[R-sig-Geo] enable parallel analysis on pixels from rasterbrick

[Jackson Rodrigues]

Dear all,

Could someone help me on performing parallel analysis on pixels from a
rasterbrick?

I would like to extract and perform  Change-Point Detection from package
trend on pixels from a rasterbrick. and write result as a netcdf file.
However, when applied to my original data it is really time demanding
(days).

So I would like some support on enabling parallel analysis, activating
other cores from my computer aiming to save some time.
I have already tried several techniques and got no satisfactory results, so
far.

I am going through packages doParallel and foreach, but I think that my
error is on selecting pixels from all layers as time series rather than
from a single layer.

Below there is a copy of my function and some syntetic data created.

Thank you all in advance,

Jackson

############
library(raster)
r <- raster(ncol=96, nrow=63, vals=runif(63*96))
n <- 672  # number of copies
s <- stack(lapply(1:n, function(i) rz<-stack(r[i]<-(r^2/3))))

Pettitt <- function(x, date, adjust = "none") {
  require("raster")
  require("trend")
  require("zoo")

#Define how many cores you want to use
UseCores <- detectCores() -1
#Register CoreCluster
cl<- makeCluster(UseCores)
registerDoParallel(cl)

    # pre allocate memory
ptt <- rep(NA, ncell(x))
    # compute Pettitt  Change-Point Detection
  #foreach(i=1:ncell(x)) %dopar% {}
for(i in 1:ncell(x)) {
    temporal <- x[i]
    if(!any(is.na(temporal))) {
      ptt[i] <- pettitt.test(x[i])[3] # Pettitt Test
    }
    cat("\r Processing :", round(i/ncell(x) * 100), "%")
  }

  PTT <- raster(nrow=nrow(x), ncol =ncol(x), crs=crs(x))
  extent(PTT) <- extent(x)
  PTT[] <- unlist(ptt)
    # write output
  raster::writeRaster(PTT, "PTT.nc", overwrite = T)
}

start <- Sys.time()
Pettitt(s, dates)
end <- Sys.time()
difftime(end,start)

Ptt<-brick("PTT.nc")
plot(Ptt)

-- 

Jackson M. Rodrigues

"In order to succeed, we must first believe that we can."

Nikos Kazantzakis

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