[R-sig-Geo] Pixel calculation using extract() in geoTiff raster: faster and free of computer lock in R

[Hugo Costa]

Hi Alexandre,

it seems to me this is a job for function 'focal' rather then 'extract'.
Even if so, I'm not sure about the speed it would take.

Cheers
Hugo

ASANTOS via R-sig-Geo <r-sig-geo using r-project.org> escreveu no dia domingo,
18/11/2018 à(s) 14:10:

> Dear R-sig-geo Members,
>
>      I've like to use R and raster package (extract() function) for
> pixel calculations (SD, Skewness and Kurtosis in 1  unit radius of a
> buffer) in a geoTiff raster, but my original geoTiff image has
> 6244(nrow), 8721(ncol) and 54453924 (ncell) dimensions. This image size
> causes slow computation process or computer lock, for example in my code
> below:
>
> ### <code r>
> #Packages
> library(raster)
> library(moments) #Measures of Skewness and Kurtosis
>
> ## Create artificial raster for my geoTiff simulation - dimensions  of
> my original geoTiff: 6244, 8721, 54453924  (nrow, ncol, ncell)
> r <- raster(nc=8721, nr=6244)
> r <- setValues(r, round(runif(ncell(r))* 255))
>
> #Extract all pixel coordinates in raster
> coord_r<-coordinates(r)
>
> #Extract standard deviation, skewness and kurtosis
> Buffer<-1
> SD<-function (x, na.rm = TRUE)
> {
> if (is.matrix(x))
>      apply(x, 2, sd, na.rm = na.rm)
> else if (is.vector(x))
>      sqrt(var(x, na.rm = na.rm))
> else if (is.data.frame(x))
>      sapply(x, sd, na.rm = na.rm)
> else sqrt(var(as.vector(x), na.rm = na.rm))
> }
> desv_pad_R<-extract(r, coord_r, buffer = Buffer, fun = SD)
> str(desv_pad_R)
> sk_R <-extract(r,coord_r,buffer=Buffer, fun=skewness, na.rm = TRUE)
> str(sk_R)
> k_R <-extract(r,coord_r,buffer=Buffer, fun=kurtosis, na.rm = TRUE)
> str(k_R)
> # <END code>
>
>      There are different approaches (eg. integration with SAGA GIS or
> GRASS, convert image to ASCII) for my problem?
>
> Thanks in advanced,
>
> Alexandre
>
> --
> ======================================================================
> Alexandre dos Santos
> Proteção Florestal
> IFMT - Instituto Federal de Educação, Ciência e Tecnologia de Mato Grosso
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>
>          alexandre.santos using cas.ifmt.edu.br
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>
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