形

更简单的形状 - 使用两个方形多边形进行测试