Solutions for lack of memory using extract() in a large raster image
I have a Core i5 CPU and 8GB RAM computer, but 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 lack of memory, for example in my code below:
### <code r>
#Packages
library(raster)
library(rgdal)
library(moments) #Measures of Skewness and Kurtosis
memory.limit(size=50000)#Increase memory
## 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))
##Create geoTiff
writeRaster(r, "r.tif", drivername="GTiff")
##Open geoTiff
r2<-raster("r.tif")
#Extract all pixel coordinates in raster
coord_r<-coordinates(r2)
#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(r2, coord_r, buffer = Buffer, fun = SD)
str(desv_pad_R)
sk_R <-extract(r2,coord_r,buffer=Buffer, fun=skewness, na.rm = TRUE)
str(sk_R)
k_R <-extract(r2,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, using RQGIS, convert image to ASCII) for my problem using the same computer and working in R?
Thanks in advanced,
r gis raster geotiff
asked Nov 20 at 17:09
Leprechault
8010
add a comment |
I have a Core i5 CPU and 8GB RAM computer, but 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 lack of memory, for example in my code below:
### <code r>
#Packages
library(raster)
library(rgdal)
library(moments) #Measures of Skewness and Kurtosis
memory.limit(size=50000)#Increase memory
## 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))
##Create geoTiff
writeRaster(r, "r.tif", drivername="GTiff")
##Open geoTiff
r2<-raster("r.tif")
#Extract all pixel coordinates in raster
coord_r<-coordinates(r2)
#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(r2, coord_r, buffer = Buffer, fun = SD)
str(desv_pad_R)
sk_R <-extract(r2,coord_r,buffer=Buffer, fun=skewness, na.rm = TRUE)
str(sk_R)
k_R <-extract(r2,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, using RQGIS, convert image to ASCII) for my problem using the same computer and working in R?
Thanks in advanced,
r gis raster geotiff
asked Nov 20 at 17:09
Leprechault
8010
add a comment |
I have a Core i5 CPU and 8GB RAM computer, but 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 lack of memory, for example in my code below:
### <code r>
#Packages
library(raster)
library(rgdal)
library(moments) #Measures of Skewness and Kurtosis
memory.limit(size=50000)#Increase memory
## 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))
##Create geoTiff
writeRaster(r, "r.tif", drivername="GTiff")
##Open geoTiff
r2<-raster("r.tif")
#Extract all pixel coordinates in raster
coord_r<-coordinates(r2)
#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(r2, coord_r, buffer = Buffer, fun = SD)
str(desv_pad_R)
sk_R <-extract(r2,coord_r,buffer=Buffer, fun=skewness, na.rm = TRUE)
str(sk_R)
k_R <-extract(r2,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, using RQGIS, convert image to ASCII) for my problem using the same computer and working in R?
Thanks in advanced,
r gis raster geotiff
asked Nov 20 at 17:09
Leprechault
8010
I have a Core i5 CPU and 8GB RAM computer, but 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 lack of memory, for example in my code below:
### <code r>
#Packages
library(raster)
library(rgdal)
library(moments) #Measures of Skewness and Kurtosis
memory.limit(size=50000)#Increase memory
## 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))
##Create geoTiff
writeRaster(r, "r.tif", drivername="GTiff")
##Open geoTiff
r2<-raster("r.tif")
#Extract all pixel coordinates in raster
coord_r<-coordinates(r2)
#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(r2, coord_r, buffer = Buffer, fun = SD)
str(desv_pad_R)
sk_R <-extract(r2,coord_r,buffer=Buffer, fun=skewness, na.rm = TRUE)
str(sk_R)
k_R <-extract(r2,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, using RQGIS, convert image to ASCII) for my problem using the same computer and working in R?
Thanks in advanced,
r gis raster geotiff
r gis raster geotiff
asked Nov 20 at 17:09
Leprechault
8010
asked Nov 20 at 17:09
Leprechault
8010
edited Nov 20 at 17:18
asked Nov 20 at 17:09
Leprechault
8010
asked Nov 20 at 17:09
Leprechault
8010
asked Nov 20 at 17:09
Leprechault
8010
8010
add a comment |
add a comment |
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