R crashes when looping with function writeRaster

Romolo,

For your questions about memory, please read vignette('raster').
r[,]=ifelse(r[,]<=(-2000), NA, r[,]/10000) # is this the culprit?
probably yes, because you are loading all the values into RAM if you do that.
Consider doing something like this:

fileDisp=list.files(getwd())
for (f in 1:length(fileDisp))  :
      r <- raster(fileDisp[f])
   # never overwrite your input files!
   # preferably also send the output to another directory
     outf <- paste0(extension(fileDisp, ''), "_out.tif"
     x <- calc(r, function(x){ x[x <= -2000] <- NA;  x/10000 }, filename=outf)
}

# or perhaps

fileDisp=list.files(getwd())
for (f in 1:length(fileDisp))  :
      r <- raster(fileDisp[f])
     NAvalue(r) <- -2000
     outf <- paste0(extension(fileDisp, ''), "_out.tif"
     x <- calc(r, function(x)  x/10000, filename=outf)
}

Robert
 Jonathan, thanks for your reply. I adjusted the code (fileAnno wasn't
correct)...

fileDisp=list.files(getwd(), full=TRUE)
for (f in 1:length(fileDisp))
{
r=raster(fileDisp[f])
r[,]=ifelse(r[,]<=(-2000), NA, r[,]/10000) # is this the culprit?
writeRaster(r,filename=fileDisp[f],format="GTiff",overwrite=TRUE)
}

Also I don't understand the behaviour (in memory managment),
for the following examples:

LayerTot = stack(fileDisp)
#ex1
MeanL=calc(LayerTot, fun=mean) #gives a memory allocation error, while...
#ex2
MeanL=mean(LayerTot) #doesn't

Furthermore, when I ran:
#ex3
ss <- calc(LayerTot,fun=myfunction)
which gives a rasterbrick, a .grd file was written into my local temporary
directory.
is it possible to force this behaviour each time I call the function "calc"
(for ex1, this could avoid the error)?

Romolo

2013/2/13 Jonathan Greenberg <jgrn at illinois.edu>

Romolo:

I feel like:
  #do some calculation on r and write it with same name
Might be the culprit.  What calculation were you doing?  Can you paste in
the code?  Creating a raster and writing a raster take almost no memory
AFAIK.

Also, your code shows the looping through the length of fileAnno, but I
don't see that defined anywhere.

--j

On Thu, Feb 7, 2013 at 2:22 AM, Romolo Salini <salinir at tiscali.it> wrote:

Dear R-sig-geo,
I'm looping the function "writeRaster", as in:

fileDisp=list.files(getwd(),full=TRUE)
for (f in 1:length(fileAnno))
  {
  r=raster(fileDisp[f])
  #do some calculation on r and write it with same name
  writeRaster(r,filename=fileDisp[f],format="GTiff",overwrite=TRUE)
  }

After about 10/15 iterations, R quits.
As it seemed to be a memory allocation problem, I tried adding
(uselessly):

rm(r)
Sys.sleep(5)

Does anybody had the same problem?

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252
[3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
[5] LC_TIME=Italian_Italy.1252

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

Sys.info()
                     sysname                      release
                   "Windows"                         "XP"

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--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007

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R crashes when looping with function writeRaster

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