空间数据和存储器

Question

我正在尝试添加geotiff，但我遇到内存问题。根据以下R错误，R正在使用所有32GB…

In writeValues(y, x, start = 1) :
  Reached total allocation of 32710Mb: see help(memory.size)

我也检查了R的属性，它是64位的，目标是…

" C: Program Files R R-3.3.0 bin x64 Rgui.exe "

版本号

R.Version() 
$platform
[1] "x86_64-w64-mingw32"
$arch
[1] "x86_64"
$os
[1] "mingw32"
$system
[1] "x86_64, mingw32"
$status
[1] ""
$major
[1] "3"
$minor
[1] "3.0"
$year
[1] "2016"
$month
[1] "05"
$day
[1] "03"
$`svn rev`
[1] "70573"
$language
[1] "R"
$version.string
[1] "R version 3.3.0 (2016-05-03)"
$nickname
[1] "Supposedly Educational"

所以看起来我的最大内存正在被r使用，我尝试在r中使用bigmemory包，所以在下面的代码中，我尝试将矩阵更改为大。矩阵，但是失败了，并且在尝试写输出文件时发生错误。有什么建议试图改变代码，以减少内存使用或尝试在包ff或bigmemory工作?

############  LOOP THROUGH AGE MAPS TO COMPILE THE NUMBER OF TIMES A CELL BURNS DURING A GIVEN SPAN OF TIME  ####################
## Empirical Fires
print("1 of 3: 2010-2015")
burn.mat<- matrix(0,nrow,ncol) #create matrix of all zero's, the dimension of your landscape  (row, col)
# Read in Historical Fire maps
for (j in 2010:2015){ #Year Loop
  age.tmp<- as.matrix(raster(paste('fr',j,'.tif',sep=''))) #read in Age Map
  burn.mat<- burn.mat+(age.tmp==1) #when something has burned in ALFRESCO empirical fire history files, AGE=1. (age.tmp==0) is a 'logic' cmd, returning a 0,1 map for True/False
  #Write the data to a geotiff
  out <- raster(burn.mat,xmn=-1692148,xmx= 1321752, ymn = 490809.9, ymx = 2245610, crs = '+proj=aea +lat_1=55 +lat_2=65 +lat_0=50 +lon_0=-154 +x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=m +no_defs')
  writeRaster(out,filename=paste(outdir,'/burn.mat.hist.1950-2007.tif',sep=''),format = 'GTiff',options='COMPRESS=LZW',datatype='FLT4S',overwrite=T)
}

Answer 1

如果您使用栅格*对象而不是矩阵，这个问题可能会消失。就像

library(raster)
r <- raster('fr2010.tif')
burn.mat <- setValues(r, 0)
for (j in 2010:2015) {
  age.tmp <- raster(paste0('fr', j, '.tif'))
  burn.mat <- burn.mat + (age.tmp==1) 
 # if age.tmp only has values of 0 and 1 use this instead:  
 # burn.mat <- burn.mat + age.tmp 
}
# write the results outside of the loop
writeRaster(burn.mat, filename=file.path(outdir, 'burn.mat.hist.1950-2007.tif'), options='COMPRESS=LZW',datatype='FLT4S',overwrite=TRUE)

不使用循环的更直接的方法

 files <- paste0('fr', 2010:2015, '.tif'))
 s <- stack(files)
 burn <- sum(s)

或

 burn <- sum(s == 1)

或者一步写入文件

 b <- calc(s, sum, filename=file.path(outdir, 'burn.mat.hist.1950-2007.tif'), options='COMPRESS=LZW', datatype='FLT4S', overwrite=TRUE)