[R-sig-Geo] Converting large RasterStack to CSVs fast

[Mohammad Abdel-Razek]

Hi
I got a function to convert ndvi raster stack to CSVs. Each stack is divided into 100 subset, which is convert to csv. The code works for small raster stack, for large ones, I cannot load them into the memory, then it takes massive time to do the task. 

is there a better way to do it? 

The code is below:

require(gdal) 
require(raster) 

exportCSV <- function () { 
  tif <- list.files(pattern='NDVI.tif$') 
  wd <- getwd() 
  ModisTile<-  substr(wd, nchar(wd)-5, nchar(wd)) 
  nImages <- length(tif) 
  cat(paste("Stacking images ...", "\n")) 
  s <- stack(tif) 
  cat(paste("Loading values to RAM memory ...", "\n")) 
#this step is skipped in case of large stacks, then it takes very long time 
  s <- readAll(s) 
#create the subsets bounding coordinates 
  borders <- extent(s) 
  Xmin <- borders at xmin 
  Xmax <- borders at xmax 
  Ymin <- borders at ymin 
  Ymax <- borders at ymax 
  xIncreament <-(Xmax-Xmin)/10 
  yIncreament <-(Ymax-Ymin)/10 
  cat(paste("Subsetting and writing NDVI values ...", "\n")) 
  for (i in 1:10) { 
    for (j in 1:10) { 
      clip_xmin <- Xmin + xIncreament*(i-1) 
      clip_xmax <- Xmin + xIncreament*i 
      clip_ymin <- Ymin + yIncreament*(j-1) 
      clip_ymax <- Ymin + yIncreament*j 
      c_xmin <- format(round(clip_xmin,6), nsmall=6) 
      c_xmax <- format(round(clip_xmax,6), nsmall=6) 
      c_ymin <- format(round(clip_ymin,6), nsmall=6) 
      c_ymax <- format(round(clip_ymax,6), nsmall=6)     
      
      subset <- extent(c(clip_xmin, clip_xmax, clip_ymin, clip_ymax)) 
      c <- crop(s, subset) 
      p <- as.data.frame(rasterToPoints(c)) 
      csvName <- paste0(ModisTile, "_Xmin_",c_xmin, "_Xmax_",c_xmax, "_Ymin_",c_ymin, "_Ymax_",c_ymax,".csv") 
      cat(paste("Writing Subset... MOIDS Tile:", ModisTile,", X", i, "Y", j, "\n")) 
      write.table(p, csvName, row.names=F, sep=";", dec=".") 
    } 
  } 
} 

Best, 
Mohammad PhD Candidate  Institute of Crop Science and Resource Protection - Crop Science Research Group
Katzenburgweg 5 - 53115 Bonn - Germany
 Tel.: +49 (0) 228 73 3258       Fax: +49 (0) 228 73 2870
abdelrazek at uni-bonn.de        http://www.lap.uni-bonn.de

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